#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	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
KAZN	23254	hgsc.bcm.edu	37	1	15428105	15428105	+	Silent	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:15428105G>A	ENST00000376030.2	+	11	1908	c.1614G>A	c.(1612-1614)ctG>ctA	p.L538L		NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	538	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.				keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						ACATTGGCCTGTCCCAGTACT	0.577																																					p.L538L		Atlas-SNP	.											.	KAZN	57	.	0			c.G1614A						PASS	.						46.0	38.0	40.0					1																	15428105		2197	4282	6479	SO:0001819	synonymous_variant	23254	exon11			TGGCCTGTCCCAG	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"""Sterile alpha motif (SAM) domain containing"""	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.1614G>A	chr1.hg19:g.15428105G>A		87.0	0.0	.		73.0	28.0	.	NM_201628	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Silent	SNP	ENST00000376030.2	hg19	CCDS152.2																																																																																			.	.	.	none		0.577	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999	
SRSF4	6429	hgsc.bcm.edu	37	1	29475201	29475201	+	Silent	SNP	G	G	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:29475201G>C	ENST00000373795.4	-	6	1440	c.1206C>G	c.(1204-1206)tcC>tcG	p.S402S	SRSF4_ENST00000466448.1_5'UTR|RP11-242O24.3_ENST00000413004.1_lincRNA|SRSF4_ENST00000546138.1_3'UTR	NM_005626.4	NP_005617.2	Q08170	SRSF4_HUMAN	serine/arginine-rich splicing factor 4	402	Arg/Ser-rich (RS domain).				gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(1)	27						ATCTGGACTGGGAGCGGTCAG	0.582																																					p.S402S		Atlas-SNP	.											.	SRSF4	44	.	0			c.C1206G						PASS	.						141.0	145.0	144.0					1																	29475201		2203	4300	6503	SO:0001819	synonymous_variant	6429	exon6			GGACTGGGAGCGG	BC002781	CCDS333.1	1p35.3	2013-02-12	2010-06-22	2010-06-22	ENSG00000116350	ENSG00000116350		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10786	protein-coding gene	gene with protein product	"""SR splicing factor 4"""	601940	"""splicing factor, arginine/serine-rich 4"""	SFRS4		8321209, 20516191	Standard	NM_005626		Approved	SRP75	uc001bro.3	Q08170	OTTHUMG00000003663	ENST00000373795.4:c.1206C>G	chr1.hg19:g.29475201G>C		74.0	0.0	.		71.0	24.0	.	NM_005626	Q5VXP1|Q9BUA4|Q9UEB5	Silent	SNP	ENST00000373795.4	hg19	CCDS333.1																																																																																			.	.	.	none		0.582	SRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010392.1	NM_005626	
EFCAB14	9813	hgsc.bcm.edu	37	1	47144277	47144277	+	Silent	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:47144277C>T	ENST00000371933.3	-	11	2320	c.1344G>A	c.(1342-1344)caG>caA	p.Q448Q	EFCAB14-AS1_ENST00000418985.1_RNA|EFCAB14_ENST00000544071.1_Intron|EFCAB14-AS1_ENST00000442839.1_RNA	NM_014774.2	NP_055589.1	O75071	EFC14_HUMAN	EF-hand calcium binding domain 14	448	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)										CATCCACGTCCTGGCCAGTCT	0.423																																					p.Q448Q		Atlas-SNP	.											.	.	.	.	0			c.G1344A						PASS	.						84.0	85.0	84.0					1																	47144277		2203	4300	6503	SO:0001819	synonymous_variant	9813	exon11			CACGTCCTGGCCA	AB007963	CCDS30706.1	1p33	2013-01-10	2012-11-29	2012-11-29	ENSG00000159658	ENSG00000159658		"""EF-hand domain containing"""	29051	protein-coding gene	gene with protein product			"""KIAA0494"""	KIAA0494		9455484	Standard	NM_014774		Approved		uc001cqk.4	O75071	OTTHUMG00000007992	ENST00000371933.3:c.1344G>A	chr1.hg19:g.47144277C>T		130.0	0.0	.		124.0	57.0	.	NM_014774	D3DQ23|Q5SXB8	Silent	SNP	ENST00000371933.3	hg19	CCDS30706.1																																																																																			.	.	.	none		0.423	EFCAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021931.1	NM_014774	
SPATA6	54558	hgsc.bcm.edu	37	1	48865170	48865170	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:48865170A>C	ENST00000371847.3	-	7	797	c.633T>G	c.(631-633)atT>atG	p.I211M	SPATA6_ENST00000371843.3_Missense_Mutation_p.I211M|SPATA6_ENST00000463938.1_5'UTR|SPATA6_ENST00000396199.3_Missense_Mutation_p.I139M	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	211					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						ATTTTGAAGAAATTGTAGGCT	0.418																																					p.I211M		Atlas-SNP	.											.	SPATA6	45	.	0			c.T633G						PASS	.						267.0	271.0	270.0					1																	48865170		2203	4300	6503	SO:0001583	missense	54558	exon7			TGAAGAAATTGTA	AK000869	CCDS551.1, CCDS65535.1, CCDS72787.1	1p32.3	2012-03-15			ENSG00000132122	ENSG00000132122			18309	protein-coding gene	gene with protein product	"""spermatogenesis-related factor-1"""	613947					Standard	XM_005270948		Approved	SRF1, FLJ10007, SRF-1	uc001crr.2	Q9NWH7	OTTHUMG00000007794	ENST00000371847.3:c.633T>G	chr1.hg19:g.48865170A>C	ENSP00000360913:p.Ile211Met	123.0	0.0	.		152.0	58.0	.	NM_019073	Q5T3N7|Q8WUE6	Missense_Mutation	SNP	ENST00000371847.3	hg19	CCDS551.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.236288	0.58886	.	.	ENSG00000132122	ENST00000371847;ENST00000371843;ENST00000396199;ENST00000371841	T;T;T;T	0.54675	2.59;2.57;2.58;0.56	5.57	0.164	0.14990	.	0.205873	0.41938	D	0.000789	T	0.53449	0.1797	L	0.43152	1.355	0.35753	D	0.819568	D;D;D;D	0.76494	0.998;0.999;0.998;0.998	D;D;D;D	0.76575	0.967;0.988;0.983;0.983	T	0.59878	-0.7371	10	0.87932	D	0	.	0.4593	0.00513	0.4101:0.1327:0.1989:0.2582	.	139;139;211;211	B4DX17;A8MU33;Q9NWH7-2;Q9NWH7	.;.;.;SPAT6_HUMAN	M	211;211;139;52	ENSP00000360913:I211M;ENSP00000360909:I211M;ENSP00000379502:I139M;ENSP00000360907:I52M	ENSP00000360907:I52M	I	-	3	3	SPATA6	48637757	0.814000	0.29104	1.000000	0.80357	0.991000	0.79684	-0.141000	0.10327	0.356000	0.24157	-0.421000	0.06004	ATT	.	.	.	none		0.418	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073	
CACHD1	57685	hgsc.bcm.edu	37	1	65107535	65107535	+	Missense_Mutation	SNP	G	G	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:65107535G>T	ENST00000371073.2	+	8	1039	c.1039G>T	c.(1039-1041)Ggc>Tgc	p.G347C	CACHD1_ENST00000290039.5_Missense_Mutation_p.G296C|CACHD1_ENST00000495994.1_3'UTR			Q5VU97	CAHD1_HUMAN	cache domain containing 1	347	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						CCTGTCAGCTGGCATTACATC	0.383																																					p.G296C		Atlas-SNP	.											.	CACHD1	125	.	0			c.G886T						PASS	.						131.0	124.0	127.0					1																	65107535		2203	4300	6503	SO:0001583	missense	57685	exon8			TCAGCTGGCATTA	AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"""von Willebrand factor type A and cache domain containing 1"""	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.1039G>T	chr1.hg19:g.65107535G>T	ENSP00000360113:p.Gly347Cys	134.0	0.0	.		174.0	27.0	.	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	hg19		.	.	.	.	.	.	.	.	.	.	G	29.1	4.979116	0.92982	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.49139	0.79;0.79	5.77	5.77	0.91146	von Willebrand factor, type A (2);	0.000000	0.85682	D	0.000000	T	0.52517	0.1739	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.57705	-0.7765	10	0.87932	D	0	-35.1798	19.9906	0.97362	0.0:0.0:1.0:0.0	.	347	Q5VU97	CAHD1_HUMAN	C	347;296	ENSP00000360113:G347C;ENSP00000290039:G296C	ENSP00000290039:G296C	G	+	1	0	CACHD1	64880123	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	9.468000	0.97676	2.729000	0.93468	0.609000	0.83330	GGC	.	.	.	none		0.383	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925	
IGSF3	3321	hgsc.bcm.edu	37	1	117122158	117122158	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:117122158G>A	ENST00000369486.3	-	10	3955	c.3190C>T	c.(3190-3192)Cgg>Tgg	p.R1064W	IGSF3_ENST00000369483.1_Missense_Mutation_p.R1084W|IGSF3_ENST00000318837.6_Missense_Mutation_p.R1084W	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1064	Ig-like C2-type 8.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				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)		ACTGTGAGCCGGTAGAGCACC	0.637																																					p.R1084W		Atlas-SNP	.											.	IGSF3	294	.	0			c.C3250T						PASS	.						48.0	50.0	49.0					1																	117122158		2203	4300	6503	SO:0001583	missense	3321	exon11			TGAGCCGGTAGAG	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.3190C>T	chr1.hg19:g.117122158G>A	ENSP00000358498:p.Arg1064Trp	68.0	0.0	.		90.0	13.0	.	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	hg19	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271626	0.59649	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.22945	1.93;1.93;1.93	4.67	2.66	0.31614	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.124838	0.53938	D	0.000043	T	0.27313	0.0670	L	0.48642	1.525	0.38363	D	0.944664	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.984	T	0.06698	-1.0812	10	0.87932	D	0	-49.5391	7.5572	0.27831	0.0:0.1593:0.5132:0.3275	.	1064;1084	O75054;A6NJZ6	IGSF3_HUMAN;.	W	1064;1084;1084	ENSP00000358498:R1064W;ENSP00000358495:R1084W;ENSP00000321184:R1084W	ENSP00000321184:R1084W	R	-	1	2	IGSF3	116923681	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	2.081000	0.41596	1.154000	0.42482	0.462000	0.41574	CGG	.	.	.	none		0.637	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
POLR3GL	84265	hgsc.bcm.edu	37	1	145457964	145457964	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:145457964G>A	ENST00000369314.1	-	4	402	c.296C>T	c.(295-297)cCg>cTg	p.P99L	POLR3GL_ENST00000369313.3_Intron	NM_032305.1	NP_115681.1	Q9BT43	RPC7L_HUMAN	polymerase (RNA) III (DNA directed) polypeptide G (32kD)-like	99					gene expression (GO:0010467)|innate immune response (GO:0045087)|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 initiation from RNA polymerase III promoter (GO:0006384)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)				endometrium(2)|large_intestine(1)|lung(1)	4	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					ATTGTCAATCGGACCTGACAT	0.483																																					p.P99L		Atlas-SNP	.											.	POLR3GL	21	.	0			c.C296T						PASS	.						175.0	140.0	152.0					1																	145457964		2203	4300	6503	SO:0001583	missense	84265	exon4			TCAATCGGACCTG	BC004355	CCDS72875.1	1q21.1	2008-02-05	2006-12-14		ENSG00000121851	ENSG00000121851			28466	protein-coding gene	gene with protein product			"""polymerase (RNA) III (DNA directed) polypeptide G (32kD) like"""			12477932	Standard	NM_032305		Approved	flj32422, MGC3200	uc001enp.1	Q9BT43	OTTHUMG00000013739	ENST00000369314.1:c.296C>T	chr1.hg19:g.145457964G>A	ENSP00000358320:p.Pro99Leu	67.0	0.0	.		88.0	34.0	.	NM_032305	B1MVG5	Missense_Mutation	SNP	ENST00000369314.1	hg19	CCDS914.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850236	0.71719	.	.	ENSG00000121851	ENST00000369314	.	.	.	5.32	4.4	0.53042	.	0.212727	0.38436	N	0.001698	T	0.56934	0.2019	M	0.77820	2.39	0.80722	D	1	D	0.69078	0.997	P	0.54026	0.74	T	0.59161	-0.7506	9	0.30078	T	0.28	-14.425	11.9585	0.52995	0.0836:0.0:0.9164:0.0	.	99	Q9BT43	RPC7L_HUMAN	L	99	.	ENSP00000358320:P99L	P	-	2	0	POLR3GL	144169321	1.000000	0.71417	0.834000	0.33040	0.955000	0.61496	4.357000	0.59436	1.471000	0.48121	0.655000	0.94253	CCG	.	.	.	none		0.483	POLR3GL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038510.1	NM_032305	
CTSK	1513	hgsc.bcm.edu	37	1	150778422	150778422	+	Missense_Mutation	SNP	G	G	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:150778422G>C	ENST00000271651.3	-	4	424	c.314C>G	c.(313-315)aCc>aGc	p.T105S	CTSK_ENST00000480670.1_5'UTR	NM_000396.3	NP_000387.1	P43235	CATK_HUMAN	cathepsin K	105					bone resorption (GO:0045453)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|intramembranous ossification (GO:0001957)|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)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|proteoglycan binding (GO:0043394)			cervix(1)|endometrium(1)|lung(4)|skin(1)	7	all_cancers(9;2.32e-51)|all_epithelial(9;3.89e-42)|all_lung(15;4.59e-35)|Lung NSC(24;1.7e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Colorectal(459;0.171)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			GATATAAAGGGTGTCATTACT	0.458																																					p.T105S		Atlas-SNP	.											.	CTSK	27	.	0			c.C314G						PASS	.						121.0	116.0	118.0					1																	150778422		2203	4300	6503	SO:0001583	missense	1513	exon4			TAAAGGGTGTCAT	BC016058	CCDS969.1	1q21	2008-02-05	2006-12-05		ENSG00000143387	ENSG00000143387		"""Cathepsins"""	2536	protein-coding gene	gene with protein product		601105	"""cathepsin K (pycnodysostosis)"""	CTSO2, CTSO, PYCD		7818555	Standard	NM_000396		Approved	PKND	uc001evp.2	P43235	OTTHUMG00000035008	ENST00000271651.3:c.314C>G	chr1.hg19:g.150778422G>C	ENSP00000271651:p.Thr105Ser	99.0	0.0	.		115.0	47.0	.	NM_000396	Q6FHS6	Missense_Mutation	SNP	ENST00000271651.3	hg19	CCDS969.1	.	.	.	.	.	.	.	.	.	.	G	2.425	-0.332121	0.05314	.	.	ENSG00000143387	ENST00000271651;ENST00000443913	D;D	0.97553	-4.43;-4.43	5.38	5.38	0.77491	.	0.289753	0.38492	N	0.001665	D	0.86234	0.5884	L	0.31120	0.905	0.38859	D	0.956449	P	0.42993	0.797	B	0.32980	0.156	D	0.87916	0.2700	10	0.02654	T	1	.	12.0088	0.53276	0.0:0.0:0.8273:0.1727	.	105	P43235	CATK_HUMAN	S	105;164	ENSP00000271651:T105S;ENSP00000405083:T164S	ENSP00000271651:T105S	T	-	2	0	CTSK	149045046	1.000000	0.71417	0.996000	0.52242	0.431000	0.31685	3.309000	0.51903	2.683000	0.91414	0.561000	0.74099	ACC	.	.	.	none		0.458	CTSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084732.1	NM_000396	
TCHH	7062	hgsc.bcm.edu	37	1	152081020	152081020	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:152081020C>T	ENST00000368804.1	-	2	4672	c.4673G>A	c.(4672-4674)cGc>cAc	p.R1558H		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1558	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTCCTCCTCGCGGAATTTTCT	0.612																																					p.R1558H		Atlas-SNP	.											.	TCHH	275	.	0			c.G4673A						PASS	.						59.0	60.0	60.0					1																	152081020		1888	4101	5989	SO:0001583	missense	7062	exon3			TCCTCGCGGAATT	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.4673G>A	chr1.hg19:g.152081020C>T	ENSP00000357794:p.Arg1558His	82.0	0.0	.		79.0	23.0	.	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	-	8.616	0.890198	0.17613	.	.	ENSG00000159450	ENST00000368804	T	0.05925	3.37	3.3	1.34	0.21922	.	.	.	.	.	T	0.05135	0.0137	L	0.46157	1.445	0.09310	N	1	D	0.89917	1.0	D	0.63192	0.912	T	0.29150	-1.0021	9	0.44086	T	0.13	-1.3601	4.0858	0.09947	0.4099:0.4715:0.0:0.1186	.	1558	Q07283	TRHY_HUMAN	H	1558	ENSP00000357794:R1558H	ENSP00000357794:R1558H	R	-	2	0	TCHH	150347644	0.000000	0.05858	0.007000	0.13788	0.032000	0.12392	-0.112000	0.10791	0.211000	0.20683	0.460000	0.39030	CGC	.	.	.	none		0.612	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
LYST	1130	hgsc.bcm.edu	37	1	235969849	235969849	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:235969849C>T	ENST00000389794.3	-	6	2761	c.2587G>A	c.(2587-2589)Gct>Act	p.A863T	LYST_ENST00000536965.1_Missense_Mutation_p.A863T|LYST_ENST00000389793.2_Missense_Mutation_p.A863T			Q99698	LYST_HUMAN	lysosomal trafficking regulator	863					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)			TCTGAATAAGCTTGCTGATGA	0.408																																					p.A863T		Atlas-SNP	.											.	LYST	370	.	0			c.G2587A						PASS	.						164.0	164.0	164.0					1																	235969849		2203	4300	6503	SO:0001583	missense	1130	exon6			AATAAGCTTGCTG	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.2587G>A	chr1.hg19:g.235969849C>T	ENSP00000374444:p.Ala863Thr	116.0	0.0	.		149.0	57.0	.	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	hg19	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	C	11.63	1.696527	0.30142	.	.	ENSG00000143669	ENST00000389794;ENST00000389793;ENST00000536965	T;T;T	0.62364	0.03;0.03;1.18	5.48	3.56	0.40772	.	1.082300	0.07038	N	0.829561	T	0.52041	0.1710	L	0.34521	1.04	0.09310	N	1	P;B	0.40660	0.726;0.005	B;B	0.39217	0.294;0.004	T	0.39440	-0.9614	10	0.45353	T	0.12	.	7.6404	0.28290	0.2933:0.6315:0.0:0.0753	.	863;863	Q99698-3;Q99698	.;LYST_HUMAN	T	863	ENSP00000374444:A863T;ENSP00000374443:A863T;ENSP00000438315:A863T	ENSP00000374443:A863T	A	-	1	0	LYST	234036472	0.000000	0.05858	0.579000	0.28588	0.710000	0.40934	0.322000	0.19576	0.648000	0.30732	0.655000	0.94253	GCT	.	.	.	none		0.408	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
ZNF695	57116	hgsc.bcm.edu	37	1	247150413	247150414	+	Missense_Mutation	DNP	TT	TT	AA			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:247150413_247150414TT>AA	ENST00000339986.7	-	4	1550_1551	c.1403_1404AA>TT	c.(1402-1404)gAA>gTT	p.E468V	ZNF695_ENST00000498046.2_Intron|ZNF695_ENST00000487338.2_Intron	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	468					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-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)			CTTTGCCACATTCTTCACATTT	0.386																																					p.E468D|p.E468V		Atlas-SNP	.											.	ZNF695	55	.	0			c.A1404T|c.A1403T						PASS	.																																			SO:0001583	missense	57116	exon4			GCCACATTCTTCA|CCACATTCTTCAC		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"""Zinc fingers, C2H2-type"", ""-"""	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000339986.7:c.1403_1404delinsAA	chr1.hg19:g.247150413_247150414delinsAA	ENSP00000341236:p.Glu468Val	69.0|68.0	0.0	.		99.0	48.0	.	NM_020394	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	hg19	CCDS44344.1																																																																																			.	.	.	none		0.386	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394	
LTBP1	4052	hgsc.bcm.edu	37	2	33525581	33525581	+	Missense_Mutation	SNP	C	C	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr2:33525581C>A	ENST00000404816.2	+	21	3652	c.3299C>A	c.(3298-3300)tCc>tAc	p.S1100Y	LTBP1_ENST00000272273.5_Missense_Mutation_p.S40Y|LTBP1_ENST00000418533.2_Missense_Mutation_p.S774Y|LTBP1_ENST00000498013.1_3'UTR|LTBP1_ENST00000404525.1_Missense_Mutation_p.S721Y|LTBP1_ENST00000402934.1_Missense_Mutation_p.S721Y|LTBP1_ENST00000354476.3_Missense_Mutation_p.S1101Y|LTBP1_ENST00000390003.4_Missense_Mutation_p.S775Y|LTBP1_ENST00000407925.1_Missense_Mutation_p.S774Y			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1100	EGF-like 9; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)				ACCGAGGGCTCCTTCAGGTGC	0.453																																					p.S1100Y		Atlas-SNP	.											.	LTBP1	317	.	0			c.C3299A						PASS	.						96.0	96.0	96.0					2																	33525581		2203	4300	6503	SO:0001583	missense	4052	exon21			AGGGCTCCTTCAG		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.3299C>A	chr2.hg19:g.33525581C>A	ENSP00000386043:p.Ser1100Tyr	81.0	0.0	.		99.0	36.0	.	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.1|24.1	4.488575|4.488575	0.84854|0.84854	.|.	.|.	ENSG00000049323|ENSG00000049323	ENST00000415140|ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273	.|D;D;D;D;D;D;D;D	.|0.95412	.|-3.7;-3.7;-3.7;-3.7;-3.7;-3.7;-3.7;-3.7	5.39|5.39	5.39|5.39	0.77823|0.77823	.|EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.|.	.|.	.|.	.|.	D|D	0.98226|0.98226	0.9413|0.9413	M|M	0.90870|0.90870	3.155|3.155	0.58432|0.58432	D|D	0.999995|0.999995	.|P;D;D;D;D;D;D	.|0.89917	.|0.879;0.999;1.0;1.0;1.0;1.0;0.999	.|P;D;D;D;D;D;D	.|0.91635	.|0.766;0.995;0.998;0.998;0.991;0.999;0.991	D|D	0.99257|0.99257	1.0889|1.0889	5|9	.|0.87932	.|D	.|0	.|.	17.9453|17.9453	0.89036|0.89036	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|40;1100;774;721;774;775;1101	.|E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	.|.;LTBP1_HUMAN;.;.;.;.;.	T|Y	62|1100;1101;775;774;721;721;774;40	.|ENSP00000386043:S1100Y;ENSP00000346467:S1101Y;ENSP00000374653:S775Y;ENSP00000393057:S774Y;ENSP00000384373:S721Y;ENSP00000385359:S721Y;ENSP00000384091:S774Y;ENSP00000272273:S40Y	.|ENSP00000272273:S40Y	P|S	+|+	1|2	0|0	LTBP1|LTBP1	33379085|33379085	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	6.468000|6.468000	0.73551|0.73551	2.532000|2.532000	0.85374|0.85374	0.555000|0.555000	0.69702|0.69702	CCT|TCC	.	.	.	none		0.453	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
ALMS1	7840	hgsc.bcm.edu	37	2	73613036	73613037	+	Missense_Mutation	DNP	GA	GA	CT	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr2:73613036_73613037GA>CT	ENST00000264448.6	+	1	151_152	c.40_41GA>CT	c.(40-42)GAg>CTg	p.E14L	ALMS1_ENST00000409009.1_Missense_Mutation_p.E14L|ALMS1_ENST00000377715.1_Missense_Mutation_p.E14L	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				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)		p.E27_E28delEE(1)		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						CGAGCTggaggaggaggaggag	0.693																																					p.E14Q|p.E14V		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C|c.A41T						PASS	.																																			SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG|TGGAGGAGGAGGA	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	Exception_encountered	chr2.hg19:g.73613036_73613037delinsCT	ENSP00000264448:p.Glu14Leu	184.0|187.0	0.0	.		314.0|321.0	26.0|32.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.	.	none		0.693	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
DHRS9	10170	hgsc.bcm.edu	37	2	169939934	169939934	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr2:169939934A>C	ENST00000327239.4	+	6	1913	c.409A>C	c.(409-411)Aac>Cac	p.N137H	DHRS9_ENST00000421653.1_5'UTR|DHRS9_ENST00000357546.2_Missense_Mutation_p.N137H|DHRS9_ENST00000436483.2_Missense_Mutation_p.N137H|DHRS9_ENST00000602501.1_Missense_Mutation_p.N137H|DHRS9_ENST00000432060.2_Missense_Mutation_p.N197H|DHRS9_ENST00000428522.1_Missense_Mutation_p.N137H|DHRS9_ENST00000412271.1_Missense_Mutation_p.N137H	NM_005771.4	NP_005762.2	Q9BPW9	DHRS9_HUMAN	dehydrogenase/reductase (SDR family) member 9	137					9-cis-retinoic acid biosynthetic process (GO:0042904)|androgen metabolic process (GO:0008209)|epithelial cell differentiation (GO:0030855)|progesterone metabolic process (GO:0042448)|retinol metabolic process (GO:0042572)	integral component of endoplasmic reticulum membrane (GO:0030176)	alcohol dehydrogenase (NAD) activity (GO:0004022)|racemase and epimerase activity (GO:0016854)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			breast(1)|endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						TATTGAAGTGAACCTGTTTGG	0.488																																					p.N137H		Atlas-SNP	.											.	DHRS9	29	.	0			c.A409C						PASS	.						148.0	136.0	140.0					2																	169939934		2203	4300	6503	SO:0001583	missense	10170	exon6			GAAGTGAACCTGT	AF067174	CCDS2231.1, CCDS74600.1	2q31.1	2011-09-14			ENSG00000073737	ENSG00000073737		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	16888	protein-coding gene	gene with protein product	"""NADP-dependent retinol dehydrogenase/reductase"", ""3-alpha hydroxysteroid dehydrogenase"", ""retinol dehydrogenase homolog"", ""short chain dehydrogenase/reductase family 9C, member 4"""	612131				11304534, 11294878, 19027726	Standard	NM_001142270		Approved	RDHL, 3alpha-HSD, RETSDR8, RDH15, SDR9C4	uc010zde.2	Q9BPW9	OTTHUMG00000132180	ENST00000327239.4:c.409A>C	chr2.hg19:g.169939934A>C	ENSP00000316670:p.Asn137His	93.0	0.0	.		96.0	12.0	.	NM_005771	B7Z416|D3DPC1|Q5RKX1|Q9NRA9|Q9NRB0	Missense_Mutation	SNP	ENST00000327239.4	hg19	CCDS2231.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.804239	0.90623	.	.	ENSG00000073737	ENST00000327239;ENST00000357546;ENST00000432060;ENST00000428522;ENST00000436483;ENST00000412271	D;D;D;D;D;D	0.94497	-3.44;-3.44;-3.44;-3.44;-3.44;-3.44	5.93	5.93	0.95920	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.98359	0.9455	H	0.97491	4.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99701	1.1004	10	0.87932	D	0	.	16.0558	0.80805	1.0:0.0:0.0:0.0	.	197;137	B7Z416;Q9BPW9	.;DHRS9_HUMAN	H	137;137;197;137;137;137	ENSP00000316670:N137H;ENSP00000350154:N137H;ENSP00000389241:N197H;ENSP00000388564:N137H;ENSP00000407167:N137H;ENSP00000407747:N137H	ENSP00000316670:N137H	N	+	1	0	DHRS9	169648180	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	9.047000	0.93823	2.281000	0.76405	0.533000	0.62120	AAC	.	.	.	none		0.488	DHRS9-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333612.3	NM_005771	
