#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
CEP104	9731	hgsc.bcm.edu	37	1	3742942	3742942	+	Silent	SNP	