MRPL44	65080	hgsc.bcm.edu	37	2	224824598	224824598	+	Missense_Mutation	SNP	A	A	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr2:224824598A>G	ENST00000258383.3	+	2	596	c.527A>G	c.(526-528)gAg>gGg	p.E176G		NM_022915.3	NP_075066.1	Q9H9J2	RM44_HUMAN	mitochondrial ribosomal protein L44	176	RNase III.				mitochondrial translational elongation (GO:0070125)|RNA processing (GO:0006396)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		all_lung(227;0.00679)|Lung NSC(271;0.00855)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;2.51e-10)|all cancers(144;7.89e-08)|Lung(261;0.00705)|LUSC - Lung squamous cell carcinoma(224;0.008)		TTGGCTGTGGAGCAGTTAACA	0.493																																					p.E176G		Atlas-SNP	.											.	MRPL44	31	.	0			c.A527G						PASS	.						116.0	114.0	114.0					2																	224824598		2203	4300	6503	SO:0001583	missense	65080	exon2			CTGTGGAGCAGTT	AK022763	CCDS2459.1	2p24.3-p24.1	2012-09-13			ENSG00000135900	ENSG00000135900		"""Mitochondrial ribosomal proteins / large subunits"""	16650	protein-coding gene	gene with protein product	"""39S ribosomal protein L44, mitochondrial"""	611849					Standard	NM_022915		Approved	FLJ12701, FLJ13990	uc002vnr.4	Q9H9J2	OTTHUMG00000133164	ENST00000258383.3:c.527A>G	chr2.hg19:g.224824598A>G	ENSP00000258383:p.Glu176Gly	106.0	0.0	.		98.0	33.0	.	NM_022915	Q53S16|Q6IA62|Q9H821	Missense_Mutation	SNP	ENST00000258383.3	hg19	CCDS2459.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.684531	0.88639	.	.	ENSG00000135900	ENST00000258383	T	0.41400	1.0	5.68	5.68	0.88126	Ribonuclease III (3);	0.157358	0.56097	D	0.000036	T	0.42899	0.1223	M	0.75447	2.3	0.58432	D	0.999996	B	0.27140	0.169	B	0.24848	0.056	T	0.33085	-0.9882	10	0.16420	T	0.52	-0.8659	13.8891	0.63726	1.0:0.0:0.0:0.0	.	176	Q9H9J2	RM44_HUMAN	G	176	ENSP00000258383:E176G	ENSP00000258383:E176G	E	+	2	0	MRPL44	224532842	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.938000	0.75904	2.160000	0.67779	0.519000	0.50382	GAG	.	.	.	none		0.493	MRPL44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256866.2	NM_022915	
ASB18	401036	hgsc.bcm.edu	37	2	237103670	237103670	+	Missense_Mutation	SNP	C	C	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr2:237103670C>G	ENST00000409749.3	-	6	1245	c.1246G>C	c.(1246-1248)Gcc>Ccc	p.A416P	ASB18_ENST00000330842.6_Missense_Mutation_p.A387P|AC079135.1_ENST00000415226.1_RNA|AC079135.1_ENST00000483218.1_RNA	NM_212556.2	NP_997721.2	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box containing 18	416	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					large_intestine(1)|lung(3)|ovary(1)|prostate(1)	6		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)		AGGGCCAAGGCAAAGAGGGAC	0.537																																					p.A416P		Atlas-SNP	.											ASB18_ENST00000409749,NS,carcinoma,0,1	ASB18	34	.	0			c.G1246C						PASS	.						63.0	78.0	73.0					2																	237103670		2115	4243	6358	SO:0001583	missense	401036	exon6			CCAAGGCAAAGAG	AK123854	CCDS46548.1	2q37.2	2013-01-10	2011-01-25		ENSG00000182177	ENSG00000182177		"""Ankyrin repeat domain containing"""	19770	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 18"""			12076535	Standard	NM_212556		Approved		uc010znh.2	Q6ZVZ8	OTTHUMG00000153086	ENST00000409749.3:c.1246G>C	chr2.hg19:g.237103670C>G	ENSP00000386532:p.Ala416Pro	169.0	0.0	.		133.0	58.0	.	NM_212556	B6ZDL7	Missense_Mutation	SNP	ENST00000409749.3	hg19	CCDS46548.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.606949	0.46527	.	.	ENSG00000182177	ENST00000330842;ENST00000409749	T;T	0.39592	1.07;1.14	4.65	2.62	0.31277	SOCS protein, C-terminal (1);	.	.	.	.	T	0.52853	0.1760	M	0.68593	2.085	0.09310	N	1	D	0.71674	0.998	D	0.64321	0.924	T	0.36114	-0.9761	9	0.42905	T	0.14	.	4.0084	0.09611	0.1654:0.5748:0.1613:0.0985	.	416	Q6ZVZ8	ASB18_HUMAN	P	387;416	ENSP00000329970:A387P;ENSP00000386532:A416P	ENSP00000329970:A387P	A	-	1	0	ASB18	236768409	0.017000	0.18338	0.127000	0.21898	0.760000	0.43138	0.042000	0.13949	1.127000	0.42034	0.561000	0.74099	GCC	.	.	.	none		0.537	ASB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329436.1	NM_212556	
IQCA1	79781	hgsc.bcm.edu	37	2	237240213	237240213	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr2:237240213T>C	ENST00000409907.3	-	18	2436	c.2162A>G	c.(2161-2163)aAt>aGt	p.N721S	IQCA1_ENST00000309507.5_Missense_Mutation_p.N718S|IQCA1_ENST00000431676.2_Missense_Mutation_p.N680S	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	721							ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						GACTCCTCCATTGCGTTCAAT	0.498																																					p.N729S		Atlas-SNP	.											.	IQCA1	170	.	0			c.A2186G						PASS	.						60.0	59.0	59.0					2																	237240213		2009	4175	6184	SO:0001583	missense	79781	exon18			CCTCCATTGCGTT	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.2162A>G	chr2.hg19:g.237240213T>C	ENSP00000387347:p.Asn721Ser	74.0	0.0	.		73.0	11.0	.	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Missense_Mutation	SNP	ENST00000409907.3	hg19	CCDS46549.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.878792	0.00537	.	.	ENSG00000132321	ENST00000409907;ENST00000457693;ENST00000309507;ENST00000431676	D;D;D	0.87887	-2.31;-2.31;-2.31	5.23	1.1	0.20463	.	1.245700	0.05677	N	0.589728	D	0.84074	0.5392	M	0.67953	2.075	0.09310	N	1	B;B;B	0.23128	0.017;0.044;0.08	B;B;B	0.23275	0.028;0.045;0.045	T	0.64993	-0.6276	10	0.30854	T	0.27	.	4.8923	0.13733	0.1115:0.0725:0.1289:0.6871	.	680;729;721	E7EWQ0;E9PH78;Q86XH1	.;.;IQCA1_HUMAN	S	721;729;718;680	ENSP00000387347:N721S;ENSP00000311951:N718S;ENSP00000407213:N680S	ENSP00000311951:N718S	N	-	2	0	IQCA1	236904952	0.059000	0.20769	0.000000	0.03702	0.153000	0.21895	1.431000	0.34925	0.289000	0.22422	0.533000	0.62120	AAT	.	.	.	none		0.498	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726	
SETD2	29072	hgsc.bcm.edu	37	3	47058732	47058732	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:47058732C>T	ENST00000409792.3	-	21	7588	c.7546G>A	c.(7546-7548)Gtt>Att	p.V2516I		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2516	Interaction with POLR2A.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TTATTCATAACACCGTGAGTC	0.478			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.V2516I		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.G7546A						PASS	.						132.0	119.0	124.0					3																	47058732		2203	4300	6503	SO:0001583	missense	29072	exon21			TCATAACACCGTG	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.7546G>A	chr3.hg19:g.47058732C>T	ENSP00000386759:p.Val2516Ile	47.0	0.0	.		72.0	67.0	.	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	25.9	4.684790	0.88639	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	D	0.91631	-2.88	5.14	5.14	0.70334	SRI, Set2 Rpb1 interacting (1);	0.000000	0.48286	D	0.000195	D	0.93413	0.7899	N	0.21448	0.665	0.80722	D	1	B;P	0.38863	0.037;0.65	B;D	0.64687	0.438;0.928	D	0.92291	0.5841	10	0.36615	T	0.2	.	18.7829	0.91941	0.0:1.0:0.0:0.0	.	2516;2516	F2Z317;Q9BYW2	.;SETD2_HUMAN	I	2516	ENSP00000386759:V2516I	ENSP00000386759:V2516I	V	-	1	0	SETD2	47033736	1.000000	0.71417	0.908000	0.35775	0.994000	0.84299	7.562000	0.82300	2.668000	0.90789	0.655000	0.94253	GTT	.	.	.	none		0.478	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
DNAJB8	165721	hgsc.bcm.edu	37	3	128181520	128181520	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:128181520T>C	ENST00000469083.1	-	2	3126	c.569A>G	c.(568-570)aAt>aGt	p.N190S	DNAJB8_ENST00000319153.3_Missense_Mutation_p.N190S|DNAJB8-AS1_ENST00000471626.1_RNA			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	190					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)		CTTGTGGCCATTGATCATCTC	0.622																																					p.N190S		Atlas-SNP	.											.	DNAJB8	34	.	0			c.A569G						PASS	.						139.0	116.0	124.0					3																	128181520		2203	4300	6503	SO:0001583	missense	165721	exon3			TGGCCATTGATCA		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.569A>G	chr3.hg19:g.128181520T>C	ENSP00000417418:p.Asn190Ser	76.0	0.0	.		87.0	73.0	.	NM_153330	B3KWV7	Missense_Mutation	SNP	ENST00000469083.1	hg19	CCDS3048.1	.	.	.	.	.	.	.	.	.	.	T	15.57	2.872026	0.51695	.	.	ENSG00000179407	ENST00000469083;ENST00000319153	T;T	0.41400	1.0;1.0	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.64713	0.2623	M	0.91140	3.18	0.58432	D	0.999995	D	0.61080	0.989	P	0.55391	0.775	T	0.74281	-0.3716	10	0.72032	D	0.01	.	12.8323	0.57752	0.0:0.0:0.0:1.0	.	190	Q8NHS0	DNJB8_HUMAN	S	190	ENSP00000417418:N190S;ENSP00000316053:N190S	ENSP00000316053:N190S	N	-	2	0	DNAJB8	129664210	1.000000	0.71417	0.531000	0.27976	0.053000	0.15095	4.000000	0.57039	1.772000	0.52199	0.459000	0.35465	AAT	.	.	.	none		0.622	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330	
TMCC1	23023	hgsc.bcm.edu	37	3	129390024	129390024	+	Silent	SNP	A	A	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:129390024A>T	ENST00000393238.3	-	4	1000	c.660T>A	c.(658-660)tcT>tcA	p.S220S	TMCC1_ENST00000432054.2_5'UTR|TMCC1_ENST00000329333.5_Silent_p.S41S|TMCC1_ENST00000426664.2_Silent_p.S106S	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	220						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						TTCCATCCACAGAGTCTGTGT	0.507																																					p.S220S		Atlas-SNP	.											.	TMCC1	105	.	0			c.T660A						PASS	.						112.0	108.0	109.0					3																	129390024		2203	4300	6503	SO:0001819	synonymous_variant	23023	exon4			ATCCACAGAGTCT	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"""Transmembrane and coiled-coil domain containing"""	29116	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 1"""			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.660T>A	chr3.hg19:g.129390024A>T		53.0	0.0	.		73.0	5.0	.	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Silent	SNP	ENST00000393238.3	hg19	CCDS33855.1																																																																																			.	.	.	none		0.507	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008	
MUC4	4585	hgsc.bcm.edu	37	3	195509651	195509651	+	Missense_Mutation	SNP	G	G	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:195509651G>T	ENST00000463781.3	-	2	9259	c.8800C>A	c.(8800-8802)Ctt>Att	p.L2934I	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L2934I|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.L2934F(1)|p.P2934S(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)		ACTGAGGAAAGGCTGGTGACA	0.577																																					p.L2934I		Atlas-SNP	.											MUC4_ENST00000463781,trunk,malignant_melanoma,0,2	MUC4	1505	.	2	Substitution - Missense(2)	skin(2)	c.C8800A						PASS	.						9.0	8.0	8.0					3																	195509651		662	1509	2171	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.8800C>A	chr3.hg19:g.195509651G>T	ENSP00000417498:p.Leu2934Ile	92.0	0.0	.		133.0	7.0	.	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	hg19	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	4.385	0.071104	0.08436	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32988	1.43;1.44	.	.	.	.	.	.	.	.	T	0.18841	0.0452	N	0.14661	0.345	0.09310	N	1	P	0.52170	0.951	P	0.48304	0.573	T	0.10776	-1.0615	7	.	.	.	.	3.7959	0.08738	0.0:0.0:0.5797:0.4203	.	2806	E7ESK3	.	I	2934	ENSP00000417498:L2934I;ENSP00000420243:L2934I	.	L	-	1	0	MUC4	196994430	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.715000	0.00385	-0.000000	0.14550	0.000000	0.15137	CTT	.	.	.	none		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
EVC	2121	hgsc.bcm.edu	37	4	5812077	5812077	+	Silent	SNP	A	A	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr4:5812077A>C	ENST00000264956.6	+	20	2978	c.2794A>C	c.(2794-2796)Agg>Cgg	p.R932R	EVC_ENST00000382674.2_Silent_p.R932R	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	932					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)				GAAGCCCCTAAGGACTAAAAG	0.562																																					p.R932R		Atlas-SNP	.											.	EVC	90	.	0			c.A2794C						PASS	.						41.0	45.0	44.0					4																	5812077		2203	4299	6502	SO:0001819	synonymous_variant	2121	exon20			CCCCTAAGGACTA	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.2794A>C	chr4.hg19:g.5812077A>C		230.0	0.0	.		226.0	96.0	.	NM_153717		Silent	SNP	ENST00000264956.6	hg19	CCDS3383.1																																																																																			.	.	.	none		0.562	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
CCNI	10983	hgsc.bcm.edu	37	4	77969741	77969741	+	Silent	SNP	A	A	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr4:77969741A>G	ENST00000237654.4	-	7	1341	c.765T>C	c.(763-765)ccT>ccC	p.P255P	CCNI_ENST00000537948.1_Silent_p.P241P	NM_006835.2	NP_006826.1	Q14094	CCNI_HUMAN	cyclin I	255					regulation of cell cycle (GO:0051726)|spermatogenesis (GO:0007283)					NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	9						CGGAATTCAGAGGCAGGGAAG	0.517																																					p.P255P		Atlas-SNP	.											.	CCNI	22	.	0			c.T765C						PASS	.						84.0	77.0	79.0					4																	77969741		2203	4300	6503	SO:0001819	synonymous_variant	10983	exon7			ATTCAGAGGCAGG	D50310	CCDS3580.1	4q21.1	2014-07-03			ENSG00000118816	ENSG00000118816			1595	protein-coding gene	gene with protein product						7493655	Standard	NM_006835		Approved	CCNI1	uc003hkm.3	Q14094	OTTHUMG00000130106	ENST00000237654.4:c.765T>C	chr4.hg19:g.77969741A>G		70.0	0.0	.		103.0	40.0	.	NM_006835	B2R6M0|B7Z6X4	Silent	SNP	ENST00000237654.4	hg19	CCDS3580.1	.	.	.	.	.	.	.	.	.	.	A	7.455	0.643541	0.14451	.	.	ENSG00000118816	ENST00000515468	.	.	.	5.9	5.9	0.94986	.	.	.	.	.	T	0.48409	0.1498	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53337	-0.8453	4	.	.	.	-12.2282	3.2125	0.06687	0.6383:0.1553:0.0749:0.1315	.	.	.	.	P	55	.	.	S	-	1	0	CCNI	78188765	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.896000	0.28377	2.251000	0.74343	0.528000	0.53228	TCT	.	.	.	none		0.517	CCNI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252412.2	NM_006835	
PTPN13	5783	hgsc.bcm.edu	37	4	87671752	87671752	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr4:87671752T>C	ENST00000411767.2	+	18	2843	c.2780T>C	c.(2779-2781)gTt>gCt	p.V927A	PTPN13_ENST00000511467.1_Missense_Mutation_p.V927A|PTPN13_ENST00000427191.2_Missense_Mutation_p.V927A|PTPN13_ENST00000436978.1_Missense_Mutation_p.V927A|PTPN13_ENST00000316707.6_Intron			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	927					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)		CCTTTATCAGTTCAAGCTGAG	0.468																																					p.V927A		Atlas-SNP	.											.	PTPN13	203	.	0			c.T2780C						PASS	.						80.0	80.0	80.0					4																	87671752		1971	4165	6136	SO:0001583	missense	5783	exon18			TATCAGTTCAAGC		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.2780T>C	chr4.hg19:g.87671752T>C	ENSP00000407249:p.Val927Ala	247.0	1.0	.		296.0	127.0	.	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	T	13.05	2.120999	0.37436	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T	0.54071	0.59;0.63;0.6;0.63	6.16	3.78	0.43462	.	0.291309	0.24089	N	0.041646	T	0.47857	0.1468	L	0.57536	1.79	0.23101	N	0.99829	B;B;B	0.16166	0.016;0.016;0.012	B;B;B	0.15870	0.014;0.004;0.009	T	0.45920	-0.9228	10	0.62326	D	0.03	.	10.2207	0.43194	0.0:0.1317:0.0:0.8683	.	927;927;927	Q12923-3;Q12923;Q12923-4	.;PTN13_HUMAN;.	A	927;927;927;927;895	ENSP00000408368:V927A;ENSP00000394794:V927A;ENSP00000407249:V927A;ENSP00000426626:V927A	ENSP00000349909:V895A	V	+	2	0	PTPN13	87890776	0.771000	0.28555	0.936000	0.37596	0.976000	0.68499	2.231000	0.43009	0.584000	0.29591	0.528000	0.53228	GTT	.	.	.	none		0.468	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
KIAA1109	84162	hgsc.bcm.edu	37	4	123226024	123226024	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr4:123226024A>C	ENST00000264501.4	+	56	9931	c.9558A>C	c.(9556-9558)gaA>gaC	p.E3186D	KIAA1109_ENST00000455637.1_Missense_Mutation_p.E3186D|KIAA1109_ENST00000388738.3_Missense_Mutation_p.E3186D			Q2LD37	K1109_HUMAN	KIAA1109	3186					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TTGAACTGGAACTTTCTAACC	0.398																																					p.E3186D		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A9558C						PASS	.						106.0	98.0	101.0					4																	123226024		1837	4090	5927	SO:0001583	missense	84162	exon54			ACTGGAACTTTCT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.9558A>C	chr4.hg19:g.123226024A>C	ENSP00000264501:p.Glu3186Asp	121.0	0.0	.		115.0	49.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.3|21.3	4.131217|4.131217	0.77549|0.77549	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000419325	T;T;T|.	0.32272|.	1.46;1.46;1.46|.	5.81|5.81	0.65|0.65	0.17812|0.17812	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53546|0.53546	0.1803|0.1803	L|L	0.55481|0.55481	1.735|1.735	0.31761|0.31761	N|N	0.63333|0.63333	P;D|.	0.67145|.	0.949;0.996|.	P;P|.	0.54499|.	0.717;0.754|.	T|T	0.59026|0.59026	-0.7531|-0.7531	10|5	0.62326|.	D|.	0.03|.	.|.	11.3914|11.3914	0.49817|0.49817	0.6293:0.0:0.3707:0.0|0.6293:0.0:0.3707:0.0	.|.	3186;3186|.	Q2LD37-6;Q2LD37|.	.;K1109_HUMAN|.	D|P	3186|1144	ENSP00000264501:E3186D;ENSP00000373390:E3186D;ENSP00000389925:E3186D|.	ENSP00000264501:E3186D|.	E|T	+|+	3|1	2|0	KIAA1109|KIAA1109	123445474|123445474	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.040000|1.040000	0.30278|0.30278	0.146000|0.146000	0.19002|0.19002	0.454000|0.454000	0.30748|0.30748	GAA|ACT	.	.	.	none		0.398	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
ANXA10	11199	hgsc.bcm.edu	37	4	169099042	169099042	+	Splice_Site	SNP	T	T	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr4:169099042T>C	ENST00000359299.3	+	8	722	c.536T>C	c.(535-537)gTc>gCc	p.V179A		NM_007193.4	NP_009124.2	Q9UJ72	ANX10_HUMAN	annexin A10	179						mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)			endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(2)	16		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0325)		ATGTTCCAGGTCCTATGGGAA	0.498																																					p.V179A		Atlas-SNP	.											.	ANXA10	44	.	0			c.T536C						PASS	.						125.0	119.0	121.0					4																	169099042		2203	4300	6503	SO:0001630	splice_region_variant	11199	exon8			TCCAGGTCCTATG	AJ238979	CCDS34096.1	4q32.3	2008-02-05			ENSG00000109511	ENSG00000109511		"""Annexins"""	534	protein-coding gene	gene with protein product		608008				10458909	Standard	NM_007193		Approved	ANX14	uc003irm.3	Q9UJ72	OTTHUMG00000161275	ENST00000359299.3:c.535-1T>C	chr4.hg19:g.169099042T>C		83.0	0.0	.		124.0	21.0	.	NM_007193	Q96IQ5|Q9UJV4	Missense_Mutation	SNP	ENST00000359299.3	hg19	CCDS34096.1	.	.	.	.	.	.	.	.	.	.	T	9.052	0.992269	0.18966	.	.	ENSG00000109511	ENST00000359299;ENST00000393751	T	0.10382	2.88	5.66	5.66	0.87406	.	0.093082	0.47093	D	0.000246	T	0.06325	0.0163	N	0.01800	-0.715	0.58432	D	0.999996	P;P	0.45634	0.863;0.656	P;B	0.48227	0.571;0.253	T	0.45804	-0.9236	10	0.07030	T	0.85	.	15.8919	0.79305	0.0:0.0:0.0:1.0	.	51;179	Q6ITU8;Q9UJ72	.;ANX10_HUMAN	A	179	ENSP00000352248:V179A	ENSP00000352248:V179A	V	+	2	0	ANXA10	169335617	1.000000	0.71417	1.000000	0.80357	0.613000	0.37349	5.611000	0.67674	2.168000	0.68352	0.533000	0.62120	GTC	.	.	.	none		0.498	ANXA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364348.2	NM_007193	Missense_Mutation
MCC	4163	hgsc.bcm.edu	37	5	112399744	112399744	+	Missense_Mutation	SNP	G	G	C	rs147869500		TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr5:112399744G>C	ENST00000302475.4	-	12	2143	c.1580C>G	c.(1579-1581)gCc>gGc	p.A527G	MCC_ENST00000514701.3_5'UTR|MCC_ENST00000408903.3_Missense_Mutation_p.A717G|MCC_ENST00000515367.2_Missense_Mutation_p.A464G	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	527					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		CACGGCAAAGGCTCCCCCACA	0.617																																					p.A717G		Atlas-SNP	.											.	MCC	234	.	0			c.C2150G						PASS	.						59.0	57.0	58.0					5																	112399744		2202	4300	6502	SO:0001583	missense	4163	exon14			GCAAAGGCTCCCC		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.1580C>G	chr5.hg19:g.112399744G>C	ENSP00000305617:p.Ala527Gly	150.0	0.0	.		150.0	67.0	.	NM_001085377	D3DT05|Q6ZR04	Missense_Mutation	SNP	ENST00000302475.4	hg19	CCDS4111.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.646288	0.67358	.	.	ENSG00000171444	ENST00000302475;ENST00000515367;ENST00000408903	T;T;T	0.35789	2.46;2.46;1.29	5.61	5.61	0.85477	.	0.056778	0.64402	D	0.000002	T	0.29783	0.0744	N	0.19112	0.55	0.80722	D	1	B;B;B	0.31817	0.231;0.341;0.231	B;B;B	0.35971	0.107;0.215;0.074	T	0.05131	-1.0904	10	0.20046	T	0.44	-12.5962	19.638	0.95744	0.0:0.0:1.0:0.0	.	527;717;527	B7Z6G0;P23508-2;P23508	.;.;CRCM_HUMAN	G	527;464;717	ENSP00000305617:A527G;ENSP00000421615:A464G;ENSP00000386227:A717G	ENSP00000305617:A527G	A	-	2	0	MCC	112427643	1.000000	0.71417	0.744000	0.31058	0.703000	0.40648	7.743000	0.85020	2.626000	0.88956	0.655000	0.94253	GCC	.	G|1.000;A|0.000	.	alt		0.617	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377	
SNCAIP	9627	hgsc.bcm.edu	37	5	121786598	121786598	+	Nonsense_Mutation	SNP	G	G	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr5:121786598G>T	ENST00000261368.8	+	10	2318	c.2056G>T	c.(2056-2058)Gag>Tag	p.E686*	CTC-210G5.1_ENST00000506053.1_RNA|SNCAIP_ENST00000261367.7_Nonsense_Mutation_p.E733*|SNCAIP_ENST00000542191.1_Nonsense_Mutation_p.E244*|CTC-210G5.1_ENST00000503529.1_RNA|SNCAIP_ENST00000504884.2_3'UTR|CTC-210G5.1_ENST00000505546.1_RNA|SNCAIP_ENST00000414317.2_Nonsense_Mutation_p.E288*|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000379533.2_Nonsense_Mutation_p.E733*|SNCAIP_ENST00000379536.2_Nonsense_Mutation_p.E626*|SNCAIP_ENST00000379538.3_Nonsense_Mutation_p.E320*|CTC-210G5.1_ENST00000509993.1_RNA|SNCAIP_ENST00000503116.2_3'UTR	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	686					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		CAACAACTCTGAGGACCCCAA	0.537																																					p.E686X		Atlas-SNP	.											.	SNCAIP	308	.	0			c.G2056T						PASS	.						53.0	54.0	54.0					5																	121786598		2203	4300	6503	SO:0001587	stop_gained	9627	exon10			AACTCTGAGGACC	AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"""Ankyrin repeat domain containing"""	11139	protein-coding gene	gene with protein product	"""synphilin"""	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.2056G>T	chr5.hg19:g.121786598G>T	ENSP00000261368:p.Glu686*	83.0	0.0	.		83.0	37.0	.	NM_005460	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Nonsense_Mutation	SNP	ENST00000261368.8	hg19	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	G	40	8.438364	0.98810	.	.	ENSG00000064692	ENST00000542191;ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000379538;ENST00000261367;ENST00000414317;ENST00000447854	.	.	.	6.06	6.06	0.98353	.	0.049549	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-32.5971	20.6208	0.99490	0.0:0.0:1.0:0.0	.	.	.	.	X	244;626;686;733;626;320;733;288;326	.	ENSP00000261367:E733X	E	+	1	0	SNCAIP	121814497	1.000000	0.71417	0.979000	0.43373	0.934000	0.57294	9.194000	0.94962	2.882000	0.98803	0.655000	0.94253	GAG	.	.	.	none		0.537	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1		
RNF14	9604	hgsc.bcm.edu	37	5	141354465	141354465	+	Missense_Mutation	SNP	C	C	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr5:141354465C>A	ENST00000394520.2	+	4	560	c.251C>A	c.(250-252)cCa>cAa	p.P84Q	RNF14_ENST00000502341.1_Intron|RNF14_ENST00000394514.2_Intron|RNF14_ENST00000394515.3_Missense_Mutation_p.P84Q|RNF14_ENST00000356143.1_Missense_Mutation_p.P84Q|RNF14_ENST00000347642.3_Missense_Mutation_p.P84Q|RNF14_ENST00000540015.1_Intron|RNF14_ENST00000394519.1_Missense_Mutation_p.P84Q|AC005740.5_ENST00000520882.1_RNA	NM_001201365.1|NM_004290.4	NP_001188294.1|NP_004281.1	Q9UBS8	RNF14_HUMAN	ring finger protein 14	84	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.				androgen receptor signaling pathway (GO:0030521)|positive regulation of transcription, DNA-templated (GO:0045893)|protein ubiquitination (GO:0016567)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|small conjugating protein ligase activity (GO:0019787)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15		all_hematologic(541;0.0536)|Ovarian(839;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		CCAGATTATCCATCCTCTTCC	0.408																																					p.P84Q		Atlas-SNP	.											.	RNF14	30	.	0			c.C251A						PASS	.						178.0	160.0	166.0					5																	141354465		2203	4300	6503	SO:0001583	missense	9604	exon4			ATTATCCATCCTC	AF060544	CCDS4270.1, CCDS4271.1	5q23.3-q31.1	2008-02-05			ENSG00000013561	ENSG00000013561		"""RING-type (C3HC4) zinc fingers"""	10058	protein-coding gene	gene with protein product		605675				10085091, 10320776	Standard	NM_183399		Approved	ARA54, HFB30, TRIAD2	uc003lmc.3	Q9UBS8	OTTHUMG00000129660	ENST00000394520.2:c.251C>A	chr5.hg19:g.141354465C>A	ENSP00000378028:p.Pro84Gln	89.0	0.0	.		102.0	57.0	.	NM_001201365	A0AV26|A6NMR2|A8MTW5|B3KN72|B7ZLV2|D3DQE4|O94793|Q6IBV0	Missense_Mutation	SNP	ENST00000394520.2	hg19	CCDS4270.1	.	.	.	.	.	.	.	.	.	.	C	32	5.149590	0.94645	.	.	ENSG00000013561	ENST00000511961;ENST00000506822;ENST00000513019;ENST00000356143;ENST00000394520;ENST00000347642;ENST00000506938;ENST00000394515;ENST00000507163;ENST00000394519	D;D;D;D;D;D;D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28;-3.28;-3.28;-3.28;-3.28;-3.28;-3.28	5.87	5.87	0.94306	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (3);	0.000000	0.85682	D	0.000000	D	0.98055	0.9359	H	0.95917	3.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98607	1.0661	10	0.87932	D	0	.	20.2084	0.98285	0.0:1.0:0.0:0.0	.	84;84	B7Z229;Q9UBS8	.;RNF14_HUMAN	Q	84	ENSP00000423420:P84Q;ENSP00000423273:P84Q;ENSP00000421780:P84Q;ENSP00000348462:P84Q;ENSP00000378028:P84Q;ENSP00000324956:P84Q;ENSP00000420837:P84Q;ENSP00000378023:P84Q;ENSP00000422527:P84Q;ENSP00000378027:P84Q	ENSP00000324956:P84Q	P	+	2	0	RNF14	141334649	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.762000	0.85270	2.774000	0.95407	0.650000	0.86243	CCA	.	.	.	none		0.408	RNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251860.2	NM_004290	
FOXQ1	94234	hgsc.bcm.edu	37	6	1313368	1313368	+	Silent	SNP	G	G	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr6:1313368G>T	ENST00000296839.2	+	1	694	c.429G>T	c.(427-429)gcG>gcT	p.A143A		NM_033260.3	NP_150285.3	Q9C009	FOXQ1_HUMAN	forkhead box Q1	143					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)		TGACGCTGGCGGAGATCAACG	0.647																																					p.A143A		Atlas-SNP	.											.	FOXQ1	8	.	0			c.G429T						PASS	.																																			SO:0001819	synonymous_variant	94234	exon1			GCTGGCGGAGATC	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.429G>T	chr6.hg19:g.1313368G>T		82.0	0.0	.		110.0	43.0	.	NM_033260	Q9NS06	Silent	SNP	ENST00000296839.2	hg19	CCDS4471.1																																																																																			.	.	.	none		0.647	FOXQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043410.1	NM_033260	
RIOK1	83732	hgsc.bcm.edu	37	6	7395375	7395375	+	Splice_Site	SNP	A	A	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr6:7395375A>G	ENST00000379834.2	+	3	873	c.366A>G	c.(364-366)ttA>ttG	p.L122L		NM_031480.2|NM_153005.1	NP_113668.2|NP_694550.1	Q9BRS2	RIOK1_HUMAN	RIO kinase 1	122							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19	Ovarian(93;0.0418)					AAATTAATTTAGGTGAGTTTA	0.388																																					p.L122L		Atlas-SNP	.											.	RIOK1	36	.	0			c.A366G						PASS	.						35.0	33.0	33.0					6																	7395375		2203	4300	6503	SO:0001630	splice_region_variant	83732	exon3			TAATTTAGGTGAG	BC006104	CCDS4500.1	6p24.3	2012-12-10	2012-12-10		ENSG00000124784	ENSG00000124784			18656	protein-coding gene	gene with protein product			"""RIO kinase 1 (yeast)"""				Standard	NM_031480		Approved	AD034, FLJ30006, bA288G3.1, RRP10	uc003mxn.3	Q9BRS2	OTTHUMG00000014207	ENST00000379834.2:c.367+1A>G	chr6.hg19:g.7395375A>G		193.0	0.0	.		240.0	90.0	.	NM_031480	B2RB28|Q8NDC8|Q96NV9	Silent	SNP	ENST00000379834.2	hg19	CCDS4500.1																																																																																			.	.	.	none		0.388	RIOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039780.2	NM_031480	Silent
KIAA0408	9729	hgsc.bcm.edu	37	6	127767703	127767703	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr6:127767703A>C	ENST00000483725.3	-	5	2097	c.1761T>G	c.(1759-1761)aaT>aaG	p.N587K	SOGA3_ENST00000481848.2_3'UTR|SOGA3_ENST00000556132.1_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	587										endometrium(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|skin(1)	28				GBM - Glioblastoma multiforme(226;0.0217)|all cancers(137;0.13)		ATTTGGTCCAATTATCCTGGA	0.413																																					p.N587K		Atlas-SNP	.											.	KIAA0408	61	.	0			c.T1761G						PASS	.						133.0	122.0	126.0					6																	127767703		2203	4300	6503	SO:0001583	missense	9729	exon5			GGTCCAATTATCC	AB007868	CCDS34531.1	6q22.33	2012-11-29			ENSG00000189367	ENSG00000189367			21636	protein-coding gene	gene with protein product							Standard	NM_014702		Approved		uc011ebs.2	Q6ZU52	OTTHUMG00000166439	ENST00000483725.3:c.1761T>G	chr6.hg19:g.127767703A>C	ENSP00000435150:p.Asn587Lys	52.0	0.0	.		73.0	30.0	.	NM_014702	B3KRE5|E1P573|O43158|Q5TF20|Q7L2M2	Missense_Mutation	SNP	ENST00000483725.3	hg19	CCDS34531.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.932558	0.00488	.	.	ENSG00000189367	ENST00000483725	T	0.22743	1.94	5.08	-6.14	0.02111	.	0.584041	0.13305	N	0.397945	T	0.01558	0.0050	N	0.19112	0.55	0.19300	N	0.999973	B	0.11235	0.004	B	0.08055	0.003	T	0.41840	-0.9486	10	0.02654	T	1	-2.2349	0.2684	0.00228	0.3125:0.2598:0.1825:0.2452	.	587	Q6ZU52	K0408_HUMAN	K	587	ENSP00000435150:N587K	ENSP00000435150:N587K	N	-	3	2	KIAA0408	127809396	0.518000	0.26234	0.068000	0.19968	0.016000	0.09150	-0.308000	0.08156	-0.860000	0.04099	-1.139000	0.01908	AAT	.	.	.	none		0.413	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042145.3	NM_014702	
GPNMB	10457	hgsc.bcm.edu	37	7	23300201	23300201	+	Missense_Mutation	SNP	A	A	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr7:23300201A>G	ENST00000381990.2	+	6	988	c.827A>G	c.(826-828)tAt>tGt	p.Y276C	GPNMB_ENST00000453162.2_Missense_Mutation_p.Y218C|GPNMB_ENST00000258733.4_Missense_Mutation_p.Y276C|GPNMB_ENST00000539136.1_Missense_Mutation_p.Y177C	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	276	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.				bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			TTCCTCAATTATTCTACCATT	0.423																																					p.Y276C		Atlas-SNP	.											.	GPNMB	88	.	0			c.A827G						PASS	.						177.0	169.0	171.0					7																	23300201		2203	4300	6503	SO:0001583	missense	10457	exon6			TCAATTATTCTAC	X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"""transmembrane glycoprotein"", ""glycoprotein NMB"", ""glycoprotein nmb-like protein"", ""osteoactivin"""	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.827A>G	chr7.hg19:g.23300201A>G	ENSP00000371420:p.Tyr276Cys	91.0	0.0	.		94.0	40.0	.	NM_002510	A4D155|Q6UVX1|Q8N1A1	Missense_Mutation	SNP	ENST00000381990.2	hg19	CCDS34610.1	.	.	.	.	.	.	.	.	.	.	A	15.34	2.803374	0.50315	.	.	ENSG00000136235	ENST00000258733;ENST00000435486;ENST00000381990;ENST00000425903;ENST00000539136;ENST00000453162	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.31	2.72	0.32119	PKD/Chitinase domain (1);PKD domain (2);	1.009820	0.07941	N	0.979323	T	0.43612	0.1255	N	0.22421	0.69	0.09310	N	1	D;P;D;D	0.63046	0.959;0.93;0.984;0.992	P;P;P;P	0.57152	0.62;0.632;0.814;0.634	T	0.32161	-0.9917	10	0.56958	D	0.05	-2.1972	8.3455	0.32270	0.6125:0.315:0.0725:0.0	.	177;218;276;276	F6SKP1;F5GY20;Q14956;Q14956-2	.;.;GPNMB_HUMAN;.	C	276;311;276;159;177;218	ENSP00000258733:Y276C;ENSP00000371420:Y276C;ENSP00000445266:Y177C;ENSP00000405586:Y218C	ENSP00000258733:Y276C	Y	+	2	0	GPNMB	23266726	0.439000	0.25610	0.635000	0.29338	0.863000	0.49368	1.693000	0.37742	0.933000	0.37291	0.533000	0.62120	TAT	.	.	.	none		0.423	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340	
BAZ1B	9031	hgsc.bcm.edu	37	7	72883924	72883924	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr7:72883924T>C	ENST00000339594.4	-	9	3127	c.2789A>G	c.(2788-2790)cAt>cGt	p.H930R	BAZ1B_ENST00000404251.1_Missense_Mutation_p.H930R	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	930					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)				AATGCTGTCATGTACCCAGCC	0.408																																					p.H930R	Esophageal Squamous(112;1167 1561 21085 43672 48228)	Atlas-SNP	.											.	BAZ1B	147	.	0			c.A2789G						PASS	.						219.0	182.0	194.0					7																	72883924		2203	4300	6503	SO:0001583	missense	9031	exon9			CTGTCATGTACCC	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.2789A>G	chr7.hg19:g.72883924T>C	ENSP00000342434:p.His930Arg	78.0	0.0	.		84.0	30.0	.	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	hg19	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.497148	0.85069	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.58940	0.3;0.3	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.64627	0.2615	L	0.34521	1.04	0.58432	D	0.999999	D	0.76494	0.999	D	0.78314	0.991	T	0.59408	-0.7460	10	0.18276	T	0.48	-22.8212	15.2154	0.73261	0.0:0.0:0.0:1.0	.	930	Q9UIG0	BAZ1B_HUMAN	R	930	ENSP00000342434:H930R;ENSP00000385442:H930R	ENSP00000342434:H930R	H	-	2	0	BAZ1B	72521860	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	7.620000	0.83070	2.198000	0.70561	0.533000	0.62120	CAT	.	.	.	none		0.408	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408	
PCLO	27445	hgsc.bcm.edu	37	7	82544242	82544242	+	Missense_Mutation	SNP	C	C	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr7:82544242C>A	ENST00000333891.9	-	7	13397	c.13060G>T	c.(13060-13062)Gtg>Ttg	p.V4354L	PCLO_ENST00000423517.2_Missense_Mutation_p.V4354L|PCLO_ENST00000437081.1_Missense_Mutation_p.V1074L	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						TTCTGGGCCACAATTGGTATT	0.502																																					p.V4354L		Atlas-SNP	.											.	PCLO	1506	.	0			c.G13060T						PASS	.						106.0	103.0	104.0					7																	82544242		1883	4123	6006	SO:0001583	missense	27445	exon7			GGGCCACAATTGG	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.13060G>T	chr7.hg19:g.82544242C>A	ENSP00000334319:p.Val4354Leu	89.0	0.0	.		95.0	40.0	.	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.612259	0.46631	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.18657	2.2;2.2	5.61	5.61	0.85477	.	.	.	.	.	T	0.40619	0.1124	L	0.52759	1.655	0.58432	D	0.999997	D;D;D	0.61697	0.959;0.99;0.99	P;P;P	0.60173	0.631;0.87;0.87	T	0.11966	-1.0566	9	0.87932	D	0	.	19.6481	0.95790	0.0:1.0:0.0:0.0	.	4285;4354;4354	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	L	4354;4354;1074	ENSP00000334319:V4354L;ENSP00000388393:V4354L	ENSP00000334319:V4354L	V	-	1	0	PCLO	82382178	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.074000	0.71253	2.651000	0.90000	0.557000	0.71058	GTG	.	.	.	none		0.502	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
TMEM176A	55365	hgsc.bcm.edu	37	7	150499366	150499366	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr7:150499366T>C	ENST00000484928.1	+	3	819	c.238T>C	c.(238-240)Tac>Cac	p.Y80H	TMEM176A_ENST00000004103.3_Missense_Mutation_p.Y80H|TMEM176B_ENST00000447204.2_5'Flank|TMEM176B_ENST00000492607.1_5'Flank|TMEM176B_ENST00000326442.5_5'Flank|TMEM176B_ENST00000450753.2_5'Flank|TMEM176A_ENST00000461345.1_Missense_Mutation_p.Y21H|TMEM176B_ENST00000434545.1_5'Flank			Q96HP8	T176A_HUMAN	transmembrane protein 176A	80					negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1)	12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CATCCGCGACTACACCCTCCT	0.572																																					p.Y80H		Atlas-SNP	.											.	TMEM176A	35	.	0			c.T238C						PASS	.						130.0	106.0	114.0					7																	150499366		2203	4300	6503	SO:0001583	missense	55365	exon3			CGCGACTACACCC	AF258340	CCDS5909.1	7q36.1	2006-09-04			ENSG00000002933	ENSG00000002933			24930	protein-coding gene	gene with protein product		610334				12097419, 8889548	Standard	NM_018487		Approved	HCA112	uc003whx.1	Q96HP8	OTTHUMG00000158114	ENST00000484928.1:c.238T>C	chr7.hg19:g.150499366T>C	ENSP00000417626:p.Tyr80His	36.0	0.0	.		49.0	21.0	.	NM_018487	D3DX00|Q9NYC7	Missense_Mutation	SNP	ENST00000484928.1	hg19	CCDS5909.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.489966	0.26686	.	.	ENSG00000002933	ENST00000484928;ENST00000004103;ENST00000461345;ENST00000475536;ENST00000468689	T;T;T;T;T	0.02301	4.35;4.35;4.35;4.35;4.35	4.6	-4.75	0.03239	.	1.935430	0.01942	N	0.042003	T	0.02688	0.0081	L	0.50333	1.59	0.09310	N	1	P	0.44309	0.832	B	0.42386	0.386	T	0.35549	-0.9784	10	0.41790	T	0.15	-0.0945	0.4154	0.00448	0.2867:0.2834:0.147:0.2828	.	80	Q96HP8	T176A_HUMAN	H	80;80;21;32;21	ENSP00000417626:Y80H;ENSP00000004103:Y80H;ENSP00000420818:Y21H;ENSP00000417834:Y32H;ENSP00000420081:Y21H	ENSP00000004103:Y80H	Y	+	1	0	TMEM176A	150130299	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.623000	0.05546	-0.960000	0.03613	0.459000	0.35465	TAC	.	.	.	none		0.572	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487	
CCDC25	55246	hgsc.bcm.edu	37	8	27605752	27605752	+	Missense_Mutation	SNP	G	G	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr8:27605752G>C	ENST00000356537.4	-	7	486	c.393C>G	c.(391-393)aaC>aaG	p.N131K	RP11-16P20.3_ENST00000521510.1_RNA|CCDC25_ENST00000539095.1_Missense_Mutation_p.N63K|CCDC25_ENST00000522915.1_Missense_Mutation_p.N63K	NM_018246.2	NP_060716.2	Q86WR0	CCD25_HUMAN	coiled-coil domain containing 25	131						extracellular vesicular exosome (GO:0070062)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0223)|KIRC - Kidney renal clear cell carcinoma(542;0.11)|Kidney(114;0.131)|Colorectal(74;0.154)		TTTCTAATCGGTTCAGGATCT	0.398																																					p.N131K		Atlas-SNP	.											.	CCDC25	14	.	0			c.C393G						PASS	.						118.0	113.0	115.0					8																	27605752		2203	4300	6503	SO:0001583	missense	55246	exon7			TAATCGGTTCAGG	AK001715	CCDS6062.2	8p21.1	2006-09-20			ENSG00000147419	ENSG00000147419			25591	protein-coding gene	gene with protein product						12477932	Standard	NM_018246		Approved	FLJ10853	uc003xgc.3	Q86WR0	OTTHUMG00000132173	ENST00000356537.4:c.393C>G	chr8.hg19:g.27605752G>C	ENSP00000348933:p.Asn131Lys	82.0	0.0	.		83.0	4.0	.	NM_018246	Q0P663|Q96SI2|Q9NV98	Missense_Mutation	SNP	ENST00000356537.4	hg19	CCDS6062.2	.	.	.	.	.	.	.	.	.	.	G	15.06	2.721188	0.48728	.	.	ENSG00000147419	ENST00000356537;ENST00000539095;ENST00000522915	.	.	.	5.61	2.78	0.32641	.	0.000000	0.85682	D	0.000000	T	0.47266	0.1436	M	0.68593	2.085	0.58432	D	0.999999	P	0.42456	0.78	B	0.38106	0.265	T	0.41805	-0.9488	9	0.54805	T	0.06	-24.9936	8.8923	0.35441	0.2473:0.0:0.7527:0.0	.	131	Q86WR0	CCD25_HUMAN	K	131;63;63	.	ENSP00000348933:N131K	N	-	3	2	CCDC25	27661671	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.658000	0.54482	0.285000	0.22329	0.655000	0.94253	AAC	.	.	.	none		0.398	CCDC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255224.1	NM_018246	
ATP6V1H	51606	hgsc.bcm.edu	37	8	54628574	54628574	+	Missense_Mutation	SNP	C	C	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr8:54628574C>G	ENST00000359530.2	-	14	1665	c.1402G>C	c.(1402-1404)Ggc>Cgc	p.G468R	ATP6V1H_ENST00000523899.1_5'UTR|ATP6V1H_ENST00000520188.1_Missense_Mutation_p.G428R|ATP6V1H_ENST00000355221.3_Missense_Mutation_p.G450R|ATP6V1H_ENST00000396774.2_Missense_Mutation_p.G468R	NM_015941.3	NP_057025.2	Q9UI12	VATH_HUMAN	ATPase, H+ transporting, lysosomal 50/57kDa, V1 subunit H	468					ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|endocytosis (GO:0006897)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|regulation of catalytic activity (GO:0050790)|regulation of defense response to virus by virus (GO:0050690)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V1 domain (GO:0000221)	enzyme regulator activity (GO:0030234)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	18		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)			AGCTGCTTGCCAAGGTATTCC	0.483																																					p.G468R		Atlas-SNP	.											.	ATP6V1H	66	.	0			c.G1402C						PASS	.						42.0	46.0	45.0					8																	54628574		2203	4298	6501	SO:0001583	missense	51606	exon14			GCTTGCCAAGGTA	AF132945	CCDS6153.1, CCDS6154.1	8q11.2	2011-05-24	2002-08-29		ENSG00000047249	ENSG00000047249		"""ATPases / V-type"""	18303	protein-coding gene	gene with protein product	"""vacuolar ATP synthase subunit H"""	608861	"""ATPase, H+ transporting, lysosomal 50/57kD, V1 subunit H"""			9620685, 10810093	Standard	NM_015941		Approved	CGI-11, SFD, VMA13, SFDalpha, SFDbeta	uc003xrm.4	Q9UI12	OTTHUMG00000164231	ENST00000359530.2:c.1402G>C	chr8.hg19:g.54628574C>G	ENSP00000352522:p.Gly468Arg	191.0	0.0	.		162.0	57.0	.	NM_015941	B3KMR0|Q6PK44|Q9H3E3|Q9Y300	Missense_Mutation	SNP	ENST00000359530.2	hg19	CCDS6153.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.268497	0.80469	.	.	ENSG00000047249	ENST00000355221;ENST00000520188;ENST00000359530;ENST00000396774	.	.	.	5.73	5.73	0.89815	.	0.205114	0.52532	D	0.000070	T	0.77452	0.4132	M	0.62723	1.935	0.80722	D	1	D;D	0.71674	0.998;0.992	D;D	0.77557	0.99;0.972	T	0.78288	-0.2262	9	0.87932	D	0	-19.1942	17.1743	0.86837	0.0:1.0:0.0:0.0	.	450;468	Q9UI12-2;Q9UI12	.;VATH_HUMAN	R	450;428;468;468	.	ENSP00000347359:G450R	G	-	1	0	ATP6V1H	54791127	1.000000	0.71417	0.999000	0.59377	0.866000	0.49608	4.271000	0.58902	2.861000	0.98227	0.655000	0.94253	GGC	.	.	.	none		0.483	ATP6V1H-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377865.1	NM_015941	
SNX16	64089	hgsc.bcm.edu	37	8	82751914	82751914	+	Missense_Mutation	SNP	C	C	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr8:82751914C>G	ENST00000345957.4	-	2	586	c.308G>C	c.(307-309)tGg>tCg	p.W103S	SNX16_ENST00000396330.2_Missense_Mutation_p.W103S|SNX16_ENST00000353788.4_Missense_Mutation_p.W103S	NM_152836.2	NP_690049.1	P57768	SNX16_HUMAN	sorting nexin 16	103					early endosome to late endosome transport (GO:0045022)|endosome to lysosome transport (GO:0008333)|protein targeting to lysosome (GO:0006622)	early endosome (GO:0005769)|extrinsic component of endosome membrane (GO:0031313)|late endosome (GO:0005770)|lysosome (GO:0005764)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			large_intestine(1)|ovary(1)|pancreas(1)|skin(2)	5						TCTATCTTCCCAATTCACTGT	0.378																																					p.W103S		Atlas-SNP	.											.	SNX16	21	.	0			c.G308C						PASS	.						152.0	142.0	146.0					8																	82751914		2203	4300	6503	SO:0001583	missense	64089	exon2			TCTTCCCAATTCA	AF305779	CCDS6234.1, CCDS6235.1	8q21.13	2011-05-03			ENSG00000104497	ENSG00000104497		"""Sorting nexins"""	14980	protein-coding gene	gene with protein product		614903				12461558, 12813048	Standard	NM_152837		Approved		uc003ycn.3	P57768	OTTHUMG00000164727	ENST00000345957.4:c.308G>C	chr8.hg19:g.82751914C>G	ENSP00000322652:p.Trp103Ser	85.0	0.0	.		78.0	33.0	.	NM_152836	A8K4D8|Q658L0|Q8N4U3	Missense_Mutation	SNP	ENST00000345957.4	hg19	CCDS6234.1	.	.	.	.	.	.	.	.	.	.	C	9.277	1.047069	0.19827	.	.	ENSG00000104497	ENST00000353788;ENST00000396330;ENST00000345957;ENST00000520618;ENST00000523757;ENST00000521810	T;T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.66;1.27	5.42	2.43	0.29744	Phox homologous domain (2);	0.782608	0.12355	N	0.476157	T	0.33000	0.0848	L	0.57536	1.79	0.47094	D	0.999312	B;B	0.30511	0.282;0.006	B;B	0.25884	0.064;0.005	T	0.08659	-1.0711	10	0.11182	T	0.66	-13.4645	15.1417	0.72615	0.4023:0.5977:0.0:0.0	.	103;103	Q658L0;P57768	.;SNX16_HUMAN	S	103;103;103;103;74;103	ENSP00000322631:W103S;ENSP00000379621:W103S;ENSP00000322652:W103S;ENSP00000428699:W103S;ENSP00000430038:W74S;ENSP00000428734:W103S	ENSP00000322652:W103S	W	-	2	0	SNX16	82914469	0.999000	0.42202	0.213000	0.23690	0.565000	0.35776	1.105000	0.31086	0.168000	0.19655	0.561000	0.74099	TGG	.	.	.	none		0.378	SNX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379929.1	NM_022133	
ZNF251	90987	hgsc.bcm.edu	37	8	145947779	145947779	+	Silent	SNP	T	T	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr8:145947779T>C	ENST00000292562.7	-	5	1541	c.1266A>G	c.(1264-1266)gaA>gaG	p.E422E	ZNF251_ENST00000524394.1_Intron	NM_138367.1	NP_612376.1	Q9BRH9	ZN251_HUMAN	zinc finger protein 251	422					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|kidney(1)|large_intestine(5)|lung(9)|stomach(1)	17	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;7.54e-38)|all cancers(56;6.19e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.198)		TCCTTACGTGTTCAGTAAGAT	0.448																																					p.E422E		Atlas-SNP	.											.	ZNF251	80	.	0			c.A1266G						PASS	.						96.0	108.0	104.0					8																	145947779		2128	4254	6382	SO:0001819	synonymous_variant	90987	exon5			TACGTGTTCAGTA	AK000435	CCDS47944.1	8q24.3	2013-01-08			ENSG00000198169	ENSG00000198169		"""Zinc fingers, C2H2-type"", ""-"""	13045	protein-coding gene	gene with protein product							Standard	NM_138367		Approved		uc003zdv.4	Q9BRH9	OTTHUMG00000165189	ENST00000292562.7:c.1266A>G	chr8.hg19:g.145947779T>C		74.0	0.0	.		89.0	18.0	.	NM_138367	Q2M219	Silent	SNP	ENST00000292562.7	hg19	CCDS47944.1																																																																																			.	.	.	none		0.448	ZNF251-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382541.1	NM_138367	
RPL35	11224	hgsc.bcm.edu	37	9	127622502	127622502	+	Missense_Mutation	SNP	A	A	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr9:127622502A>G	ENST00000348462.3	-	3	230	c.182T>C	c.(181-183)aTt>aCt	p.I61T	ARPC5L_ENST00000353214.2_5'Flank|RPL35_ENST00000373570.4_Missense_Mutation_p.I61T	NM_007209.3	NP_009140.1	P42766	RL35_HUMAN	ribosomal protein L35	61					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)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|large_intestine(1)|lung(1)|ovary(1)	4				GBM - Glioblastoma multiforme(294;0.182)		AGTCTGGTTAATAACTGTGAG	0.498																																					p.I61T		Atlas-SNP	.											.	RPL35	11	.	0			c.T182C						PASS	.						89.0	86.0	87.0					9																	127622502		2203	4300	6503	SO:0001583	missense	11224	exon3			TGGTTAATAACTG	U12465	CCDS6858.1	9q34.1	2011-04-06			ENSG00000136942	ENSG00000136942		"""L ribosomal proteins"""	10344	protein-coding gene	gene with protein product	"""60S ribosomal protein L35"""					11401437	Standard	NM_007209		Approved	L35	uc004boy.1	P42766	OTTHUMG00000020659	ENST00000348462.3:c.182T>C	chr9.hg19:g.127622502A>G	ENSP00000259469:p.Ile61Thr	66.0	0.0	.		92.0	37.0	.	NM_007209	A8K4V7|Q4VBY5|Q5JTN5|Q6IBC7|Q96QJ7|Q9BYF4	Missense_Mutation	SNP	ENST00000348462.3	hg19	CCDS6858.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.547839	0.86022	.	.	ENSG00000136942	ENST00000348462	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.76154	0.3948	M	0.90309	3.105	0.80722	D	1	P	0.45011	0.848	P	0.49085	0.6	T	0.81824	-0.0755	9	0.66056	D	0.02	.	14.7041	0.69176	1.0:0.0:0.0:0.0	.	61	P42766	RL35_HUMAN	T	61	.	ENSP00000259469:I61T	I	-	2	0	RPL35	126662323	1.000000	0.71417	0.999000	0.59377	0.861000	0.49209	8.770000	0.91746	2.125000	0.65367	0.459000	0.35465	ATT	.	.	.	none		0.498	RPL35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054035.1	NM_007209	
LAMC3	10319	hgsc.bcm.edu	37	9	133901739	133901739	+	Silent	SNP	C	C	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr9:133901739C>A	ENST00000361069.4	+	2	574	c.441C>A	c.(439-441)atC>atA	p.I147I	LAMC3_ENST00000480883.1_3'UTR	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	147	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				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)		GCTTTGCCATCTACAAGCGCA	0.617																																					p.I147I		Atlas-SNP	.											.	LAMC3	167	.	0			c.C441A						PASS	.						42.0	46.0	45.0					9																	133901739		2203	4300	6503	SO:0001819	synonymous_variant	10319	exon2			TGCCATCTACAAG	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.441C>A	chr9.hg19:g.133901739C>A		146.0	0.0	.		137.0	53.0	.	NM_006059	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	hg19	CCDS6938.1																																																																																			.	.	.	none		0.617	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
DIP2C	22982	hgsc.bcm.edu	37	10	327182	327182	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr10:327182A>C	ENST00000280886.6	-	36	4463	c.4376T>G	c.(4375-4377)aTt>aGt	p.I1459S	RNA5SP298_ENST00000364991.1_RNA	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1459						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CGAGGTCTCAATGTCGATTGG	0.542																																					p.I1459S		Atlas-SNP	.											.	DIP2C	195	.	0			c.T4376G						PASS	.						179.0	144.0	156.0					10																	327182		2203	4300	6503	SO:0001583	missense	22982	exon36			GTCTCAATGTCGA	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.4376T>G	chr10.hg19:g.327182A>C	ENSP00000280886:p.Ile1459Ser	74.0	0.0	.		84.0	39.0	.	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.004268	0.93287	.	.	ENSG00000151240	ENST00000280886;ENST00000535541	T	0.19806	2.12	5.89	5.89	0.94794	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.52273	0.1724	M	0.85945	2.785	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.59327	-0.7475	10	0.87932	D	0	-38.0194	16.3123	0.82883	1.0:0.0:0.0:0.0	.	1459	Q9Y2E4	DIP2C_HUMAN	S	1459;384	ENSP00000280886:I1459S	ENSP00000280886:I1459S	I	-	2	0	DIP2C	317182	1.000000	0.71417	0.999000	0.59377	0.916000	0.54674	9.339000	0.96797	2.254000	0.74563	0.459000	0.35465	ATT	.	.	.	none		0.542	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974	
C10orf67	256815	hgsc.bcm.edu	37	10	23622020	23622020	+	Silent	SNP	A	A	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr10:23622020A>G	ENST00000323327.4	-	2	368	c.301T>C	c.(301-303)Ttg>Ctg	p.L101L		NM_153714.2	NP_714925.2	Q8IYJ2	CJ067_HUMAN	chromosome 10 open reading frame 67	101								p.L101M(1)		central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)	5						GATGAACTCAATTCTTTTACT	0.343																																					p.L101L		Atlas-SNP	.											C10orf67,NS,carcinoma,0,1	C10orf67	21	.	1	Substitution - Missense(1)	lung(1)	c.T301C						PASS	.						119.0	112.0	114.0					10																	23622020		1838	4082	5920	SO:0001819	synonymous_variant	256815	exon2			AACTCAATTCTTT	BC035732	CCDS44365.1	10p12.31	2012-05-31			ENSG00000179133	ENSG00000179133			28716	protein-coding gene	gene with protein product						12477932	Standard	NM_153714		Approved	MGC46732	uc010qcx.2	Q8IYJ2	OTTHUMG00000017818	ENST00000323327.4:c.301T>C	chr10.hg19:g.23622020A>G		115.0	0.0	.		136.0	61.0	.	NM_153714	A8MUP9|Q5SWD4	Silent	SNP	ENST00000323327.4	hg19	CCDS44365.1																																																																																			.	.	.	none		0.343	C10orf67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047213.1	NM_153714	
WAC	51322	hgsc.bcm.edu	37	10	28906628	28906628	+	Missense_Mutation	SNP	C	C	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr10:28906628C>G	ENST00000354911.4	+	13	1950	c.1789C>G	c.(1789-1791)Cac>Gac	p.H597D	WAC_ENST00000375664.4_Missense_Mutation_p.H552D|WAC_ENST00000375646.1_Missense_Mutation_p.H445D|WAC_ENST00000347934.4_Missense_Mutation_p.H494D	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil	597					cellular response to DNA damage stimulus (GO:0006974)|G1 DNA damage checkpoint (GO:0044783)|histone H2B conserved C-terminal lysine ubiquitination (GO:0071894)|histone monoubiquitination (GO:0010390)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	chromatin binding (GO:0003682)|RNA polymerase II core binding (GO:0000993)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|urinary_tract(1)	32						GGGAACTATTCACATGTCCGA	0.313																																					p.H597D		Atlas-SNP	.											.	WAC	77	.	0			c.C1789G						PASS	.						38.0	41.0	40.0					10																	28906628		2203	4300	6503	SO:0001583	missense	51322	exon13			ACTATTCACATGT	AK055852	CCDS7159.1, CCDS7160.1, CCDS7161.1	10p12.1	2007-05-17	2003-03-19		ENSG00000095787	ENSG00000095787			17327	protein-coding gene	gene with protein product		615049	"""WW domain-containing adaptor with coiled coil"""			11827461	Standard	NR_024557		Approved	Wwp4, FLJ31290, PRO1741, BM-016, MGC10753	uc001iuf.3	Q9BTA9	OTTHUMG00000017872	ENST00000354911.4:c.1789C>G	chr10.hg19:g.28906628C>G	ENSP00000346986:p.His597Asp	264.0	0.0	.		240.0	105.0	.	NM_016628	A8K2A9|C9JBT9|D3DRW5|D3DRW6|D3DRW7|Q53EN9|Q5JU75|Q5JU77|Q5VXK0|Q5VXK2|Q8TCK1|Q96DP3|Q96FW6|Q96JI3	Missense_Mutation	SNP	ENST00000354911.4	hg19	CCDS7159.1	.	.	.	.	.	.	.	.	.	.	C	18.03	3.531433	0.64972	.	.	ENSG00000095787	ENST00000375664;ENST00000375646;ENST00000347934;ENST00000354911	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.57	5.57	0.84162	.	0.093685	0.85682	D	0.000000	T	0.35393	0.0930	L	0.34521	1.04	0.80722	D	1	P;P;P	0.42620	0.764;0.785;0.652	B;B;B	0.36418	0.224;0.182;0.112	T	0.24119	-1.0169	10	0.54805	T	0.06	-10.4861	19.5403	0.95271	0.0:1.0:0.0:0.0	.	552;494;597	Q9BTA9-2;Q9BTA9-5;Q9BTA9	.;.;WAC_HUMAN	D	552;445;494;597	ENSP00000364816:H552D;ENSP00000364797:H445D;ENSP00000311106:H494D;ENSP00000346986:H597D	ENSP00000311106:H494D	H	+	1	0	WAC	28946634	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.667000	0.68067	2.619000	0.88677	0.655000	0.94253	CAC	.	.	.	none		0.313	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000047371.1	NM_100264	
CUEDC2	79004	hgsc.bcm.edu	37	10	104184908	104184908	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr10:104184908G>A	ENST00000369937.4	-	2	183	c.38C>T	c.(37-39)gCc>gTc	p.A13V	CUEDC2_ENST00000465409.1_5'Flank	NM_024040.2	NP_076945.2	Q9H467	CUED2_HUMAN	CUE domain containing 2	13						cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(1)|stomach(1)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.122)		Epithelial(162;9.17e-09)|all cancers(201;2.16e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		CTGGACAAAGGCAAGGAGGGC	0.622																																					p.A13V		Atlas-SNP	.											.	CUEDC2	22	.	0			c.C38T						PASS	.						63.0	67.0	65.0					10																	104184908		2085	4206	6291	SO:0001583	missense	79004	exon2			ACAAAGGCAAGGA	BC000262	CCDS41566.1	10q24.32	2008-10-23	2004-03-04	2004-03-05	ENSG00000107874	ENSG00000107874			28352	protein-coding gene	gene with protein product		614142	"""chromosome 10 open reading frame 66"""	C10orf66		12477932	Standard	NM_024040		Approved	MGC2491	uc001kvn.2	Q9H467	OTTHUMG00000018958	ENST00000369937.4:c.38C>T	chr10.hg19:g.104184908G>A	ENSP00000358953:p.Ala13Val	16.0	0.0	.		35.0	13.0	.	NM_024040	D3DR88|Q9BWG8	Missense_Mutation	SNP	ENST00000369937.4	hg19	CCDS41566.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.126576	0.37533	.	.	ENSG00000107874	ENST00000369937	D	0.89485	-2.52	5.3	0.711	0.18162	.	0.533792	0.20404	N	0.092995	T	0.77170	0.4091	N	0.12182	0.205	0.09310	N	0.99999	B	0.20887	0.049	B	0.16722	0.016	T	0.68569	-0.5374	10	0.52906	T	0.07	-2.1406	10.7668	0.46299	0.0:0.4683:0.4178:0.1139	.	13	Q9H467	CUED2_HUMAN	V	13	ENSP00000358953:A13V	ENSP00000358953:A13V	A	-	2	0	CUEDC2	104174898	0.958000	0.32768	0.710000	0.30468	0.970000	0.65996	1.729000	0.38115	0.568000	0.29311	0.555000	0.69702	GCC	.	.	.	none		0.622	CUEDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050060.1	NM_024040	
COL17A1	1308	hgsc.bcm.edu	37	10	105793812	105793812	+	Silent	SNP	T	T	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr10:105793812T>A	ENST00000353479.5	-	52	4337	c.4047A>T	c.(4045-4047)gcA>gcT	p.A1349A	COL17A1_ENST00000369733.3_Silent_p.A1267A	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1349	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		CTTCTGCTGCTGCCCCATAGC	0.602																																					p.A1349A		Atlas-SNP	.											.	COL17A1	149	.	0			c.A4047T						PASS	.						83.0	79.0	80.0					10																	105793812		2203	4300	6503	SO:0001819	synonymous_variant	1308	exon52			TGCTGCTGCCCCA	M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"""Collagens"""	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.4047A>T	chr10.hg19:g.105793812T>A		212.0	0.0	.		258.0	98.0	.	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Silent	SNP	ENST00000353479.5	hg19	CCDS7554.1																																																																																			.	.	.	none		0.602	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494	
RRM1	6240	hgsc.bcm.edu	37	11	4144483	4144483	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:4144483C>T	ENST00000300738.5	+	12	1393	c.1189C>T	c.(1189-1191)Cag>Tag	p.Q397*	RRM1_ENST00000534285.1_Nonsense_Mutation_p.Q175*|RRM1_ENST00000423050.2_Nonsense_Mutation_p.Q300*|RRM1_ENST00000537197.1_Nonsense_Mutation_p.Q59*|RRM1_ENST00000528470.1_3'UTR	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	397					cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	CATTGAGTCTCAGACGGAAAC	0.433																																					p.Q397X	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.C1189T						PASS	.						100.0	99.0	99.0					11																	4144483		2201	4298	6499	SO:0001587	stop_gained	6240	exon12			GAGTCTCAGACGG	X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"""ribonucleotide reductase M1 polypeptide"""			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.1189C>T	chr11.hg19:g.4144483C>T	ENSP00000300738:p.Gln397*	169.0	0.0	.		217.0	98.0	.	NM_001033	Q9UNN2	Nonsense_Mutation	SNP	ENST00000300738.5	hg19	CCDS7750.1	.	.	.	.	.	.	.	.	.	.	C	38	6.853298	0.97885	.	.	ENSG00000167325	ENST00000300738;ENST00000423050;ENST00000536894;ENST00000534285;ENST00000543838;ENST00000537197	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-10.9476	18.8429	0.92192	0.0:1.0:0.0:0.0	.	.	.	.	X	397;300;310;175;175;59	.	ENSP00000300738:Q397X	Q	+	1	0	RRM1	4101059	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	7.487000	0.81328	2.706000	0.92434	0.563000	0.77884	CAG	.	.	.	none		0.433	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033	
TRIM3	10612	hgsc.bcm.edu	37	11	6470304	6470304	+	Missense_Mutation	SNP	G	G	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:6470304G>T	ENST00000525074.1	-	12	2583	c.2189C>A	c.(2188-2190)gCt>gAt	p.A730D	TRIM3_ENST00000359518.3_Missense_Mutation_p.A730D|TRIM3_ENST00000536344.1_Missense_Mutation_p.A611D|TRIM3_ENST00000537602.1_Missense_Mutation_p.A652D|TRIM3_ENST00000345851.3_Missense_Mutation_p.A730D	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	730					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)		GCCAGCATCAGCCACCACCAC	0.562																																					p.A730D	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.C2189A						PASS	.						88.0	74.0	79.0					11																	6470304		2201	4296	6497	SO:0001583	missense	10612	exon12			GCATCAGCCACCA	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.2189C>A	chr11.hg19:g.6470304G>T	ENSP00000433102:p.Ala730Asp	63.0	0.0	.		95.0	5.0	.	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Missense_Mutation	SNP	ENST00000525074.1	hg19	CCDS7764.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.461615	0.84425	.	.	ENSG00000110171	ENST00000525074;ENST00000345851;ENST00000336043;ENST00000537602;ENST00000359518;ENST00000536344	T;T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26;-1.26	4.8	4.8	0.61643	Six-bladed beta-propeller, TolB-like (1);	0.066417	0.64402	D	0.000011	D	0.90665	0.7072	M	0.92122	3.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.92909	0.6346	10	0.87932	D	0	-11.2897	16.6192	0.84925	0.0:0.0:1.0:0.0	.	611;730	F5H2Q8;O75382	.;TRIM3_HUMAN	D	730;730;719;652;730;611	ENSP00000433102:A730D;ENSP00000340797:A730D;ENSP00000441091:A652D;ENSP00000352508:A730D;ENSP00000445460:A611D	ENSP00000337094:A719D	A	-	2	0	TRIM3	6426880	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.591000	0.98241	2.492000	0.84095	0.563000	0.77884	GCT	.	.	.	none		0.562	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458	
HPS5	11234	hgsc.bcm.edu	37	11	18333543	18333543	+	Missense_Mutation	SNP	C	C	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:18333543C>A	ENST00000349215.3	-	3	414	c.137G>T	c.(136-138)tGg>tTg	p.W46L	HPS5_ENST00000396253.3_5'UTR|HPS5_ENST00000531848.1_5'UTR|HPS5_ENST00000438420.2_5'UTR	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	46					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CAAAGCCAACCATTTCCGAGA	0.433									Hermansky-Pudlak syndrome																												p.W46L		Atlas-SNP	.											.	HPS5	70	.	0			c.G137T						PASS	.						112.0	117.0	115.0					11																	18333543		2199	4293	6492	SO:0001583	missense	11234	exon3	Familial Cancer Database	HPS, HPS1-8	GCCAACCATTTCC	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.137G>T	chr11.hg19:g.18333543C>A	ENSP00000265967:p.Trp46Leu	86.0	0.0	.		82.0	35.0	.	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	hg19	CCDS7836.1	.	.	.	.	.	.	.	.	.	.	C	32	5.109237	0.94292	.	.	ENSG00000110756	ENST00000349215	T	0.59906	0.23	5.4	5.4	0.78164	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.67961	0.2949	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.68618	-0.5361	10	0.51188	T	0.08	.	19.5422	0.95278	0.0:1.0:0.0:0.0	.	62;46	Q8IZE8;Q9UPZ3	.;HPS5_HUMAN	L	46	ENSP00000265967:W46L	ENSP00000265967:W46L	W	-	2	0	HPS5	18290119	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.403000	0.79983	2.695000	0.91970	0.561000	0.74099	TGG	.	.	.	none		0.433	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	
SLC3A2	6520	hgsc.bcm.edu	37	11	62652107	62652108	+	Missense_Mutation	DNP	GC	GC	AT			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:62652107_62652108GC>AT	ENST00000377890.2	+	8	1234_1235	c.1066_1067GC>AT	c.(1066-1068)GCa>ATa	p.A356I	SLC3A2_ENST00000536981.1_5'UTR|SLC3A2_ENST00000377889.2_Missense_Mutation_p.A294I|SLC3A2_ENST00000377891.2_Missense_Mutation_p.A357I|SLC3A2_ENST00000538682.1_3'UTR|SLC3A2_ENST00000338663.7_Missense_Mutation_p.A255I|SLC3A2_ENST00000377892.1_Missense_Mutation_p.A387I|SLC3A2_ENST00000535296.1_Missense_Mutation_p.A325I	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	356					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|carbohydrate metabolic process (GO:0005975)|cell growth (GO:0016049)|ion transport (GO:0006811)|leucine import (GO:0060356)|leukocyte migration (GO:0050900)|response to exogenous dsRNA (GO:0043330)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|tryptophan transport (GO:0015827)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|double-stranded RNA binding (GO:0003725)|neutral amino acid transmembrane transporter activity (GO:0015175)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						TTTCTAGGATGCATCCTCATTC	0.485											OREG0021032	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A357T|p.A357V		Atlas-SNP	.											.	SLC3A2	55	.	0			c.G1069A|c.C1070T						PASS	.																																			SO:0001583	missense	6520	exon8			TAGGATGCATCCT|AGGATGCATCCTC		CCDS8039.2, CCDS31588.1, CCDS31589.1, CCDS31590.1	11q12-q22	2013-07-19	2013-07-19		ENSG00000168003	ENSG00000168003		"""Solute carriers"""	11026	protein-coding gene	gene with protein product	"""antigen identified by monoclonal antibodies 4F2, TRA1.10, TROP4, and T43"", ""antigen defined by monoclonal antibody 4F2"", ""heavy chain"", ""4F2 heavy chain"", ""CD98 heavy chain"", ""monoclonal antibody 44D7"", ""4F2 cell-surface antigen heavy chain"", ""lymphocyte activation antigen 4F2 large subunit"""	158070	"""solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2"""	MDU1		3036867	Standard	NM_001012662		Approved	4T2HC, 4F2, NACAE, CD98, CD98HC, 4F2HC	uc001nwd.3	P08195	OTTHUMG00000074091	Exception_encountered	chr11.hg19:g.62652107_62652108delinsAT	ENSP00000367122:p.Ala356Ile	85.0|83.0	0.0	.	1062	67.0|69.0	25.0	.	NM_001012662	Q13543	Missense_Mutation	SNP	ENST00000377890.2	hg19	CCDS8039.2																																																																																			.	.	.	none		0.485	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661	
NUMA1	4926	hgsc.bcm.edu	37	11	71720100	71720100	+	Silent	SNP	A	A	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:71720100A>G	ENST00000393695.3	-	19	5302	c.4971T>C	c.(4969-4971)caT>caC	p.H1657H	NUMA1_ENST00000358965.6_Silent_p.H1643H|NUMA1_ENST00000351960.6_Silent_p.H521H	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						GCTGTAGCTCATGGCCCAGCC	0.597			T	RARA	APL																																p.H1657H		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.T4971C						PASS	.						53.0	50.0	51.0					11																	71720100		2200	4293	6493	SO:0001819	synonymous_variant	4926	exon19			TAGCTCATGGCCC	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.4971T>C	chr11.hg19:g.71720100A>G		49.0	0.0	.		59.0	27.0	.	NM_006185		Silent	SNP	ENST00000393695.3	hg19	CCDS31633.1	.	.	.	.	.	.	.	.	.	.	A	8.322	0.824515	0.16678	.	.	ENSG00000137497	ENST00000541584	.	.	.	5.56	-7.2	0.01495	.	.	.	.	.	T	0.47377	0.1442	.	.	.	0.45777	D	0.998668	.	.	.	.	.	.	T	0.51140	-0.8743	4	.	.	.	.	7.7891	0.29110	0.5762:0.1983:0.0:0.2256	.	.	.	.	T	488	.	.	M	-	2	0	NUMA1	71397748	0.006000	0.16342	0.638000	0.29380	0.961000	0.63080	-0.491000	0.06474	-1.624000	0.01556	0.459000	0.35465	ATG	.	.	.	none		0.597	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
INPPL1	3636	hgsc.bcm.edu	37	11	71942228	71942228	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:71942228C>T	ENST00000298229.2	+	12	1696	c.1492C>T	c.(1492-1494)Cgc>Tgc	p.R498C	INPPL1_ENST00000541756.1_Missense_Mutation_p.R256C|INPPL1_ENST00000538751.1_Missense_Mutation_p.R256C	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	498					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)	p.R498S(1)		breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						TCTGGATTACCGCCCGGTGAG	0.597																																					p.R498C		Atlas-SNP	.											.	INPPL1	120	.	1	Substitution - Missense(1)	lung(1)	c.C1492T						PASS	.						71.0	81.0	78.0					11																	71942228		2199	4290	6489	SO:0001583	missense	3636	exon12			GATTACCGCCCGG	Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"""Sterile alpha motif (SAM) domain containing"", ""SH2 domain containing"""	6080	protein-coding gene	gene with protein product	"""51C protein"""	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.1492C>T	chr11.hg19:g.71942228C>T	ENSP00000298229:p.Arg498Cys	31.0	0.0	.		36.0	16.0	.	NM_001567	B2RTX5|Q13577|Q13578	Missense_Mutation	SNP	ENST00000298229.2	hg19	CCDS8213.1	.	.	.	.	.	.	.	.	.	.	c	23.4	4.416629	0.83449	.	.	ENSG00000165458	ENST00000298229;ENST00000541756;ENST00000538751	T;T;T	0.80824	-1.42;-1.42;-1.42	5.81	5.81	0.92471	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.123775	0.56097	D	0.000033	D	0.82884	0.5134	N	0.17764	0.52	0.52099	D	0.999943	D	0.76494	0.999	D	0.65573	0.936	D	0.84613	0.0679	10	0.59425	D	0.04	.	18.6606	0.91470	0.0:1.0:0.0:0.0	.	498	O15357	SHIP2_HUMAN	C	498;256;256	ENSP00000298229:R498C;ENSP00000446360:R256C;ENSP00000444619:R256C	ENSP00000298229:R498C	R	+	1	0	INPPL1	71619876	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.557000	0.67313	2.746000	0.94184	0.655000	0.94253	CGC	.	.	.	none		0.597	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567	
RAB6A	5870	hgsc.bcm.edu	37	11	73471628	73471628	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:73471628A>T	ENST00000336083.3	-	1	508	c.53T>A	c.(52-54)tTc>tAc	p.F18Y	RAB6A_ENST00000310653.6_Missense_Mutation_p.F18Y|RAB6A_ENST00000541588.1_Missense_Mutation_p.F18Y|RP11-707G14.1_ENST00000540547.1_RNA|RAB6A_ENST00000536566.1_5'Flank	NM_198896.1	NP_942599.1	P20340	RAB6A_HUMAN	RAB6A, member RAS oncogene family	18					antigen processing and presentation (GO:0019882)|early endosome to Golgi transport (GO:0034498)|GTP catabolic process (GO:0006184)|minus-end-directed organelle transport along microtubule (GO:0072385)|peptidyl-cysteine methylation (GO:0018125)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|protein domain specific binding (GO:0019904)			large_intestine(2)|lung(2)	4						CTCCCCCAGGAACACCAGCTT	0.682																																					p.F18Y		Atlas-SNP	.											.	RAB6A	17	.	0			c.T53A						PASS	.						35.0	31.0	32.0					11																	73471628		2200	4292	6492	SO:0001583	missense	5870	exon1			CCCAGGAACACCA	AF130986	CCDS8223.1, CCDS8224.1, CCDS58155.1, CCDS58156.1	11q13.3	2008-08-08			ENSG00000175582	ENSG00000175582		"""RAB, member RAS oncogene"""	9786	protein-coding gene	gene with protein product		179513		RAB6			Standard	NM_001243718		Approved		uc001ouf.3	P20340	OTTHUMG00000134308	ENST00000336083.3:c.53T>A	chr11.hg19:g.73471628A>T	ENSP00000336850:p.Phe18Tyr	226.0	0.0	.		248.0	99.0	.	NM_002869	A8K133|B7Z772|F5H668|Q1W5D8|Q5U0A8|Q9UBE4	Missense_Mutation	SNP	ENST00000336083.3	hg19	CCDS8224.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.2|28.2	4.895232|4.895232	0.91962|0.91962	.|.	.|.	ENSG00000175582|ENSG00000175582	ENST00000310653;ENST00000336083;ENST00000393571;ENST00000541588;ENST00000540771;ENST00000539750;ENST00000535748;ENST00000542366|ENST00000400470	T;T;T;T|.	0.80123|.	-1.34;-1.34;-1.34;-0.49|.	4.89|4.89	4.89|4.89	0.63831|0.63831	Small GTP-binding protein domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80701|0.80701	0.4673|0.4673	M|M	0.91663|0.91663	3.23|3.23	0.80722|0.80722	D|D	1|1	P;D;B;B|.	0.67145|.	0.786;0.996;0.184;0.153|.	P;D;B;B|.	0.76071|.	0.733;0.987;0.239;0.199|.	D|D	0.84953|0.84953	0.0872|0.0872	10|5	0.87932|.	D|.	0|.	.|.	12.527|12.527	0.56091|0.56091	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	18;18;18;18|.	Q1W5D8;F5H3K7;P20340;P20340-2|.	.;.;RAB6A_HUMAN;.|.	Y|T	18|10	ENSP00000311449:F18Y;ENSP00000336850:F18Y;ENSP00000445350:F18Y;ENSP00000438842:F18Y|.	ENSP00000311449:F18Y|.	F|S	-|-	2|1	0|0	RAB6A|RAB6A	73149276|73149276	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.895000|6.895000	0.75660|0.75660	2.051000|2.051000	0.60960|0.60960	0.528000|0.528000	0.53228|0.53228	TTC|TCC	.	.	.	none		0.682	RAB6A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259241.2		
C2CD3	26005	hgsc.bcm.edu	37	11	73850650	73850650	+	Splice_Site	SNP	C	C	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:73850650C>G	ENST00000334126.7	-	4	933	c.707G>C	c.(706-708)aGg>aCg	p.R236T	C2CD3_ENST00000539061.1_Splice_Site_p.R236T|C2CD3_ENST00000313663.7_Splice_Site_p.R236T			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	236					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)					TGGTAATTACCTCGGAGTGGT	0.408																																					p.R236T		Atlas-SNP	.											.	C2CD3	288	.	0			c.G707C						PASS	.						294.0	291.0	292.0					11																	73850650		2200	4293	6493	SO:0001630	splice_region_variant	26005	exon4			AATTACCTCGGAG	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.707+1G>C	chr11.hg19:g.73850650C>G		91.0	0.0	.		84.0	23.0	.	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	C	13.04	2.117645	0.37339	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000289350;ENST00000539061	T;T	0.11385	2.78;2.81	5.02	4.11	0.48088	.	0.236148	0.42548	D	0.000694	T	0.28067	0.0692	M	0.73598	2.24	0.34355	D	0.690345	D;D	0.71674	0.995;0.998	P;D	0.68621	0.841;0.959	T	0.40117	-0.9580	9	.	.	.	.	9.0399	0.36311	0.0:0.9009:0.0:0.0991	.	236;236	Q4AC94;Q4AC94-1	C2CD3_HUMAN;.	T	236	ENSP00000334379:R236T;ENSP00000323339:R236T	.	R	-	2	0	C2CD3	73528298	1.000000	0.71417	1.000000	0.80357	0.454000	0.32378	2.454000	0.44979	1.355000	0.45865	0.644000	0.83932	AGG	.	.	.	none		0.408	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	Missense_Mutation
FUT4	2526	hgsc.bcm.edu	37	11	94277973	94277973	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:94277973A>T	ENST00000358752.2	+	1	957	c.674A>T	c.(673-675)gAc>gTc	p.D225V	RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA	NM_002033.3	NP_002024.1	P22083	FUT4_HUMAN	fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid-specific)	225					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	cell periphery (GO:0071944)|cell surface (GO:0009986)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(2)|endometrium(2)|lung(1)|skin(2)|upper_aerodigestive_tract(1)	8		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CTGCTCACCGACCGCGCGTCC	0.736																																					p.D225V		Atlas-SNP	.											.	FUT4	17	.	0			c.A674T						PASS	.						6.0	7.0	6.0					11																	94277973		1699	3465	5164	SO:0001583	missense	2526	exon1			TCACCGACCGCGC		CCDS8301.1	11q21	2013-02-26			ENSG00000196371	ENSG00000196371		"""CD molecules"", ""Fucosyltransferases"""	4015	protein-coding gene	gene with protein product	"""ELAM ligand fucosyltransferase"", ""galactoside 3-L-fucosyltransferase"""	104230		CD15, FCT3A, ELFT		1702034	Standard	NM_002033		Approved	FUC-TIV	uc001pez.3	P22083	OTTHUMG00000167795	ENST00000358752.2:c.674A>T	chr11.hg19:g.94277973A>T	ENSP00000351602:p.Asp225Val	53.0	0.0	.		32.0	14.0	.	NM_002033	B2RMS0	Missense_Mutation	SNP	ENST00000358752.2	hg19	CCDS8301.1	.	.	.	.	.	.	.	.	.	.	a	20.8	4.052660	0.75960	.	.	ENSG00000196371	ENST00000358752	T	0.29917	1.55	4.4	3.17	0.36434	.	0.122950	0.52532	D	0.000062	T	0.57740	0.2074	M	0.88906	2.99	0.58432	D	0.999999	D	0.89917	1.0	D	0.79784	0.993	T	0.65504	-0.6152	10	0.87932	D	0	.	10.5091	0.44851	0.8375:0.1625:0.0:0.0	.	225	P22083	FUT4_HUMAN	V	225	ENSP00000351602:D225V	ENSP00000351602:D225V	D	+	2	0	FUT4	93917621	0.998000	0.40836	0.773000	0.31616	0.629000	0.37895	3.825000	0.55730	1.739000	0.51704	0.363000	0.22086	GAC	.	.	.	none		0.736	FUT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396327.2	NM_002033	
KMT2A	4297	hgsc.bcm.edu	37	11	118390700	118390700	+	Missense_Mutation	SNP	C	C	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:118390700C>G	ENST00000389506.5	+	33	11341	c.11341C>G	c.(11341-11343)Ctg>Gtg	p.L3781V	KMT2A_ENST00000354520.4_Missense_Mutation_p.L3743V|RP11-770J1.3_ENST00000556583.1_RNA|RP11-770J1.3_ENST00000554407.1_RNA|RP11-770J1.3_ENST00000532597.1_RNA|RP11-770J1.3_ENST00000525992.2_RNA|KMT2A_ENST00000534358.1_Missense_Mutation_p.L3784V|RP11-770J1.3_ENST00000528578.1_RNA			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3781					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										GTTTAACTTCCTGGCTTCTAA	0.418																																					p.L3784V		Atlas-SNP	.											.	MLL	548	.	0			c.C11350G						PASS	.						93.0	90.0	91.0					11																	118390700		2200	4295	6495	SO:0001583	missense	4297	exon33			AACTTCCTGGCTT	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.11341C>G	chr11.hg19:g.118390700C>G	ENSP00000374157:p.Leu3781Val	42.0	0.0	.		66.0	38.0	.	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	C	14.63	2.593068	0.46214	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.84442	-1.85;-1.85;-1.81	5.9	4.02	0.46733	.	0.000000	0.64402	D	0.000002	D	0.91690	0.7373	M	0.86953	2.85	0.48975	D	0.999731	D;D	0.69078	0.997;0.997	D;D	0.78314	0.991;0.991	D	0.91550	0.5256	10	0.87932	D	0	.	8.9014	0.35497	0.0:0.7699:0.0:0.2301	.	3784;3781	E9PQG7;Q03164	.;MLL1_HUMAN	V	3784;3781;3743;2691	ENSP00000436786:L3784V;ENSP00000374157:L3781V;ENSP00000346516:L3743V	ENSP00000346516:L3743V	L	+	1	2	MLL	117895910	0.990000	0.36364	1.000000	0.80357	0.967000	0.64934	0.319000	0.19522	2.786000	0.95864	0.563000	0.77884	CTG	.	.	.	none		0.418	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
CLEC4C	170482	hgsc.bcm.edu	37	12	7890038	7890038	+	Missense_Mutation	SNP	G	G	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr12:7890038G>C	ENST00000542353.1	-	5	858	c.368C>G	c.(367-369)aCc>aGc	p.T123S	CLEC4C_ENST00000354629.5_Missense_Mutation_p.T92S|CLEC4C_ENST00000360345.3_Missense_Mutation_p.T123S|CLEC4C_ENST00000540085.1_Missense_Mutation_p.T92S	NM_130441.2	NP_569708.1	Q8WTT0	CLC4C_HUMAN	C-type lectin domain family 4, member C	123	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				Kidney(36;0.0915)		TTCTTCCCTGGTGTTGATCAC	0.408																																					p.T123S		Atlas-SNP	.											.	CLEC4C	44	.	0			c.C368G						PASS	.						128.0	126.0	127.0					12																	7890038		2203	4300	6503	SO:0001583	missense	170482	exon5			TCCCTGGTGTTGA	AF325460	CCDS8583.1, CCDS8584.1	12p13.2-p12.3	2008-02-05	2004-02-13	2005-02-11	ENSG00000198178	ENSG00000198178		"""C-type lectin domain containing"", ""CD molecules"""	13258	protein-coding gene	gene with protein product		606677	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 7"""	CLECSF11, CLECSF7		11031109, 11536172	Standard	NM_130441		Approved	HECL, DLEC, BDCA2, CD303	uc001qth.1	Q8WTT0	OTTHUMG00000168441	ENST00000542353.1:c.368C>G	chr12.hg19:g.7890038G>C	ENSP00000440428:p.Thr123Ser	53.0	0.0	.		53.0	19.0	.	NM_130441	D3DUU3|Q3T1C3|Q6UXS8|Q8WXX8	Missense_Mutation	SNP	ENST00000542353.1	hg19	CCDS8583.1	.	.	.	.	.	.	.	.	.	.	G	6.168	0.399249	0.11696	.	.	ENSG00000198178	ENST00000542353;ENST00000354629;ENST00000540085;ENST00000360345;ENST00000537530;ENST00000543765	T;T;T;T;T;T	0.12569	2.67;2.67;2.67;2.67;2.67;2.67	2.62	0.51	0.16983	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.11110	0.0271	N	0.13327	0.33	0.09310	N	1	P;D	0.54047	0.518;0.964	B;P	0.57152	0.103;0.814	T	0.05321	-1.0892	9	0.02654	T	1	.	8.1294	0.31018	0.0:0.4976:0.5024:0.0	.	92;123	Q8WTT0-2;Q8WTT0	.;CLC4C_HUMAN	S	123;92;92;123;45;83	ENSP00000440428:T123S;ENSP00000346648:T92S;ENSP00000445338:T92S;ENSP00000353500:T123S;ENSP00000438649:T45S;ENSP00000442457:T83S	ENSP00000346648:T92S	T	-	2	0	CLEC4C	7781305	0.403000	0.25319	0.038000	0.18304	0.029000	0.11900	0.490000	0.22403	0.123000	0.18342	0.603000	0.83216	ACC	.	.	.	none		0.408	CLEC4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399750.1	NM_203503	
RASSF3	283349	hgsc.bcm.edu	37	12	65078565	65078565	+	Splice_Site	SNP	A	A	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr12:65078565A>C	ENST00000542104.1	+	2	231		c.e2-1		RASSF3_ENST00000336061.2_Splice_Site	NM_178169.3	NP_835463.1	Q86WH2	RASF3_HUMAN	Ras association (RalGDS/AF-6) domain family member 3						signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Lung(2;0.00133)|LUAD - Lung adenocarcinoma(6;0.0665)|LUSC - Lung squamous cell carcinoma(43;0.132)	GBM - Glioblastoma multiforme(28;0.0611)		TTTTTCTTCTAGGATGTTGAG	0.443																																					.		Atlas-SNP	.											.	RASSF3	18	.	0			c.112-2A>C						PASS	.						93.0	88.0	90.0					12																	65078565		2203	4300	6503	SO:0001630	splice_region_variant	283349	exon2			TCTTCTAGGATGT		CCDS8969.1	12q14.2	2008-02-22	2008-02-22		ENSG00000153179	ENSG00000153179			14271	protein-coding gene	gene with protein product		607019					Standard	NM_178169		Approved		uc001ssd.3	Q86WH2	OTTHUMG00000168812	ENST00000542104.1:c.112-1A>C	chr12.hg19:g.65078565A>C		71.0	0.0	.		65.0	30.0	.	NM_178169	Q86WH1	Splice_Site	SNP	ENST00000542104.1	hg19	CCDS8969.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.241139	0.79912	.	.	ENSG00000153179	ENST00000542104;ENST00000336061	.	.	.	5.01	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0409	0.71791	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RASSF3	63364832	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.594000	0.82698	2.014000	0.59158	0.459000	0.35465	.	.	.	.	none		0.443	RASSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401161.1		Intron
RAB21	23011	hgsc.bcm.edu	37	12	72176413	72176413	+	Silent	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr12:72176413G>A	ENST00000261263.3	+	6	766	c.510G>A	c.(508-510)gaG>gaA	p.E170E		NM_014999.2	NP_055814.1	Q9UL25	RAB21_HUMAN	RAB21, member RAS oncogene family	170					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						AAGGAATTGAGGAACTCTTTC	0.284																																					p.E170E		Atlas-SNP	.											.	RAB21	17	.	0			c.G510A						PASS	.						105.0	109.0	107.0					12																	72176413		2203	4298	6501	SO:0001819	synonymous_variant	23011	exon6			AATTGAGGAACTC	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.510G>A	chr12.hg19:g.72176413G>A		174.0	0.0	.		201.0	88.0	.	NM_014999	Q14466|Q569H3	Silent	SNP	ENST00000261263.3	hg19	CCDS9003.1																																																																																			.	.	.	none		0.284	RAB21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404855.1		
GALNT4	8693	hgsc.bcm.edu	37	12	89917333	89917333	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr12:89917333C>T	ENST00000529983.2	-	1	1250	c.994G>A	c.(994-996)Gaa>Aaa	p.E332K	POC1B_ENST00000313546.3_Intron|POC1B_ENST00000541909.1_Intron|POC1B_ENST00000549035.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|GALNT4_ENST00000413530.1_Missense_Mutation_p.E160K|POC1B-GALNT4_ENST00000547474.1_3'UTR|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000393179.4_Intron|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.E329K	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	332	Catalytic subdomain B.				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						CCCCACACTTCCATTCCTGTG	0.498																																					p.E332K		Atlas-SNP	.											.	GALNT4	38	.	0			c.G994A						PASS	.						183.0	185.0	184.0					12																	89917333		2024	4193	6217	SO:0001583	missense	8693	exon1			ACACTTCCATTCC	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.994G>A	chr12.hg19:g.89917333C>T	ENSP00000436604:p.Glu332Lys	106.0	0.0	.		101.0	37.0	.	NM_003774	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	hg19	CCDS53817.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.871294	0.91587	.	.	ENSG00000259075;ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000413530;ENST00000529983	T;D;T	0.82711	-0.23;-1.64;-0.23	5.85	5.85	0.93711	.	.	.	.	.	D	0.90133	0.6917	M	0.64260	1.97	0.80722	D	1	D;D	0.71674	0.998;0.997	D;P	0.70016	0.967;0.896	D	0.90223	0.4273	9	0.72032	D	0.01	.	19.1613	0.93533	0.0:1.0:0.0:0.0	.	329;332	F8VUJ3;Q8N4A0	.;GALT4_HUMAN	K	329;160;332	ENSP00000447852:E329K;ENSP00000389686:E160K;ENSP00000436604:E332K	ENSP00000436604:E332K	E	-	1	0	GALNT4;RP11-1109F11.4	88441464	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.760000	0.85248	2.768000	0.95171	0.655000	0.94253	GAA	.	.	.	none		0.498	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
MYBPC1	4604	hgsc.bcm.edu	37	12	102043137	102043137	+	Missense_Mutation	SNP	G	G	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr12:102043137G>C	ENST00000550270.1	+	13	1221	c.1221G>C	c.(1219-1221)aaG>aaC	p.K407N	MYBPC1_ENST00000550501.1_Intron|MYBPC1_ENST00000536007.1_Missense_Mutation_p.K388N|RP11-755O11.2_ENST00000552081.1_RNA|MYBPC1_ENST00000551300.1_Missense_Mutation_p.K308N|MYBPC1_ENST00000441232.1_Missense_Mutation_p.K407N|MYBPC1_ENST00000549145.1_Missense_Mutation_p.K420N|MYBPC1_ENST00000547405.1_Missense_Mutation_p.K381N|MYBPC1_ENST00000360610.2_Missense_Mutation_p.K407N|MYBPC1_ENST00000361685.2_Missense_Mutation_p.K432N|RP11-755O11.2_ENST00000547027.1_RNA|MYBPC1_ENST00000361466.2_Missense_Mutation_p.K432N|MYBPC1_ENST00000553190.1_Missense_Mutation_p.K407N|MYBPC1_ENST00000392934.3_Missense_Mutation_p.K394N|MYBPC1_ENST00000547509.1_Missense_Mutation_p.K393N|MYBPC1_ENST00000541119.1_Missense_Mutation_p.K395N|MYBPC1_ENST00000452455.2_Missense_Mutation_p.K407N|MYBPC1_ENST00000545503.2_Missense_Mutation_p.K407N			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	407	Ig-like C2-type 3.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						GAGCAACAAAGGCTGATGCTG	0.393																																					p.K432N		Atlas-SNP	.											.	MYBPC1	235	.	0			c.G1296C						PASS	.						186.0	169.0	175.0					12																	102043137		2203	4300	6503	SO:0001583	missense	4604	exon15			AACAAAGGCTGAT		CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7549	protein-coding gene	gene with protein product		160794	"""myosin-binding protein C, slow-type"""			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.1221G>C	chr12.hg19:g.102043137G>C	ENSP00000449702:p.Lys407Asn	83.0	0.0	.		100.0	41.0	.	NM_206819	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	hg19	CCDS9085.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.637917	0.29157	.	.	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000360610;ENST00000392934;ENST00000547509;ENST00000361685;ENST00000549145;ENST00000553190;ENST00000540770;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466;ENST00000551300;ENST00000550270	T;T;T;T;T;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;0.93;0.93;0.93;0.93;0.93	5.98	2.17	0.27698	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000063	T	0.50769	0.1635	L	0.53249	1.67	0.43971	D	0.996657	P;D;P;D;D;P;P;D;P;P;P	0.53885	0.924;0.963;0.578;0.963;0.963;0.924;0.954;0.963;0.794;0.954;0.954	P;P;P;P;P;P;P;P;P;P;P	0.60886	0.875;0.848;0.648;0.848;0.88;0.875;0.81;0.88;0.637;0.81;0.81	T	0.39354	-0.9618	10	0.45353	T	0.12	.	8.746	0.34587	0.4881:0.0:0.5119:0.0	.	388;395;407;407;394;381;407;407;432;432;420	B7ZL02;B7ZL10;E7EWS6;B7ZL09;E7ESM5;Q17RR7;Q00872-3;Q00872;G3XAE8;Q00872-2;F8VZY0	.;.;.;.;.;.;.;MYPC1_HUMAN;.;.;.	N	381;407;407;407;394;393;432;420;407;432;407;388;395;432;308;407	ENSP00000448175:K381N;ENSP00000400908:K407N;ENSP00000388989:K407N;ENSP00000353822:K407N;ENSP00000376665:K394N;ENSP00000447362:K393N;ENSP00000354845:K432N;ENSP00000447660:K420N;ENSP00000447900:K407N;ENSP00000440034:K407N;ENSP00000446128:K388N;ENSP00000442847:K395N;ENSP00000354849:K432N;ENSP00000447116:K308N;ENSP00000449702:K407N	ENSP00000353822:K407N	K	+	3	2	MYBPC1	100567268	1.000000	0.71417	0.973000	0.42090	0.037000	0.13140	1.952000	0.40343	0.138000	0.18790	-0.469000	0.05056	AAG	.	.	.	none		0.393	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1		
AMER2	219287	hgsc.bcm.edu	37	13	25744451	25744451	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr13:25744451A>T	ENST00000515384.1	-	1	1974	c.1307T>A	c.(1306-1308)cTa>cAa	p.L436Q	AMER2-AS1_ENST00000413501.1_lincRNA|AMER2_ENST00000381853.3_Missense_Mutation_p.L317Q|AMER2_ENST00000357816.2_Missense_Mutation_p.L317Q			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	436					ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)										GAACTCCTGTAGATAGGTGTC	0.647																																					p.L436Q		Atlas-SNP	.											.	.	.	.	0			c.T1307A						PASS	.						33.0	27.0	29.0					13																	25744451		2203	4300	6503	SO:0001583	missense	219287	exon1			TCCTGTAGATAGG	AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"""-"""	26360	protein-coding gene	gene with protein product		614659	"""family with sequence similarity 123A"""	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.1307T>A	chr13.hg19:g.25744451A>T	ENSP00000426528:p.Leu436Gln	48.0	0.0	.		65.0	36.0	.	NM_152704	Q5RL80|Q5VX56|Q8N593|Q96NN5	Missense_Mutation	SNP	ENST00000515384.1	hg19	CCDS53859.1	.	.	.	.	.	.	.	.	.	.	A	18.88	3.717353	0.68844	.	.	ENSG00000165566	ENST00000357816;ENST00000381853;ENST00000515384	T;T;T	0.19938	2.11;2.11;2.11	4.42	4.42	0.53409	.	0.139225	0.50627	D	0.000113	T	0.43389	0.1245	M	0.66939	2.045	0.47476	D	0.999435	D;D	0.76494	0.999;0.999	D;D	0.77004	0.989;0.98	T	0.42327	-0.9458	10	0.87932	D	0	-31.152	12.9998	0.58667	1.0:0.0:0.0:0.0	.	436;317	Q8N7J2;Q8N7J2-2	F123A_HUMAN;.	Q	317;317;436	ENSP00000350469:L317Q;ENSP00000371277:L317Q;ENSP00000426528:L436Q	ENSP00000350469:L317Q	L	-	2	0	FAM123A	24642451	1.000000	0.71417	0.446000	0.26920	0.834000	0.47266	7.158000	0.77470	1.849000	0.53698	0.459000	0.35465	CTA	.	.	.	none		0.647	AMER2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370229.1	NM_152704	
FRY	10129	hgsc.bcm.edu	37	13	32705963	32705963	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr13:32705963C>T	ENST00000380250.3	+	8	1367	c.871C>T	c.(871-873)Ctt>Ttt	p.L291F		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	291						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)		TGAGGCCTCTCTTCAGTTTAT	0.418																																					p.L291F		Atlas-SNP	.											.	FRY	312	.	0			c.C871T						PASS	.						130.0	117.0	121.0					13																	32705963		1876	4115	5991	SO:0001583	missense	10129	exon8			GCCTCTCTTCAGT	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.871C>T	chr13.hg19:g.32705963C>T	ENSP00000369600:p.Leu291Phe	110.0	0.0	.		139.0	55.0	.	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	hg19	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	C	6.462	0.453397	0.12283	.	.	ENSG00000073910	ENST00000380250;ENST00000267067	T	0.20463	2.07	5.8	5.8	0.92144	.	0.059737	0.64402	D	0.000001	T	0.06005	0.0156	N	0.00054	-2.38	0.80722	D	1	B	0.06786	0.001	B	0.11329	0.006	T	0.50693	-0.8798	10	0.87932	D	0	.	20.0586	0.97663	0.0:1.0:0.0:0.0	.	291	Q5TBA9	FRY_HUMAN	F	291;219	ENSP00000369600:L291F	ENSP00000267067:L219F	L	+	1	0	FRY	31603963	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.745000	0.68672	2.741000	0.93983	0.650000	0.86243	CTT	.	.	.	none		0.418	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
RTN1	6252	hgsc.bcm.edu	37	14	60074162	60074162	+	Missense_Mutation	SNP	A	A	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr14:60074162A>G	ENST00000267484.5	-	4	2149	c.1814T>C	c.(1813-1815)tTt>tCt	p.F605S	RTN1_ENST00000342503.4_Missense_Mutation_p.F37S|RTN1_ENST00000395090.1_Missense_Mutation_p.F22S|RTN1_ENST00000557422.1_5'UTR	NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	605	Reticulon. {ECO:0000255|PROSITE- ProRule:PRU00170}.				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)		GAAACTCCCAAACACGATGCC	0.597																																					p.F605S		Atlas-SNP	.											.	RTN1	139	.	0			c.T1814C						PASS	.						56.0	52.0	53.0					14																	60074162		2203	4300	6503	SO:0001583	missense	6252	exon4			CTCCCAAACACGA	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.1814T>C	chr14.hg19:g.60074162A>G	ENSP00000267484:p.Phe605Ser	78.0	0.0	.		81.0	40.0	.	NM_021136	Q16800|Q16801|Q5BKZ4|Q9BQ59	Missense_Mutation	SNP	ENST00000267484.5	hg19	CCDS9740.1	.	.	.	.	.	.	.	.	.	.	A	32	5.148436	0.94603	.	.	ENSG00000139970	ENST00000432103;ENST00000267484;ENST00000395090;ENST00000342503;ENST00000433623	T;T;T	0.54071	0.59;0.59;0.59	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.78375	0.4273	M	0.89840	3.065	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;0.994	T	0.83082	-0.0137	10	0.87932	D	0	.	16.4943	0.84223	1.0:0.0:0.0:0.0	.	22;605;37	A8MT72;Q16799;Q16799-3	.;RTN1_HUMAN;.	S	185;605;22;37;531	ENSP00000267484:F605S;ENSP00000378525:F22S;ENSP00000340716:F37S	ENSP00000267484:F605S	F	-	2	0	RTN1	59143915	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	9.339000	0.96797	2.291000	0.77112	0.533000	0.62120	TTT	.	.	.	none		0.597	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2		
ZFP36L1	677	hgsc.bcm.edu	37	14	69256832	69256832	+	Silent	SNP	G	G	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr14:69256832G>T	ENST00000439696.2	-	2	736	c.435C>A	c.(433-435)cgC>cgA	p.R145R	ZFP36L1_ENST00000555997.1_3'UTR|ZFP36L1_ENST00000336440.3_Silent_p.R145R	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1	145					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|T cell differentiation in thymus (GO:0033077)|vasculogenesis (GO:0001570)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|kidney(1)|large_intestine(1)|liver(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(1)	21				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GGGTCAGGCTGCGGAGCTCGT	0.632											OREG0022753	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R214R		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.C642A						PASS	.						80.0	78.0	79.0					14																	69256832		2203	4300	6503	SO:0001819	synonymous_variant	677	exon3			CAGGCTGCGGAGC	X79066	CCDS9791.1	14q22-q24	2012-11-27	2012-11-27	2001-11-23		ENSG00000185650		"""RING-type (C3HC4) zinc fingers"""	1107	protein-coding gene	gene with protein product		601064	"""zinc finger protein, C3H type, 36-like 1"", ""zinc finger protein 36, C3H type-like 1"""	BRF1		8024689	Standard	NM_004926		Approved	RNF162B, Berg36, ERF1, TIS11B, cMG1	uc021rve.1	Q07352		ENST00000439696.2:c.435C>A	chr14.hg19:g.69256832G>T		68.0	0.0	.	1113	94.0	38.0	.	NM_001244701	Q13851	Silent	SNP	ENST00000439696.2	hg19	CCDS9791.1																																																																																			.	.	.	none		0.632	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1		
SERPINA4	5267	hgsc.bcm.edu	37	14	95030170	95030170	+	Silent	SNP	C	C	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr14:95030170C>A	ENST00000557004.1	+	2	772	c.351C>A	c.(349-351)gtC>gtA	p.V117V	SERPINA5_ENST00000553780.1_Intron|SERPINA4_ENST00000298841.5_Silent_p.V117V|SERPINA4_ENST00000555095.1_Silent_p.V117V			P29622	KAIN_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4	117					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(28)|ovary(3)|skin(1)|urinary_tract(1)	46				COAD - Colon adenocarcinoma(157;0.211)		AGTCCGATGTCCATAGGGGCT	0.627																																					p.V117V		Atlas-SNP	.											.	SERPINA4	81	.	0			c.C351A						PASS	.						68.0	67.0	67.0					14																	95030170		2203	4300	6503	SO:0001819	synonymous_variant	5267	exon2			CGATGTCCATAGG	L19684	CCDS9927.1	14q32.13	2014-02-18	2005-08-18		ENSG00000100665	ENSG00000100665		"""Serine (or cysteine) peptidase inhibitors"""	8948	protein-coding gene	gene with protein product		147935	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4"""	PI4		8227002, 24172014	Standard	NM_001289032		Approved	KST, KAL, KLST, kallistatin	uc001ydk.3	P29622	OTTHUMG00000170859	ENST00000557004.1:c.351C>A	chr14.hg19:g.95030170C>A		26.0	0.0	.		50.0	23.0	.	NM_006215	Q53XB5|Q86TR9|Q96BZ5	Silent	SNP	ENST00000557004.1	hg19	CCDS9927.1																																																																																			.	.	.	none		0.627	SERPINA4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410718.1	NM_006215	
HERC2	8924	hgsc.bcm.edu	37	15	28459417	28459417	+	Splice_Site	SNP	C	C	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr15:28459417C>G	ENST00000261609.7	-	41	6468	c.6360G>C	c.(6358-6360)gaG>gaC	p.E2120D		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)		TCAGCGTGGACTCTGAGGAGG	0.677																																					p.E2120D		Atlas-SNP	.											.	HERC2	501	.	0			c.G6360C						PASS	.						17.0	18.0	18.0					15																	28459417		2190	4275	6465	SO:0001630	splice_region_variant	8924	exon41			CGTGGACTCTGAG	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.6359-1G>C	chr15.hg19:g.28459417C>G		72.0	0.0	.		98.0	47.0	.	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	5.854	0.341694	0.11069	.	.	ENSG00000128731	ENST00000261609	T	0.39056	1.1	4.75	-4.8	0.03190	.	0.205916	0.40064	N	0.001188	T	0.25005	0.0607	L	0.44542	1.39	0.80722	D	1	B	0.17667	0.023	B	0.12156	0.007	T	0.13150	-1.0520	10	0.15066	T	0.55	.	8.6363	0.33950	0.0:0.2967:0.1043:0.599	.	2120	O95714	HERC2_HUMAN	D	2120	ENSP00000261609:E2120D	ENSP00000261609:E2120D	E	-	3	2	HERC2	26133012	0.743000	0.28239	0.501000	0.27601	0.127000	0.20565	-0.241000	0.08940	-0.791000	0.04486	0.484000	0.47621	GAG	.	.	.	none		0.677	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	Missense_Mutation
DMXL2	23312	hgsc.bcm.edu	37	15	51792075	51792075	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr15:51792075C>T	ENST00000251076.5	-	18	3633	c.3346G>A	c.(3346-3348)Gag>Aag	p.E1116K	RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000543779.2_Missense_Mutation_p.E1116K|DMXL2_ENST00000449909.3_Intron	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1116						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)		AAAACCCACTCTGATCCTCCT	0.378																																					p.E1116K		Atlas-SNP	.											.	DMXL2	262	.	0			c.G3346A						PASS	.						73.0	66.0	68.0					15																	51792075		2194	4293	6487	SO:0001583	missense	23312	exon18			CCCACTCTGATCC	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.3346G>A	chr15.hg19:g.51792075C>T	ENSP00000251076:p.Glu1116Lys	95.0	0.0	.		128.0	53.0	.	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	hg19	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.243914	0.58995	.	.	ENSG00000104093	ENST00000251076;ENST00000543779	T;T	0.29397	1.57;1.57	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.37571	0.1008	M	0.75615	2.305	0.80722	D	1	B;P	0.35745	0.067;0.518	B;B	0.33846	0.076;0.171	T	0.23583	-1.0184	10	0.32370	T	0.25	.	19.0754	0.93159	0.0:1.0:0.0:0.0	.	1116;1116	F5GWF1;Q8TDJ6	.;DMXL2_HUMAN	K	1116	ENSP00000251076:E1116K;ENSP00000441858:E1116K	ENSP00000251076:E1116K	E	-	1	0	DMXL2	49579367	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.461000	0.80834	2.497000	0.84241	0.591000	0.81541	GAG	.	.	.	none		0.378	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
CELF6	60677	hgsc.bcm.edu	37	15	72581548	72581548	+	Missense_Mutation	SNP	G	G	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr15:72581548G>C	ENST00000569547.1	-	8	1032	c.961C>G	c.(961-963)Ctg>Gtg	p.L321V	CELF6_ENST00000543764.2_Missense_Mutation_p.L205V|CELF6_ENST00000395258.2_Missense_Mutation_p.L208V|CELF6_ENST00000567083.1_Missense_Mutation_p.L321V|CELF6_ENST00000569311.1_5'Flank|CELF6_ENST00000539635.1_Missense_Mutation_p.L182V|RP11-106M3.2_ENST00000379915.4_RNA|RP11-106M3.3_ENST00000570175.1_RNA|CELF6_ENST00000287202.5_Missense_Mutation_p.L321V			Q96J87	CELF6_HUMAN	CUGBP, Elav-like family member 6	321					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(2)	13						TGGGGGGTCAGAGGGCCGAAT	0.682																																					p.L321V		Atlas-SNP	.											.	CELF6	30	.	0			c.C961G						PASS	.						14.0	19.0	18.0					15																	72581548		2190	4274	6464	SO:0001583	missense	60677	exon8			GGGTCAGAGGGCC	AF425606	CCDS10242.1, CCDS53955.1, CCDS53956.1	15q24	2013-02-12	2010-02-19	2010-02-19	ENSG00000140488	ENSG00000140488		"""RNA binding motif (RRM) containing"""	14059	protein-coding gene	gene with protein product		612681	"""Bruno (Drosophila) -like 6, RNA binding protein"", ""bruno-like 6, RNA binding protein (Drosophila)"""	BRUNOL6		10893231	Standard	NM_052840		Approved		uc002auh.2	Q96J87	OTTHUMG00000133444	ENST00000569547.1:c.961C>G	chr15.hg19:g.72581548G>C	ENSP00000454749:p.Leu321Val	47.0	0.0	.		65.0	30.0	.	NM_001172684	B4DG28|B4DJB6|Q6PII4|Q6ZNJ7|Q8N607	Missense_Mutation	SNP	ENST00000569547.1	hg19	CCDS10242.1	.	.	.	.	.	.	.	.	.	.	G	10.09	1.255375	0.22965	.	.	ENSG00000140488	ENST00000287202;ENST00000437872;ENST00000543764;ENST00000379915;ENST00000395258;ENST00000539635	T;T;T;T	0.21191	2.02;2.26;2.27;3.74	5.02	2.07	0.26955	.	0.555812	0.15029	U	0.284567	T	0.16041	0.0386	L	0.39147	1.195	0.40996	D	0.984894	B;B;B;B;B	0.33103	0.096;0.096;0.357;0.397;0.096	B;B;B;B;B	0.38683	0.021;0.021;0.279;0.085;0.021	T	0.11743	-1.0575	10	0.16420	T	0.52	-6.9448	4.6841	0.12750	0.2282:0.0:0.6166:0.1551	.	321;205;208;182;321	B4DJB6;B4DG28;Q96J87-2;B3KWE6;Q96J87	.;.;.;.;CELF6_HUMAN	V	321;321;205;172;208;182	ENSP00000287202:L321V;ENSP00000439956:L205V;ENSP00000378677:L208V;ENSP00000443162:L182V	ENSP00000287202:L321V	L	-	1	2	CELF6	70368602	0.358000	0.24947	0.999000	0.59377	0.664000	0.39144	0.682000	0.25335	0.147000	0.19030	0.491000	0.48974	CTG	.	.	.	none		0.682	CELF6-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000420180.1	NM_052840	
ANPEP	290	hgsc.bcm.edu	37	15	90349809	90349809	+	Silent	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr15:90349809G>A	ENST00000300060.6	-	2	319	c.6C>T	c.(4-6)gcC>gcT	p.A2A		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	2					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)	AGAAGCCCTTGGCCATGGTGA	0.632																																					p.A2A	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.C6T						PASS	.						27.0	27.0	27.0					15																	90349809		2199	4295	6494	SO:0001819	synonymous_variant	290	exon2			GCCCTTGGCCATG	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.6C>T	chr15.hg19:g.90349809G>A		63.0	0.0	.		58.0	7.0	.	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Silent	SNP	ENST00000300060.6	hg19	CCDS10356.1																																																																																			.	.	.	none		0.632	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1		
CHTF18	63922	hgsc.bcm.edu	37	16	842327	842327	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr16:842327G>A	ENST00000262315.9	+	10	1369	c.1306G>A	c.(1306-1308)Gag>Aag	p.E436K	CHTF18_ENST00000317063.6_Missense_Mutation_p.E631K|CHTF18_ENST00000455171.2_Missense_Mutation_p.E464K	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	436					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				GGTCATCGATGAGATCGACGG	0.692																																					p.E436K		Atlas-SNP	.											.	CHTF18	52	.	0			c.G1306A						PASS	.						23.0	31.0	28.0					16																	842327		1939	4039	5978	SO:0001583	missense	63922	exon10			ATCGATGAGATCG	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"""ATPases / AAA-type"""	18435	protein-coding gene	gene with protein product		613201	"""chromosome 16 open reading frame 41"""	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.1306G>A	chr16.hg19:g.842327G>A	ENSP00000262315:p.Glu436Lys	172.0	0.0	.		166.0	24.0	.	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	hg19	CCDS45371.1	.	.	.	.	.	.	.	.	.	.	g	36	5.735393	0.96865	.	.	ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315	D;D;D	0.97870	-4.58;-4.58;-4.58	5.19	5.19	0.71726	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.99351	0.9772	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	0.98516	1.0621	10	0.49607	T	0.09	-36.8096	17.2796	0.87124	0.0:0.0:1.0:0.0	.	464;436	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	K	631;464;436	ENSP00000313029:E631K;ENSP00000406252:E464K;ENSP00000262315:E436K	ENSP00000262315:E436K	E	+	1	0	CHTF18	782328	1.000000	0.71417	0.993000	0.49108	0.880000	0.50808	9.500000	0.97977	2.416000	0.81992	0.457000	0.33378	GAG	.	.	.	none		0.692	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
C16orf72	29035	hgsc.bcm.edu	37	16	9210571	9210571	+	Silent	SNP	A	A	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr16:9210571A>G	ENST00000327827.7	+	4	1027	c.630A>G	c.(628-630)ccA>ccG	p.P210P		NM_014117.2	NP_054836.2	Q14CZ0	CP072_HUMAN	chromosome 16 open reading frame 72	210										endometrium(4)|large_intestine(2)|lung(2)	8						CGAGTACCCCAGGCTCTCCTA	0.423																																					p.P210P		Atlas-SNP	.											.	C16orf72	26	.	0			c.A630G						PASS	.						192.0	182.0	185.0					16																	9210571		2197	4300	6497	SO:0001819	synonymous_variant	29035	exon4			TACCCCAGGCTCT	AK123266	CCDS10538.1	16p13.2	2012-11-19			ENSG00000182831	ENSG00000182831			30103	protein-coding gene	gene with protein product						8889548	Standard	NM_014117		Approved	FLJ41272, PRO0149	uc002czm.3	Q14CZ0	OTTHUMG00000178147	ENST00000327827.7:c.630A>G	chr16.hg19:g.9210571A>G		108.0	0.0	.		106.0	47.0	.	NM_014117		Silent	SNP	ENST00000327827.7	hg19	CCDS10538.1																																																																																			.	.	.	none		0.423	C16orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440760.2	NM_014117	
CNGB1	1258	hgsc.bcm.edu	37	16	57957180	57957180	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr16:57957180G>A	ENST00000251102.8	-	18	1700	c.1640C>T	c.(1639-1641)aCt>aTt	p.T547I	CNGB1_ENST00000564448.1_Missense_Mutation_p.T541I	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	547					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						GTCTCACTCAGTGTCCTTCGG	0.582																																					p.T547I	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.C1640T						PASS	.						49.0	51.0	50.0					16																	57957180		1885	4109	5994	SO:0001583	missense	1258	exon18			CACTCAGTGTCCT	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.1640C>T	chr16.hg19:g.57957180G>A	ENSP00000251102:p.Thr547Ile	30.0	0.0	.		36.0	16.0	.	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	hg19	CCDS42169.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.659448	0.47467	.	.	ENSG00000070729	ENST00000251102	T	0.29142	1.58	4.97	1.69	0.24217	.	0.655524	0.13615	N	0.374836	T	0.25754	0.0627	L	0.46157	1.445	0.09310	N	0.999999	P	0.50710	0.938	P	0.45195	0.473	T	0.10520	-1.0626	10	0.42905	T	0.14	.	3.9819	0.09498	0.1996:0.0:0.6032:0.1972	.	547	Q14028	CNGB1_HUMAN	I	547	ENSP00000251102:T547I	ENSP00000251102:T547I	T	-	2	0	CNGB1	56514681	0.012000	0.17670	0.616000	0.29078	0.522000	0.34438	1.527000	0.35975	0.681000	0.31386	0.655000	0.94253	ACT	.	.	.	none		0.582	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
GUCY2D	3000	hgsc.bcm.edu	37	17	7907255	7907255	+	Silent	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:7907255C>T	ENST00000254854.4	+	3	957	c.807C>T	c.(805-807)acC>acT	p.T269T		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	269					intracellular signal transduction (GO:0035556)|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)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			skin(1)	1		Prostate(122;0.157)				TGGGCCTGACCGATGGCTCCC	0.662																																					p.T269T		Atlas-SNP	.											.	GUCY2D	82	.	0			c.C807T						PASS	.						94.0	88.0	90.0					17																	7907255		2203	4300	6503	SO:0001819	synonymous_variant	3000	exon3			CCTGACCGATGGC	L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"""cone rod dystrophy 6"""	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.807C>T	chr17.hg19:g.7907255C>T		106.0	0.0	.		106.0	20.0	.	NM_000180	Q6LEA7	Silent	SNP	ENST00000254854.4	hg19	CCDS11127.1																																																																																			.	.	.	none		0.662	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2		
TMIGD1	388364	hgsc.bcm.edu	37	17	28656425	28656425	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:28656425G>A	ENST00000328886.4	-	3	277	c.205C>T	c.(205-207)Cga>Tga	p.R69*	TMIGD1_ENST00000538566.2_Nonsense_Mutation_p.R69*	NM_206832.1	NP_996663.1	Q6UXZ0	TMIG1_HUMAN	transmembrane and immunoglobulin domain containing 1	69	Ig-like C2-type 1.					integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(1)|lung(5)|skin(2)	12						CCCTCCTCTCGGTACCAGAGC	0.443																																					p.R69X		Atlas-SNP	.											.	TMIGD1	38	.	0			c.C205T						PASS	.						123.0	111.0	115.0					17																	28656425		2203	4300	6503	SO:0001587	stop_gained	388364	exon3			CCTCTCGGTACCA	AY358153	CCDS32605.1	17q11.2	2013-01-29	2006-07-05	2006-07-05		ENSG00000182271		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	32431	protein-coding gene	gene with protein product				TMIGD		12975309	Standard	NM_206832		Approved	UNQ9372	uc002hfa.1	Q6UXZ0		ENST00000328886.4:c.205C>T	chr17.hg19:g.28656425G>A	ENSP00000332404:p.Arg69*	73.0	0.0	.		91.0	5.0	.	NM_206832	A8K2K1|Q6ZMC6	Nonsense_Mutation	SNP	ENST00000328886.4	hg19	CCDS32605.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.947315	0.92593	.	.	ENSG00000182271	ENST00000328886;ENST00000538566	.	.	.	5.52	2.21	0.28008	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.1084	14.2699	0.66145	0.0:0.0:0.5014:0.4986	.	.	.	.	X	69	.	ENSP00000332404:R69X	R	-	1	2	TMIGD1	25680551	1.000000	0.71417	0.988000	0.46212	0.980000	0.70556	1.621000	0.36986	0.196000	0.20367	0.579000	0.79373	CGA	.	.	.	none		0.443	TMIGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447955.1	NM_206832	
NF1	4763	hgsc.bcm.edu	37	17	29483033	29483033	+	Missense_Mutation	SNP	T	T	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:29483033T>G	ENST00000358273.4	+	2	476	c.93T>G	c.(91-93)caT>caG	p.H31Q	NF1_ENST00000356175.3_Missense_Mutation_p.H31Q|NF1_ENST00000431387.4_Missense_Mutation_p.H31Q	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	31			H -> R (in NF1; dbSNP:rs199474725). {ECO:0000269|PubMed:15060124}.		actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AGAACACACATACCAAAGTCA	0.318			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.H31Q		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)	c.T93G						PASS	.						89.0	81.0	84.0					17																	29483033		2203	4300	6503	SO:0001583	missense	4763	exon2	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	CACACATACCAAA		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.93T>G	chr17.hg19:g.29483033T>G	ENSP00000351015:p.His31Gln	141.0	0.0	.		201.0	84.0	.	NM_001128147	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	T	11.32	1.605044	0.28623	.	.	ENSG00000196712	ENST00000431387;ENST00000358273;ENST00000356175	T;T;T	0.08720	3.06;3.32;3.47	4.95	2.37	0.29283	.	0.000000	0.85682	D	0.000000	T	0.11324	0.0276	L	0.38692	1.165	0.80722	D	1	D;B;D;D	0.69078	0.96;0.179;0.997;0.96	D;B;D;D	0.78314	0.962;0.039;0.991;0.962	T	0.44877	-0.9299	10	0.02654	T	1	.	4.7551	0.13080	0.0:0.4884:0.0:0.5116	.	31;31;31;31	P21359-2;P21359;Q14931;P21359-3	.;NF1_HUMAN;.;.	Q	31	ENSP00000412921:H31Q;ENSP00000351015:H31Q;ENSP00000348498:H31Q	ENSP00000348498:H31Q	H	+	3	2	NF1	26507159	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.637000	0.61346	0.836000	0.34901	-0.376000	0.06991	CAT	.	.	.	none		0.318	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
PEX12	5193	hgsc.bcm.edu	37	17	33904061	33904062	+	Missense_Mutation	DNP	TG	TG	CA			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:33904061_33904062TG>CA	ENST00000225873.4	-	2	1282_1283	c.675_676CA>TG	c.(673-678)gcCAgg>gcTGgg	p.R226G	RP11-1094M14.11_ENST00000592381.1_lincRNA	NM_000286.2	NP_000277.1	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	226					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	integral component of peroxisomal membrane (GO:0005779)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(8)	18				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCTTACCTCCTGGCTGGTTGCT	0.45																																					p.R226G|p.A225A		Atlas-SNP	.											.	PEX12	36	.	0			c.A676G|c.C675T						PASS	.																																			SO:0001583	missense	5193	exon2			ACCTCCTGGCTGG|CCTCCTGGCTGGT	U91521	CCDS11296.1	17q21.1	2011-02-10			ENSG00000108733	ENSG00000108733			8854	protein-coding gene	gene with protein product		601758				9090384	Standard	NM_000286		Approved		uc002hjp.3	O00623	OTTHUMG00000132951	ENST00000225873.4:c.675_676delinsCA	chr17.hg19:g.33904061_33904062delinsCA	ENSP00000225873:p.Arg226Gly	28.0|29.0	0.0	.		50.0	20.0	.	NM_000286	B2R6M2	Missense_Mutation|Silent	SNP	ENST00000225873.4	hg19	CCDS11296.1																																																																																			.	.	.	none		0.450	PEX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256489.2	NM_000286	
KRTAP17-1	83902	hgsc.bcm.edu	37	17	39471747	39471747	+	Silent	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:39471747G>A	ENST00000334202.3	-	1	200	c.156C>T	c.(154-156)tgC>tgT	p.C52C		NM_031964.1	NP_114170.1	Q9BYP8	KR171_HUMAN	keratin associated protein 17-1	52						intermediate filament (GO:0005882)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			acgatccgcagcagctgcccc	0.687																																					p.C52C		Atlas-SNP	.											.	KRTAP17-1	14	.	0			c.C156T						PASS	.						15.0	20.0	19.0					17																	39471747		2181	4269	6450	SO:0001819	synonymous_variant	83902	exon1			TCCGCAGCAGCTG	AJ406952	CCDS11387.1	17q21.2	2013-06-20			ENSG00000186860	ENSG00000186860		"""Keratin associated proteins"""	18917	protein-coding gene	gene with protein product							Standard	NM_031964		Approved	KAP17.1	uc002hwj.3	Q9BYP8	OTTHUMG00000133433	ENST00000334202.3:c.156C>T	chr17.hg19:g.39471747G>A		72.0	0.0	.		59.0	28.0	.	NM_031964		Silent	SNP	ENST00000334202.3	hg19	CCDS11387.1																																																																																			.	.	.	none		0.687	KRTAP17-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257296.1		
KIF18B	146909	hgsc.bcm.edu	37	17	43003847	43003847	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:43003847C>T	ENST00000593135.1	-	15	2484	c.2387G>A	c.(2386-2388)cGc>cAc	p.R796H	KIF18B_ENST00000339151.4_Missense_Mutation_p.R799H|KIF18B_ENST00000590129.1_Missense_Mutation_p.R817H|KIF18B_ENST00000438933.2_Missense_Mutation_p.R808H|KIF18B_ENST00000587309.1_Missense_Mutation_p.R808H	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B	808					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|regulation of cell division (GO:0051302)	astral microtubule (GO:0000235)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule plus-end (GO:0035371)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	21		Prostate(33;0.155)				GATGCGGCTGCGGCCATGGGA	0.607																																					p.R808H		Atlas-SNP	.											.	KIF18B	63	.	0			c.G2423A						PASS	.						30.0	37.0	35.0					17																	43003847		2020	4182	6202	SO:0001583	missense	146909	exon15			CGGCTGCGGCCAT		CCDS45709.1, CCDS58555.1, CCDS45709.2	17q21.31	2014-09-04			ENSG00000186185			"""Kinesins"""	27102	protein-coding gene	gene with protein product		614570				16084724	Standard	NM_001264573		Approved		uc010wjh.3	Q86Y91	OTTHUMG00000179867	ENST00000593135.1:c.2387G>A	chr17.hg19:g.43003847C>T	ENSP00000465992:p.Arg796His	66.0	0.0	.		56.0	16.0	.	NM_001264573	A6NJI2|B7ZM49|B9EGM8|D5L6I1	Missense_Mutation	SNP	ENST00000593135.1	hg19	CCDS45709.2	.	.	.	.	.	.	.	.	.	.	C	13.25	2.179701	0.38511	.	.	ENSG00000186185	ENST00000438933;ENST00000339151;ENST00000376982	T;T	0.76709	-1.02;-1.04	5.18	-2.42	0.06542	.	.	.	.	.	T	0.69396	0.3106	M	0.65975	2.015	0.09310	N	1	B;B;B	0.28439	0.036;0.212;0.212	B;B;B	0.22880	0.007;0.042;0.042	T	0.53358	-0.8450	9	0.22109	T	0.4	.	9.4947	0.38982	0.0:0.4552:0.0:0.5448	.	808;805;817	Q86Y91;Q86Y91-3;Q86Y91-2	KI18B_HUMAN;.;.	H	808;799;808	ENSP00000412798:R808H;ENSP00000341466:R799H	ENSP00000341466:R799H	R	-	2	0	KIF18B	40359373	0.002000	0.14202	0.103000	0.21229	0.889000	0.51656	-0.800000	0.04555	-0.501000	0.06605	-0.345000	0.07892	CGC	.	.	.	none		0.607	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	NM_001080443	
FASN	2194	hgsc.bcm.edu	37	17	80047168	80047168	+	Silent	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:80047168G>A	ENST00000306749.2	-	13	2276	c.2058C>T	c.(2056-2058)ttC>ttT	p.F686F		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	686	Acyl and malonyl transferases. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	TGGCCTCCATGAAGTAGGAGT	0.637																																					p.F686F	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C2058T						PASS	.						52.0	49.0	50.0					17																	80047168		2200	4300	6500	SO:0001819	synonymous_variant	2194	exon13			CTCCATGAAGTAG	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	3594	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 27X, member 1"""	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.2058C>T	chr17.hg19:g.80047168G>A		98.0	0.0	.		93.0	51.0	.	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	hg19	CCDS11801.1																																																																																			.	.	.	none		0.637	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
RALBP1	10928	hgsc.bcm.edu	37	18	9535920	9535920	+	Silent	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr18:9535920G>A	ENST00000019317.4	+	10	2176	c.1953G>A	c.(1951-1953)aaG>aaA	p.K651K	RALBP1_ENST00000383432.3_Silent_p.K651K			Q15311	RBP1_HUMAN	ralA binding protein 1	651					ATP catabolic process (GO:0006200)|chemotaxis (GO:0006935)|positive regulation of Cdc42 GTPase activity (GO:0043089)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|transport (GO:0006810)	cytosol (GO:0005829)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ATPase activity, coupled to movement of substances (GO:0043492)|GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	14					Carbamazepine(DB00564)|Doxorubicin(DB00997)|Sorafenib(DB00398)|Vincristine(DB00541)	GGGATAGGAAGGAGACGTCCA	0.627																																					p.K651K		Atlas-SNP	.											.	RALBP1	48	.	0			c.G1953A						PASS	.						20.0	23.0	22.0					18																	9535920		2199	4291	6490	SO:0001819	synonymous_variant	10928	exon10			TAGGAAGGAGACG	L42542	CCDS11845.1	18p11.22	2006-04-22			ENSG00000017797	ENSG00000017797			9841	protein-coding gene	gene with protein product		605801				7673236	Standard	NM_006788		Approved	RLIP76, RIP1, RIP	uc002koc.3	Q15311	OTTHUMG00000131596	ENST00000019317.4:c.1953G>A	chr18.hg19:g.9535920G>A		192.0	0.0	.		174.0	65.0	.	NM_006788	D3DUI0	Silent	SNP	ENST00000019317.4	hg19	CCDS11845.1																																																																																			.	.	.	none		0.627	RALBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254479.1	NM_006788	
PPP4R1	9989	hgsc.bcm.edu	37	18	9570630	9570630	+	Silent	SNP	A	A	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr18:9570630A>T	ENST00000400556.3	-	11	1171	c.1098T>A	c.(1096-1098)acT>acA	p.T366T	PPP4R1_ENST00000400555.3_Silent_p.T349T	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	366					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						GATCTGAAGGAGTATCCTCTG	0.423																																					p.T366T	Melanoma(188;1232 2082 5061 11948 35994)	Atlas-SNP	.											.	PPP4R1	63	.	0			c.T1098A						PASS	.						89.0	87.0	88.0					18																	9570630		1898	4108	6006	SO:0001819	synonymous_variant	9989	exon11			TGAAGGAGTATCC	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.1098T>A	chr18.hg19:g.9570630A>T		43.0	0.0	.		59.0	33.0	.	NM_001042388	Q99774|Q9UNQ7	Silent	SNP	ENST00000400556.3	hg19	CCDS42412.1																																																																																			.	.	.	none		0.423	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134	
DOT1L	84444	hgsc.bcm.edu	37	19	2210838	2210838	+	Silent	SNP	G	G	T	rs563972624		TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:2210838G>T	ENST00000398665.3	+	14	1371	c.1335G>T	c.(1333-1335)gcG>gcT	p.A445A	AC004490.1_ENST00000585593.1_RNA	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	445					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)		CTCAGACGGCGGCCTCCTCAC	0.687																																					p.A445A		Atlas-SNP	.											.	DOT1L	205	.	0			c.G1335T						PASS	.						21.0	27.0	25.0					19																	2210838		1979	4136	6115	SO:0001819	synonymous_variant	84444	exon14			GACGGCGGCCTCC	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.1335G>T	chr19.hg19:g.2210838G>T		126.0	0.0	.		119.0	55.0	.	NM_032482	O60379|Q96JL1	Silent	SNP	ENST00000398665.3	hg19	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	G	6.432	0.447875	0.12223	.	.	ENSG00000104885	ENST00000440640	.	.	.	4.84	-9.68	0.00528	.	.	.	.	.	T	0.16128	0.0388	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.09552	-1.0669	4	.	.	.	-12.4482	3.2203	0.06713	0.4213:0.2469:0.2445:0.0872	.	.	.	.	L	232	.	.	R	+	2	0	DOT1L	2161838	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.301000	0.01137	-2.984000	0.00282	-1.134000	0.01955	CGG	.	.	.	none		0.687	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482	
MUC16	94025	hgsc.bcm.edu	37	19	9011358	9011358	+	Missense_Mutation	SNP	G	G	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:9011358G>T	ENST00000397910.4	-	36	39078	c.38875C>A	c.(38875-38877)Ccc>Acc	p.P12959T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12961	SEA 6. {ECO:0000255|PROSITE- ProRule:PRU00188}.				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						AGGGTGTAGGGGCCCAGCTCT	0.547																																					p.P12959T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C38875A						PASS	.						228.0	200.0	209.0					19																	9011358		1988	4172	6160	SO:0001583	missense	94025	exon36			TGTAGGGGCCCAG	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.38875C>A	chr19.hg19:g.9011358G>T	ENSP00000381008:p.Pro12959Thr	87.0	0.0	.		96.0	23.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	8.336	0.827704	0.16749	.	.	ENSG00000181143	ENST00000397910;ENST00000441155	T	0.24151	1.87	2.76	-0.411	0.12370	.	.	.	.	.	T	0.30634	0.0771	L	0.51914	1.62	.	.	.	P	0.44659	0.84	P	0.51999	0.687	T	0.40059	-0.9583	8	0.87932	D	0	-4.8865	5.7224	0.17995	0.3682:0.0:0.6318:0.0	.	12959	B5ME49	.	T	12959;112	ENSP00000381008:P12959T	ENSP00000381008:P12959T	P	-	1	0	MUC16	8872358	0.000000	0.05858	0.441000	0.26858	0.242000	0.25591	-0.041000	0.12084	-0.157000	0.11059	0.305000	0.20034	CCC	.	.	.	none		0.547	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
HOOK2	29911	hgsc.bcm.edu	37	19	12878236	12878236	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:12878236G>A	ENST00000397668.3	-	14	1419	c.1346C>T	c.(1345-1347)gCc>gTc	p.A449V	HOOK2_ENST00000589965.1_Intron|HOOK2_ENST00000264827.5_Missense_Mutation_p.A449V	NM_013312.2	NP_037444.2	Q96ED9	HOOK2_HUMAN	hook microtubule-tethering protein 2	449	Sufficient for interaction with microtubules.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	centrosome (GO:0005813)|FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(5)|skin(1)	20						GATCTCTGCGGCTAAGTTATC	0.627																																					p.A449V		Atlas-SNP	.											.	HOOK2	73	.	0			c.C1346T						PASS	.						53.0	58.0	57.0					19																	12878236		1880	4105	5985	SO:0001583	missense	29911	exon14			TCTGCGGCTAAGT	AF044924	CCDS42507.1, CCDS42508.1	19p13.2	2013-08-21	2013-08-21						19885	protein-coding gene	gene with protein product		607824	"""hook homolog 2 (Drosophila)"""			9927460	Standard	NM_013312		Approved	HK2	uc002muy.2	Q96ED9		ENST00000397668.3:c.1346C>T	chr19.hg19:g.12878236G>A	ENSP00000380785:p.Ala449Val	67.0	0.0	.		75.0	29.0	.	NM_001100176	O60562	Missense_Mutation	SNP	ENST00000397668.3	hg19	CCDS42508.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.939222	0.92526	.	.	ENSG00000095066	ENST00000397668;ENST00000264827	T;T	0.25085	1.82;1.82	5.51	5.51	0.81932	.	0.109656	0.64402	D	0.000010	T	0.52565	0.1742	M	0.80982	2.52	0.46749	D	0.99918	D;D	0.60160	0.984;0.987	P;D	0.63488	0.861;0.915	T	0.56300	-0.8002	10	0.66056	D	0.02	-3.622	16.9614	0.86273	0.0:0.0:1.0:0.0	.	449;449	Q96ED9-2;Q96ED9	.;HOOK2_HUMAN	V	449	ENSP00000380785:A449V;ENSP00000264827:A449V	ENSP00000264827:A449V	A	-	2	0	HOOK2	12739236	1.000000	0.71417	0.995000	0.50966	0.836000	0.47400	6.624000	0.74243	2.607000	0.88179	0.650000	0.86243	GCC	.	.	.	none		0.627	HOOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451008.1	NM_013312	
MYO9B	4650	hgsc.bcm.edu	37	19	17270210	17270210	+	Silent	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:17270210G>A	ENST00000594824.1	+	8	1482	c.1335G>A	c.(1333-1335)aaG>aaA	p.K445K	MYO9B_ENST00000397274.2_Silent_p.K445K|CTD-3032J10.2_ENST00000599360.1_RNA|MYO9B_ENST00000595618.1_Silent_p.K445K|CTD-3032J10.2_ENST00000597216.1_RNA			Q13459	MYO9B_HUMAN	myosin IXB	445	Myosin motor.				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						AACAGGTGAAGCGAGAAATCT	0.542																																					p.K445K		Atlas-SNP	.											.	MYO9B	264	.	0			c.G1335A						PASS	.						77.0	77.0	77.0					19																	17270210		1958	4148	6106	SO:0001819	synonymous_variant	4650	exon8			GGTGAAGCGAGAA		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.1335G>A	chr19.hg19:g.17270210G>A		78.0	0.0	.		86.0	36.0	.	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	hg19																																																																																				.	.	.	none		0.542	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
ZNF574	64763	hgsc.bcm.edu	37	19	42583233	42583233	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:42583233C>T	ENST00000600245.1	+	2	1130	c.475C>T	c.(475-477)Cct>Tct	p.P159S	ZNF574_ENST00000222339.7_Missense_Mutation_p.P249S|CTB-59C6.3_ENST00000594531.1_RNA|ZNF574_ENST00000359044.4_Missense_Mutation_p.P159S			Q6ZN55	ZN574_HUMAN	zinc finger protein 574	159					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(4)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20		Prostate(69;0.059)				GGCTCCTGCCCCTGTTGTCCT	0.637																																					p.P159S		Atlas-SNP	.											.	ZNF574	57	.	0			c.C475T						PASS	.						49.0	57.0	54.0					19																	42583233		2203	4300	6503	SO:0001583	missense	64763	exon2			CCTGCCCCTGTTG	AK074788	CCDS12596.1	19q13.2	2013-09-20			ENSG00000105732	ENSG00000105732		"""Zinc fingers, C2H2-type"""	26166	protein-coding gene	gene with protein product						12477932	Standard	NM_022752		Approved	FLJ22059	uc002osm.4	Q6ZN55	OTTHUMG00000182751	ENST00000600245.1:c.475C>T	chr19.hg19:g.42583233C>T	ENSP00000469029:p.Pro159Ser	100.0	0.0	.		90.0	33.0	.	NM_022752	Q6IPE0|Q6ZN10|Q7L5Z5|Q8NCE3|Q9H6N0	Missense_Mutation	SNP	ENST00000600245.1	hg19	CCDS12596.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.151603	0.57151	.	.	ENSG00000105732	ENST00000222339;ENST00000359044	T;T	0.06849	3.25;3.29	4.23	3.12	0.35913	.	0.240652	0.33813	N	0.004523	T	0.04861	0.0131	N	0.08118	0	0.26252	N	0.978701	B;P	0.40180	0.202;0.705	B;B	0.38327	0.099;0.271	T	0.38329	-0.9666	10	0.42905	T	0.14	-10.3235	13.0485	0.58942	0.0:0.8377:0.1623:0.0	.	159;248	Q6ZN55;Q6ZN55-2	ZN574_HUMAN;.	S	249;159	ENSP00000222339:P249S;ENSP00000351939:P159S	ENSP00000222339:P249S	P	+	1	0	ZNF574	47275073	0.001000	0.12720	0.701000	0.30321	0.747000	0.42532	0.256000	0.18351	2.186000	0.69663	0.591000	0.81541	CCT	.	.	.	none		0.637	ZNF574-002	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463458.1	NM_022752	
PTPRH	5794	hgsc.bcm.edu	37	19	55718205	55718205	+	Silent	SNP	A	A	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:55718205A>C	ENST00000376350.3	-	3	226	c.204T>G	c.(202-204)acT>acG	p.T68T	PTPRH_ENST00000588559.1_5'UTR|PTPRH_ENST00000263434.5_Silent_p.T68T	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	68	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CGCCGTCTCCAGTACACTGAA	0.572																																					p.T68T		Atlas-SNP	.											.	PTPRH	139	.	0			c.T204G						PASS	.						147.0	122.0	130.0					19																	55718205		2203	4300	6503	SO:0001819	synonymous_variant	5794	exon3			GTCTCCAGTACAC		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.204T>G	chr19.hg19:g.55718205A>C		136.0	0.0	.		180.0	65.0	.	NM_001161440	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Silent	SNP	ENST00000376350.3	hg19	CCDS33110.1																																																																																			.	.	.	none		0.572	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
DUXA	503835	hgsc.bcm.edu	37	19	57665813	57665813	+	Silent	SNP	A	A	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:57665813A>G	ENST00000554048.2	-	6	581	c.582T>C	c.(580-582)agT>agC	p.S194S		NM_001012729.1	NP_001012747.1	A6NLW8	DUXA_HUMAN	double homeobox A	194					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	17		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0123)		AATGAGAGTCACTAGTGAAGT	0.418																																					p.S194S		Atlas-SNP	.											.	DUXA	46	.	0			c.T582C						PASS	.						135.0	116.0	123.0					19																	57665813		2203	4300	6503	SO:0001819	synonymous_variant	503835	exon6			AGAGTCACTAGTG		CCDS33126.1	19q13.43	2012-10-04			ENSG00000258873	ENSG00000258873		"""Homeoboxes / PRD class"""	32179	protein-coding gene	gene with protein product		611168					Standard	NM_001012729		Approved		uc002qoa.1	A6NLW8	OTTHUMG00000170714	ENST00000554048.2:c.582T>C	chr19.hg19:g.57665813A>G		101.0	0.0	.		98.0	39.0	.	NM_001012729		Silent	SNP	ENST00000554048.2	hg19	CCDS33126.1																																																																																			.	.	.	none		0.418	DUXA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410075.3	NM_001012729	
TMC2	117532	hgsc.bcm.edu	37	20	2618130	2618130	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr20:2618130T>C	ENST00000358864.1	+	19	2411	c.2396T>C	c.(2395-2397)gTt>gCt	p.V799A		NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	799					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						CTCCGTGAAGTTGAGAAGAGT	0.458																																					p.V799A		Atlas-SNP	.											.	TMC2	121	.	0			c.T2396C						PASS	.						90.0	88.0	89.0					20																	2618130		2203	4300	6503	SO:0001583	missense	117532	exon19			GTGAAGTTGAGAA	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.2396T>C	chr20.hg19:g.2618130T>C	ENSP00000351732:p.Val799Ala	66.0	0.0	.		75.0	8.0	.	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	hg19	CCDS13029.2	.	.	.	.	.	.	.	.	.	.	T	7.729	0.698802	0.15106	.	.	ENSG00000149488	ENST00000358864	T	0.62105	0.05	5.04	3.93	0.45458	.	0.185575	0.43416	D	0.000570	T	0.51550	0.1681	L	0.45581	1.43	0.22762	N	0.998764	B	0.02656	0.0	B	0.06405	0.002	T	0.43523	-0.9386	10	0.39692	T	0.17	-3.1255	8.6117	0.33806	0.1709:0.0:0.0:0.8291	.	799	Q8TDI7	TMC2_HUMAN	A	799	ENSP00000351732:V799A	ENSP00000351732:V799A	V	+	2	0	TMC2	2566130	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	1.282000	0.33226	1.007000	0.39238	-0.336000	0.08194	GTT	.	.	.	none		0.458	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2		
PARD6B	84612	hgsc.bcm.edu	37	20	49354458	49354458	+	Missense_Mutation	SNP	A	A	G			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr20:49354458A>G	ENST00000371610.2	+	2	374	c.131A>G	c.(130-132)tAt>tGt	p.Y44C	PARD6B_ENST00000396039.1_Missense_Mutation_p.Y44C	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	44	OPR.				axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction assembly (GO:0007043)|cell-cell junction organization (GO:0045216)|establishment or maintenance of cell polarity (GO:0007163)|protein complex assembly (GO:0006461)|regulation of cell migration (GO:0030334)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				NS(1)|breast(1)|endometrium(1)|kidney(4)|lung(3)|urinary_tract(1)	11						GAGGAGTTTTATGGATTACTA	0.333																																					p.Y44C		Atlas-SNP	.											.	PARD6B	31	.	0			c.A131G						PASS	.						80.0	79.0	79.0					20																	49354458		2203	4300	6503	SO:0001583	missense	84612	exon2			AGTTTTATGGATT	AB044555	CCDS33485.1	20q13.13	2013-08-28	2013-08-28		ENSG00000124171	ENSG00000124171			16245	protein-coding gene	gene with protein product		608975	"""par-6 (partitioning defective 6, C.elegans) homolog beta"", ""par-6 partitioning defective 6 homolog beta (C. elegans)"""			11260256	Standard	NM_032521		Approved	PAR-6B	uc002xvo.3	Q9BYG5	OTTHUMG00000032732	ENST00000371610.2:c.131A>G	chr20.hg19:g.49354458A>G	ENSP00000360672:p.Tyr44Cys	104.0	0.0	.		132.0	50.0	.	NM_032521	A2A2A7|Q9Y510	Missense_Mutation	SNP	ENST00000371610.2	hg19	CCDS33485.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.151060	0.78001	.	.	ENSG00000124171	ENST00000371610;ENST00000396039	T;T	0.21734	1.99;1.99	5.92	5.92	0.95590	Phox/Bem1p (2);	0.000000	0.85682	D	0.000000	T	0.36663	0.0975	M	0.64567	1.98	0.80722	D	1	B	0.33583	0.418	P	0.46510	0.519	T	0.08764	-1.0706	10	0.49607	T	0.09	-29.6811	15.5593	0.76229	1.0:0.0:0.0:0.0	.	44	Q9BYG5	PAR6B_HUMAN	C	44	ENSP00000360672:Y44C;ENSP00000379354:Y44C	ENSP00000360672:Y44C	Y	+	2	0	PARD6B	48787865	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	8.920000	0.92779	2.277000	0.76020	0.528000	0.53228	TAT	.	.	.	none		0.333	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521	
ATP9A	10079	hgsc.bcm.edu	37	20	50217801	50217801	+	Silent	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr20:50217801C>T	ENST00000338821.5	-	28	3357	c.3093G>A	c.(3091-3093)aaG>aaA	p.K1031K	ATP9A_ENST00000402822.1_Silent_p.K910K|ATP9A_ENST00000311637.5_Silent_p.K895K	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	1031					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|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)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						TTCGCAGGTACTTGAGGACAT	0.567																																					p.K1031K		Atlas-SNP	.											.	ATP9A	135	.	0			c.G3093A						PASS	.						89.0	64.0	73.0					20																	50217801		2203	4300	6503	SO:0001819	synonymous_variant	10079	exon28			CAGGTACTTGAGG	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"""ATPases / P-type"""	13540	protein-coding gene	gene with protein product		609126	"""ATPase, Class II, type 9A"""			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.3093G>A	chr20.hg19:g.50217801C>T		113.0	0.0	.		148.0	8.0	.	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Silent	SNP	ENST00000338821.5	hg19	CCDS33489.1																																																																																			.	.	.	none		0.567	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045	
SLC7A4	6545	hgsc.bcm.edu	37	22	21385638	21385638	+	Missense_Mutation	SNP	G	G	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr22:21385638G>C	ENST00000382932.2	-	2	531	c.464C>G	c.(463-465)aCc>aGc	p.T155S	AC002472.11_ENST00000450652.1_RNA|MIR649_ENST00000384843.1_RNA|SLC7A4_ENST00000403586.1_Missense_Mutation_p.T155S	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	155				THVGSWQVPLLGHYPDFLAAGIILLASAFVSCGARVSS -> DPRGFLAGAPPGPLPGLPGCWHHPPWPLPLSPVEPACPP (in Ref. 1; CAA04263). {ECO:0000305}.	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)	ACCCACGTGGGTCTCAGTGAA	0.622																																					p.T155S		Atlas-SNP	.											.	SLC7A4	50	.	0			c.C464G						PASS	.						34.0	36.0	35.0					22																	21385638		2203	4300	6503	SO:0001583	missense	6545	exon2			ACGTGGGTCTCAG	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.464C>G	chr22.hg19:g.21385638G>C	ENSP00000372390:p.Thr155Ser	30.0	0.0	.		34.0	11.0	.	NM_004173	Q0P5U2|Q3KNQ6|Q4VC45|Q6IBY8|Q96H88	Missense_Mutation	SNP	ENST00000382932.2	hg19	CCDS33608.1	.	.	.	.	.	.	.	.	.	.	G	4.566	0.105214	0.08731	.	.	ENSG00000099960	ENST00000403586;ENST00000382932	D;D	0.90004	-2.6;-2.6	5.28	4.26	0.50523	Amino acid permease domain (1);	0.304735	0.34025	N	0.004331	T	0.78710	0.4326	N	0.20766	0.605	0.26027	N	0.981795	B	0.02656	0.0	B	0.06405	0.002	T	0.60337	-0.7283	10	0.12103	T	0.63	.	11.768	0.51941	0.0862:0.0:0.9138:0.0	.	155	O43246	CTR4_HUMAN	S	155	ENSP00000384278:T155S;ENSP00000372390:T155S	ENSP00000372390:T155S	T	-	2	0	SLC7A4	19715638	1.000000	0.71417	0.071000	0.20095	0.025000	0.11179	2.808000	0.47963	1.351000	0.45789	0.561000	0.74099	ACC	.	.	.	none		0.622	SLC7A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320467.1	NM_004173	
MN1	4330	hgsc.bcm.edu	37	22	28194900	28194900	+	Silent	SNP	T	T	C	rs202212250|rs530519178	byFrequency	TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr22:28194900T>C	ENST00000302326.4	-	1	2586	c.1632A>G	c.(1630-1632)caA>caG	p.Q544Q		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	544	Poly-Gln.				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						gctgctgctgttgctgttgct	0.647			T	ETV6	"""AML, meningioma"""								C|||	5	0.000998403	0.0023	0.0	5008	,	,		12597	0.0		0.0	False		,,,				2504	0.002				p.Q544Q		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"""L, O"""	.	MN1	122	.	0			c.A1632G						PASS	.																																			SO:0001819	synonymous_variant	4330	exon1			CTGCTGTTGCTGT	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.1632A>G	chr22.hg19:g.28194900T>C		39.0	0.0	.		63.0	7.0	.	NM_002430	A9Z1V9	Silent	SNP	ENST00000302326.4	hg19	CCDS42998.1																																																																																			.	.	.	none		0.647	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430	
RANGAP1	5905	hgsc.bcm.edu	37	22	41650402	41650402	+	Silent	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr22:41650402C>T	ENST00000455915.2	-	10	2639	c.1170G>A	c.(1168-1170)gaG>gaA	p.E390E	RANGAP1_ENST00000407260.4_Silent_p.E335E|RANGAP1_ENST00000356244.3_Silent_p.E390E|RANGAP1_ENST00000405486.1_Silent_p.E390E			P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	390	Asp/Glu-rich (highly acidic).				mitotic cell cycle (GO:0000278)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear pore (GO:0005643)|perinuclear region of cytoplasm (GO:0048471)	Ran GTPase activator activity (GO:0005098)	p.E390E(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						cctcctcctcctcttcttcct	0.562																																					p.E390E		Atlas-SNP	.											RANGAP1,NS,carcinoma,0,2	RANGAP1	47	.	1	Substitution - coding silent(1)	kidney(1)	c.G1170A						PASS	.						233.0	159.0	184.0					22																	41650402		2203	4300	6503	SO:0001819	synonymous_variant	5905	exon11			CTCCTCCTCTTCT	X82260	CCDS14012.1	22q13	2013-01-17			ENSG00000100401	ENSG00000100401			9854	protein-coding gene	gene with protein product		602362	"""segregation distorter homolog (Drosophila)"""	SD		7878053	Standard	NM_002883		Approved	Fug1, KIAA1835	uc003azu.3	P46060	OTTHUMG00000150940	ENST00000455915.2:c.1170G>A	chr22.hg19:g.41650402C>T		50.0	1.0	.		51.0	4.0	.	NM_002883	Q96JJ2	Silent	SNP	ENST00000455915.2	hg19	CCDS14012.1																																																																																			.	.	.	none		0.562	RANGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320606.1	NM_002883	
PLXNB2	23654	hgsc.bcm.edu	37	22	50722099	50722099	+	Silent	SNP	G	G	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr22:50722099G>A	ENST00000449103.1	-	15	2642	c.2502C>T	c.(2500-2502)gaC>gaT	p.D834D	PLXNB2_ENST00000359337.4_Silent_p.D834D|PLXNB2_ENST00000496720.1_5'UTR			O15031	PLXB2_HUMAN	plexin B2	834	IPT/TIG 1.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TCCTCTGGATGTCCCCTGCTT	0.647																																					p.D834D		Atlas-SNP	.											.	PLXNB2	172	.	0			c.C2502T						PASS	.						31.0	37.0	35.0					22																	50722099		1973	4137	6110	SO:0001819	synonymous_variant	23654	exon15			CTGGATGTCCCCT		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.2502C>T	chr22.hg19:g.50722099G>A		76.0	0.0	.		70.0	32.0	.	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	hg19	CCDS43035.1																																																																																			.	.	.	none		0.647	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
ZBED1	9189	hgsc.bcm.edu	37	X	2407032	2407032	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chrX:2407032A>C	ENST00000381223.4	-	2	1932	c.1729T>G	c.(1729-1731)Tcc>Gcc	p.S577A	DHRSX_ENST00000334651.5_Intron|ZBED1_ENST00000381222.2_Missense_Mutation_p.S577A|ZBED1_ENST00000515319.1_5'Flank|ZBED1_ENST00000381218.3_Missense_Mutation_p.S577A	NM_001171135.1|NM_001171136.1|NM_004729.3	NP_001164606.1|NP_001164607.1|NP_004720.1	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	577					metabolic process (GO:0008152)	nuclear chromosome (GO:0000228)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transposase activity (GO:0004803)			endometrium(8)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	25		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)				ACCTTCTGGGACTTGAAGTTG	0.607																																					p.S577A		Atlas-SNP	.											.	ZBED1	64	.	0			c.T1729G						PASS	.						120.0	106.0	111.0					X																	2407032		2203	4296	6499	SO:0001583	missense	9189	exon2			TCTGGGACTTGAA	AB018328	CCDS14118.1	Xp22.33 and Yp11	2013-05-03	2004-01-14	2004-01-16	ENSG00000214717	ENSG00000214717		"""Pseudoautosomal regions / PAR1"", ""Zinc fingers, BED-type"""	447	protein-coding gene	gene with protein product		300178	"""Ac-like transposable element"""	ALTE		9872452, 9887332, 23533661	Standard	NM_001171135		Approved	TRAMP, KIAA0785, DREF, hDREF	uc004cqh.2	O96006	OTTHUMG00000021069	ENST00000381223.4:c.1729T>G	chrX.hg19:g.2407032A>C	ENSP00000370621:p.Ser577Ala	95.0	0.0	.		72.0	46.0	.	NM_001171135	Q96BY4	Missense_Mutation	SNP	ENST00000381223.4	hg19	CCDS14118.1	.	.	.	.	.	.	.	.	.	.	A	9.895	1.205342	0.22205	.	.	ENSG00000214717	ENST00000381223;ENST00000381222;ENST00000381218	T;T;T	0.22539	1.95;1.95;1.95	2.97	1.67	0.24075	HAT dimerisation (1);Ribonuclease H-like (1);	0.126167	0.34750	U	0.003715	T	0.11110	0.0271	.	.	.	0.09310	N	1	B	0.18013	0.025	B	0.20577	0.03	T	0.36335	-0.9752	9	0.15066	T	0.55	.	8.2493	0.31708	0.7999:0.2001:0.0:0.0	.	577	O96006	ZBED1_HUMAN	A	577	ENSP00000370621:S577A;ENSP00000370620:S577A;ENSP00000370616:S577A	ENSP00000370616:S577A	S	-	1	0	ZBED1	2417032	1.000000	0.71417	0.572000	0.28498	0.482000	0.33219	4.352000	0.59404	0.015000	0.14971	0.373000	0.22412	TCC	.	.	.	none		0.607	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729	
GPR34	2857	hgsc.bcm.edu	37	X	41555847	41555847	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chrX:41555847T>A	ENST00000378142.4	+	3	1245	c.961T>A	c.(961-963)Tgc>Agc	p.C321S	CASK_ENST00000442742.2_Intron|GPR34_ENST00000378138.5_Missense_Mutation_p.C321S|CASK_ENST00000378154.1_Intron|CASK_ENST00000378163.1_Intron|CASK_ENST00000421587.2_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000378158.1_Intron	NM_001097579.1|NM_005300.3	NP_001091048.1|NP_005291.1	Q9UPC5	GPR34_HUMAN	G protein-coupled receptor 34	321					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	14						TTTCAATAGTTGCTTAGATCC	0.368																																					p.C321S		Atlas-SNP	.											.	GPR34	42	.	0			c.T961A						PASS	.						124.0	102.0	110.0					X																	41555847		2202	4300	6502	SO:0001583	missense	2857	exon3			AATAGTTGCTTAG	AF039686	CCDS14258.1	Xp11.4	2012-08-21			ENSG00000171659	ENSG00000171659		"""GPCR / Class A : Orphans"""	4490	protein-coding gene	gene with protein product		300241				10395919, 10036181	Standard	NM_005300		Approved		uc004dfq.4	Q9UPC5	OTTHUMG00000021375	ENST00000378142.4:c.961T>A	chrX.hg19:g.41555847T>A	ENSP00000367384:p.Cys321Ser	117.0	0.0	.		131.0	99.0	.	NM_001097579	O95853	Missense_Mutation	SNP	ENST00000378142.4	hg19	CCDS14258.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.529560	0.64860	.	.	ENSG00000171659	ENST00000378142;ENST00000378138;ENST00000535368	T;T	0.61510	0.1;0.1	5.73	5.73	0.89815	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.80465	0.4628	M	0.89840	3.065	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84706	0.0731	10	0.72032	D	0.01	-13.9692	14.9871	0.71356	0.0:0.0:0.0:1.0	.	321	Q9UPC5	GPR34_HUMAN	S	321;321;274	ENSP00000367384:C321S;ENSP00000367378:C321S	ENSP00000367378:C321S	C	+	1	0	GPR34	41440791	1.000000	0.71417	0.961000	0.40146	0.777000	0.43975	7.694000	0.84235	1.922000	0.55676	0.481000	0.45027	TGC	.	.	.	none		0.368	GPR34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056264.1	NM_005300	
MT-CO1	4512	hgsc.bcm.edu	37	M	6665	6665	+	Silent	SNP	C	C	T			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chrM:6665C>T	ENST00000361624.2	+	1	762	c.762C>T	c.(760-762)atC>atT	p.I254I	MT-TK_ENST00000387421.1_RNA|MT-CO2_ENST00000361739.1_5'Flank|MT-TA_ENST00000387392.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TD_ENST00000387419.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TY_ENST00000387409.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	254					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|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 IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						TTCGGAATAATCTCCCATATT	0.428																																					p.I254I		Atlas-SNP	.											.	.	.	.	0			c.C762T						PASS	.																																			SO:0001819	synonymous_variant	5742	exon1			AATAATCTCCCAT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.762C>T	chrM.hg19:g.6665C>T		16.0	0.0	.		104.0	79.0	.	ENST00000361624	Q34770	Silent	SNP	ENST00000361624.2	hg19																																																																																				.	.	.	none		0.428	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024028	
ZNF490	57474	hgsc.bcm.edu	37	19	12691823	12691824	+	Frame_Shift_Del	DEL	GG	GG	-			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:12691823_12691824delGG	ENST00000311437.6	-	5	1187_1188	c.1065_1066delCC	c.(1063-1068)acccacfs	p.H356fs	CTD-2192J16.20_ENST00000593682.1_5'Flank|ZNF490_ENST00000465656.1_5'Flank	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	356					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(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						ACTCCGGTGTGGGTTTTCACGT	0.431																																					p.356_356del		Atlas-Indel,Pindel	.											.	ZNF490	42	.	0			c.1066_1067del						PASS	.																																			SO:0001589	frameshift_variant	57474	exon5			.	AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033		"""Zinc fingers, C2H2-type"", ""-"""	23705	protein-coding gene	gene with protein product							Standard	NM_020714		Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.1065_1066delCC	chr19.hg19:g.12691823_12691824delGG	ENSP00000311521:p.His356fs	78.0	0.0	0		84.0	40.0	0.47619	NM_020714		Frame_Shift_Del	DEL	ENST00000311437.6	hg19	CCDS12272.1																																																																																			.	.	.	none		0.431	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714	
NPC2	10577	hgsc.bcm.edu	37	14	74953056	74953057	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr14:74953056_74953057delTG	ENST00000555619.1	-	2	402_403	c.165_166delCA	c.(163-168)tacagcfs	p.YS55fs	NPC2_ENST00000541064.1_Frame_Shift_Del_p.YS55fs|NPC2_ENST00000557510.1_Frame_Shift_Del_p.YS55fs|NPC2_ENST00000238633.2_Frame_Shift_Del_p.YS55fs|NPC2_ENST00000434013.2_Frame_Shift_Del_p.YS55fs	NM_006432.3	NP_006423.1	P61916	NPC2_HUMAN	Niemann-Pick disease, type C2	55					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)		ACATTGACGCTGTAAGACTGTC	0.441																																					p.56_56del	Pancreas(93;260 1497 8575 30964 48133)	Atlas-Indel,Pindel	.											.	NPC2	9	.	0			c.166_167del	GRCh37	CM057462	NPC2	M		PASS	.																																			SO:0001589	frameshift_variant	10577	exon2			.	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.165_166delCA	chr14.hg19:g.74953056_74953057delTG	ENSP00000451112:p.Tyr55fs	54.0	0.0	0		62.0	29.0	0.467742	NM_006432	B4DQV7|Q15668|Q29413	Frame_Shift_Del	DEL	ENST00000555619.1	hg19	CCDS32121.1																																																																																			.	.	.	none		0.441	NPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412346.1	NM_006432	
IPP	3652	hgsc.bcm.edu	37	1	46206791	46206792	+	Frame_Shift_Ins	INS	-	-	CC			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:46206791_46206792insCC	ENST00000396478.3	-	3	607_608	c.505_506insGG	c.(505-507)gttfs	p.V169fs		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	169						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					TCCACTATGAACCTCCAAGAAA	0.406																																					p.V169fs		Atlas-Indel,Pindel	.											.	IPP	66	.	0			c.506_507insGG						PASS	.																																			SO:0001589	frameshift_variant	3652	exon3			.	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.504_505dupGG	chr1.hg19:g.46206792_46206793dupCC	ENSP00000379739:p.Val169fs	105.0	0.0	0		133.0	56.0	0.421053	NM_001145349	A2A6V4|D3DQ11|Q8N5C3	Frame_Shift_Ins	INS	ENST00000396478.3	hg19	CCDS30702.1																																																																																			.	.	.	none		0.406	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897	
GLTSCR1	29998	hgsc.bcm.edu	37	19	48197404	48197404	+	Frame_Shift_Del	DEL	C	C	-			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:48197404delC	ENST00000396720.3	+	8	2510	c.2316delC	c.(2314-2316)ggcfs	p.G772fs	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	772										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		AGGGCCCAGGCCCCTCTTCGT	0.726																																					p.G772fs		Atlas-Indel,Pindel	.											.	GLTSCR1	79	.	0			c.2315delG						PASS	.						1.0	1.0	1.0					19																	48197404		834	1989	2823	SO:0001589	frameshift_variant	29998	exon8			.	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.2316delC	chr19.hg19:g.48197404delC	ENSP00000379946:p.Gly772fs	91.0	0.0	0		82.0	24.0	0.292683	NM_015711	A8MW01	Frame_Shift_Del	DEL	ENST00000396720.3	hg19	CCDS46134.1																																																																																			.	.	.	none		0.726	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711	
LRIG1	26018	hgsc.bcm.edu	37	3	66431274	66431274	+	Frame_Shift_Del	DEL	G	G	-	rs375884681		TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:66431274delG	ENST00000273261.3	-	18	3306	c.2782delC	c.(2782-2784)cggfs	p.R928fs	LRIG1_ENST00000496559.2_5'UTR|SLC25A26_ENST00000536651.1_3'UTR|LRIG1_ENST00000383703.3_Frame_Shift_Del_p.R905fs	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	928					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)		CATACGACCCGGCCACCGTGT	0.597																																					p.R928fs		Atlas-Indel,Pindel	.											.	LRIG1	138	.	0			c.2783delG						PASS	.						51.0	54.0	53.0					3																	66431274		2203	4300	6503	SO:0001589	frameshift_variant	26018	exon18			.	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.2782delC	chr3.hg19:g.66431274delG	ENSP00000273261:p.Arg928fs	49.0	0.0	0		59.0	21.0	0.355932	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Frame_Shift_Del	DEL	ENST00000273261.3	hg19	CCDS33783.1																																																																																			.	.	.	none		0.597	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
SETD2	29072	hgsc.bcm.edu	37	3	47058730	47058730	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:47058730delA	ENST00000409792.3	-	21	7590	c.7548delT	c.(7546-7548)gttfs	p.V2516fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2516	Interaction with POLR2A.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CCTTATTCATAACACCGTGAG	0.473			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.M2517X		Atlas-INDEL	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.7549delA						PASS	.						135.0	122.0	126.0					3																	47058730		2203	4300	6503	SO:0001589	frameshift_variant	29072	exon21			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.7548delT	chr3.hg19:g.47058730delA	ENSP00000386759:p.Val2516fs	46.0	0.0	0		71.0	65.0	0.915493	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.473	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
FMNL3	91010	hgsc.bcm.edu	37	12	50047553	50047554	+	Frame_Shift_Ins	INS	-	-	TT			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr12:50047553_50047554insTT	ENST00000293590.5	-	12	1408_1409	c.1175_1176insAA	c.(1174-1176)aatfs	p.N392fs	FMNL3_ENST00000550488.1_Frame_Shift_Ins_p.N392fs|FMNL3_ENST00000335154.5_Frame_Shift_Ins_p.N392fs|FMNL3_ENST00000352151.5_Frame_Shift_Ins_p.N341fs			Q8IVF7	FMNL3_HUMAN	formin-like 3	392	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)	GTPase activating protein binding (GO:0032794)			breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						CCAGGGCTACATTCTTGGTCTC	0.53																																					p.N392fs		Atlas-Indel,Pindel	.											FMNL3_ENST00000335154,colon,carcinoma,0,2	FMNL3	137	.	0			c.1176_1177insAA						PASS	.																																			SO:0001589	frameshift_variant	91010	exon12			.	AK128195	CCDS41780.1, CCDS44874.1	12q13.12	2006-04-10							23698	protein-coding gene	gene with protein product						12684686	Standard	NM_198900		Approved	DKFZp762B245, MGC45819, WBP3	uc001ruv.1	Q8IVF7	OTTHUMG00000169651	ENST00000293590.5:c.1174_1175dupAA	chr12.hg19:g.50047554_50047555dupTT	ENSP00000293590:p.Asn392fs	91.0	0.0	0		83.0	30.0	0.361446	NM_175736	B0JZA7|Q6ZRJ1	Frame_Shift_Ins	INS	ENST00000293590.5	hg19																																																																																				.	.	.	none		0.530	FMNL3-201	KNOWN	basic	protein_coding	protein_coding		NM_175736	
BSG	682	hgsc.bcm.edu	37	19	581506	581506	+	Frame_Shift_Del	DEL	C	C	-			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:581506delC	ENST00000333511.3	+	6	1054	c.984delC	c.(982-984)ttcfs	p.F328fs	BSG_ENST00000346916.4_Frame_Shift_Del_p.F148fs|BSG_ENST00000353555.4_Frame_Shift_Del_p.F212fs|BSG_ENST00000545507.2_Frame_Shift_Del_p.F119fs	NM_001728.3	NP_001719.2	P35613	BASI_HUMAN	basigin (Ok blood group)	328				F -> L (in Ref. 2; BAC76828). {ECO:0000305}.	blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular metabolic process (GO:0044237)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis of dentin-containing tooth (GO:0042475)|protein targeting to plasma membrane (GO:0072661)|pyruvate metabolic process (GO:0006090)|response to cAMP (GO:0051591)|response to mercury ion (GO:0046689)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|lung(1)	5		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)		TCTGGCCCTTCCTGGGCATCG	0.672																																					p.F328fs		Atlas-Indel,Pindel	.											.	BSG	48	.	0			c.983delT						PASS	.						28.0	27.0	27.0					19																	581506		2185	4293	6478	SO:0001589	frameshift_variant	682	exon6			.	L10240	CCDS12032.1, CCDS12033.1, CCDS12034.1, CCDS58635.1	19p13.3	2014-07-19	2014-01-02		ENSG00000172270	ENSG00000172270		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1116	protein-coding gene	gene with protein product	"""Ok blood group"""	109480	"""basigin"""	OK		8404035, 7812975	Standard	NM_198591		Approved	EMMPRIN, CD147	uc002loz.4	P35613		ENST00000333511.3:c.984delC	chr19.hg19:g.581506delC	ENSP00000333769:p.Phe328fs	77.0	0.0	0		77.0	31.0	0.402597	NM_001728	A6NJW1|D3YLG5|Q7Z796|Q8IZL7	Frame_Shift_Del	DEL	ENST00000333511.3	hg19	CCDS12033.1																																																																																			.	.	.	none		0.672	BSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438630.2	NM_001728	
TRIM53AP	642569	hgsc.bcm.edu	37	11	89732825	89732825	+	IGR	DEL	G	G	-			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:89732825delG								TRIM49D1 (77890 upstream) : TRIM49C (31448 downstream)																							CACAGTCTATGGTGACTGGGT	0.453																																					.		Atlas-INDEL	.											.	.	.	.	0			.						PASS	.																																			SO:0001628	intergenic_variant	642569	.			.																													chr11.hg19:g.89732825delG		490.0	0.0	0		493.0	103.0	0.208925	.		RNA	DEL		hg19																																																																																				.	.	.	none	0	0.453								
SCFD1	23256	hgsc.bcm.edu	37	14	31142532	31142533	+	Frame_Shift_Ins	INS	-	-	AA			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr14:31142532_31142533insAA	ENST00000458591.2	+	12	1292_1293	c.1065_1066insAA	c.(1066-1068)aaafs	p.K356fs	SCFD1_ENST00000396629.2_Frame_Shift_Ins_p.K264fs|SCFD1_ENST00000544052.2_Frame_Shift_Ins_p.K289fs|SCFD1_ENST00000541123.1_Frame_Shift_Ins_p.K171fs|SCFD1_ENST00000421551.3_Frame_Shift_Ins_p.K297fs	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1	356					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle docking involved in exocytosis (GO:0006904)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi transport complex (GO:0017119)|Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)	syntaxin binding (GO:0019905)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		AAGATGAGGTCAAACGACTTAA	0.356																																					p.V355fs		Atlas-Indel,Pindel	.											.	SCFD1	43	.	0			c.1065_1066insAA						PASS	.																																			SO:0001589	frameshift_variant	23256	exon12			.	AF110646	CCDS9639.1, CCDS45092.1, CCDS58308.1	14q12	2006-04-04	2004-01-15	2004-01-16	ENSG00000092108	ENSG00000092108			20726	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 163"""	C14orf163			Standard	NM_016106		Approved	RA410, KIAA0917, STXBP1L2, SLY1	uc001wqm.2	Q8WVM8	OTTHUMG00000029420	ENST00000458591.2:c.1066_1067dupAA	chr14.hg19:g.31142533_31142534dupAA	ENSP00000390783:p.Lys356fs	251.0	0.0	0		289.0	112.0	0.387543	NM_016106	A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Frame_Shift_Ins	INS	ENST00000458591.2	hg19	CCDS9639.1																																																																																			.	.	.	none		0.356	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835	
PEX12	5193	hgsc.bcm.edu	37	17	33904058	33904058	+	Splice_Site	DEL	T	T	-			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:33904058delT	ENST00000225873.4	-	2	1286	c.679delA	c.(679-681)agt>gt	p.S227fs	RP11-1094M14.11_ENST00000592381.1_lincRNA	NM_000286.2	NP_000277.1	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	227					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	integral component of peroxisomal membrane (GO:0005779)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(8)	18				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AGGCCTTACCTCCTGGCTGGT	0.448																																					p.S227fs		Atlas-INDEL	.											.	PEX12	36	.	0			c.680delG						PASS	.						98.0	90.0	92.0					17																	33904058		2203	4300	6503	SO:0001630	splice_region_variant	5193	exon2			.	U91521	CCDS11296.1	17q21.1	2011-02-10			ENSG00000108733	ENSG00000108733			8854	protein-coding gene	gene with protein product		601758				9090384	Standard	NM_000286		Approved		uc002hjp.3	O00623	OTTHUMG00000132951	ENST00000225873.4:c.680+1A>-	chr17.hg19:g.33904058delT		29.0	0.0	0		48.0	19.0	0.395833	NM_000286	B2R6M2	Frame_Shift_Del	DEL	ENST00000225873.4	hg19	CCDS11296.1																																																																																			.	.	.	none		0.448	PEX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256489.2	NM_000286	Frame_Shift_Del
KIF4B	285643	hgsc.bcm.edu	37	5	154395330	154395330	+	Frame_Shift_Del	DEL	C	C	-			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr5:154395330delC	ENST00000435029.4	+	1	2071	c.1911delC	c.(1909-1911)aacfs	p.N637fs		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	637					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)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CCAAGCTGAACCAAGAGATAT	0.418																																					p.N637fs		Atlas-Indel,Pindel	.											.	KIF4B	307	.	0			c.1910delA						PASS	.						154.0	150.0	151.0					5																	154395330		2203	4300	6503	SO:0001589	frameshift_variant	285643	exon1			.	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"""Kinesins"""	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.1911delC	chr5.hg19:g.154395330delC	ENSP00000387875:p.Asn637fs	321.0	0.0	0		413.0	173.0	0.418886	NM_001099293		Frame_Shift_Del	DEL	ENST00000435029.4	hg19	CCDS47324.1																																																																																			.	.	.	none		0.418	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1		
PRPF40A	55660	hgsc.bcm.edu	37	2	153551067	153551069	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr2:153551067_153551069delGCT	ENST00000410080.1	-	3	825_827	c.284_286delAGC	c.(283-288)cagcct>cct	p.Q95del		NM_017892.3	NP_060362.3	O75400	PR40A_HUMAN	PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)	122					cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|mRNA processing (GO:0006397)|regulation of cell shape (GO:0008360)|regulation of cytokinesis (GO:0032465)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|prostate(1)|urinary_tract(1)	21						GGTAAGGCAGGCTGCATGGAAGC	0.325																																					p.95_96del		Atlas-Indel,Pindel	.											.	PRPF40A	149	.	0			c.285_287del						PASS	.																																			SO:0001651	inframe_deletion	55660	exon3			.	AF049523	CCDS46430.1	2q23.3	2010-01-25	2007-01-12	2006-01-13	ENSG00000196504	ENSG00000196504			16463	protein-coding gene	gene with protein product		612941	"""formin-binding protein 3"", ""formin binding protein 3"", ""PRP40 pre-mRNA processing factor 40 homolog A (yeast)"""	FNBP3		9724750, 12460579	Standard	NM_017892		Approved	FLJ20585, FBP11, HYPA, NY-REN-6, HIP10, FBP-11, FLAF1, Prp40	uc002tyh.4	O75400	OTTHUMG00000154031	ENST00000410080.1:c.284_286delAGC	chr2.hg19:g.153551067_153551069delGCT	ENSP00000386458:p.Gln95del	448.0	0.0	0		446.0	45.0	0.100897	NM_017892	O43856|O75404|Q8TBQ1|Q9H782|Q9NWU9|Q9P0Q2|Q9Y5A8	In_Frame_Del	DEL	ENST00000410080.1	hg19	CCDS46430.1																																																																																			.	.	.	none		0.325	PRPF40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333559.2	XM_371575	
ZNF596	169270	hgsc.bcm.edu	37	8	195728	195728	+	Frame_Shift_Del	DEL	T	T	-			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr8:195728delT	ENST00000398612.1	+	6	1264	c.881delT	c.(880-882)cttfs	p.L294fs	ZNF596_ENST00000308811.4_Frame_Shift_Del_p.L294fs|ZNF596_ENST00000320552.2_Frame_Shift_Del_p.L224fs	NM_001042415.1|NM_001042416.1	NP_001035880.1|NP_001035881.1	Q8TC21	ZN596_HUMAN	zinc finger protein 596	294					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)		TGCTCTGACCTTAGAAAACAT	0.388																																					p.L294fs		Atlas-Indel,Pindel	.											.	ZNF596	34	.	0			c.880delC						PASS	.						62.0	58.0	60.0					8																	195728		2203	4300	6503	SO:0001589	frameshift_variant	169270	exon6			.	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.881delT	chr8.hg19:g.195728delT	ENSP00000381613:p.Leu294fs	113.0	0.0	0		138.0	58.0	0.42029	NM_001042415	B2R8P4|O95015|Q8N9X0	Frame_Shift_Del	DEL	ENST00000398612.1	hg19	CCDS5951.2																																																																																			.	.	.	none		0.388	ZNF596-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195858.4	NM_173539	
STRIP1	85369	hgsc.bcm.edu	37	1	110577332	110577364	+	In_Frame_Del	DEL	CCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	CCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	-			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	CCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	CCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:110577332_110577364delCCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	ENST00000369795.3	+	1	95_127	c.73_105delCCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	c.(73-105)ccgccggcagccgcacagccaccacccggggcadel	p.PPAAAQPPPGA25del	STRIP1_ENST00000369796.1_Intron|STRIP1_ENST00000369794.2_In_Frame_Del_p.PPAAAQPPPGA25del	NM_033088.3	NP_149079.2	Q5VSL9	STRP1_HUMAN	striatin interacting protein 1	25	Pro-rich.				cortical actin cytoskeleton organization (GO:0030866)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)											GCCACCTCCGCCGCCGGCAGCCGCACAGCCACCAcccggggcaccgcgggccg	0.712																																					p.24_35del		Pindel	.											.	STRIP1	1	.	0			c.72_104del						PASS	.																																			SO:0001651	inframe_deletion	85369	exon1			.	AK027649	CCDS30798.1, CCDS59197.1	1p13.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000143093	ENSG00000143093			25916	protein-coding gene	gene with protein product	"""FAR11 factor arrest 11 homolog A (yeast)"""		"""family with sequence similarity 40, member A"""	FAM40A		11214970, 12588993, 22782902, 22298706, 18782753	Standard	NM_033088		Approved	FLJ14743, KIAA1761, FAR11A	uc001dza.2	Q5VSL9	OTTHUMG00000170607	ENST00000369795.3:c.73_105delCCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	chr1.hg19:g.110577332_110577364delCCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	ENSP00000358810:p.Pro25_Ala35del	208.0	0.0	.		229.0	12.0	0.052	NM_033088	Q0V925|Q5VSL8|Q658K2|Q6ZV31|Q8N598|Q96SN2|Q9C0A2	In_Frame_Del	DEL	ENST00000369795.3	hg19	CCDS30798.1																																																																																			.	.	.	none		0.712	STRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032213.1	NM_033088	
SETD2	29072	hgsc.bcm.edu	37	3	47058731	47058732	+	Frame_Shift_Del	DEL	AC	AC	-			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:47058731_47058732delAC	ENST00000409792.3	-	21	7588_7589	c.7546_7547delGT	c.(7546-7548)gttfs	p.V2516fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2516	Interaction with POLR2A.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CTTATTCATAACACCGTGAGTC	0.48			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.2516_2516del		Pindel	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.7547_7548del						PASS	.																																			SO:0001589	frameshift_variant	29072	exon21			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.7546_7547delGT	chr3.hg19:g.47058733_47058734delAC	ENSP00000386759:p.Val2516fs	46.0	0.0	.		72.0	43.0	0.597	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.480	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
PBRM1	55193	hgsc.bcm.edu	37	3	52678783	52678784	+	Frame_Shift_Ins	INS	-	-	T	rs369874660		TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:52678783_52678784insT	ENST00000296302.7	-	8	836_837	c.835_836insA	c.(835-837)atafs	p.I279fs	PBRM1_ENST00000410007.1_Frame_Shift_Ins_p.I279fs|PBRM1_ENST00000409057.1_Frame_Shift_Ins_p.I279fs|PBRM1_ENST00000356770.4_Frame_Shift_Ins_p.I279fs|PBRM1_ENST00000409114.3_Frame_Shift_Ins_p.I279fs|PBRM1_ENST00000394830.3_Frame_Shift_Ins_p.I279fs|PBRM1_ENST00000337303.4_Frame_Shift_Ins_p.I279fs|PBRM1_ENST00000409767.1_Frame_Shift_Ins_p.I279fs			Q86U86	PB1_HUMAN	polybromo 1	279					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.I279fs*4(7)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		Catataaaatatttttttaatt	0.361			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																p.I279fs		Pindel	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	7	Deletion - Frameshift(7)	kidney(7)	c.836_837insA						PASS	.																																			SO:0001589	frameshift_variant	55193	exon9			.	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.836dupA	chr3.hg19:g.52678790_52678790dupT	ENSP00000296302:p.Ile279fs	44.0	0.0	.		40.0	25.0	0.625	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Ins	INS	ENST00000296302.7	hg19																																																																																				.	.	.	none		0.361	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
PEX12	5193	hgsc.bcm.edu	37	17	33904058	33904062	+	Splice_Site	DEL	TCCTG	TCCTG	-			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	TCCTG	TCCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:33904058_33904062delTCCTG	ENST00000225873.4	-	2	1282_1286	c.675_679delCAGGA	c.(673-681)gccaggagt>gcgt	p.RS226fs	RP11-1094M14.11_ENST00000592381.1_lincRNA	NM_000286.2	NP_000277.1	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	226					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	integral component of peroxisomal membrane (GO:0005779)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(8)	18				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AGGCCTTACCTCCTGGCTGGTTGCT	0.449																																					p.226_227del		Pindel	.											.	PEX12	36	.	0			c.676_680del						PASS	.																																			SO:0001630	splice_region_variant	5193	exon2			.	U91521	CCDS11296.1	17q21.1	2011-02-10			ENSG00000108733	ENSG00000108733			8854	protein-coding gene	gene with protein product		601758				9090384	Standard	NM_000286		Approved		uc002hjp.3	O00623	OTTHUMG00000132951	ENST00000225873.4:c.680+1CAGGA>-	chr17.hg19:g.33904058_33904062delTCCTG		30.0	0.0	.		49.0	11.0	0.224	NM_000286	B2R6M2	Frame_Shift_Del	DEL	ENST00000225873.4	hg19	CCDS11296.1																																																																																			.	.	.	none		0.449	PEX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256489.2	NM_000286	Frame_Shift_Del
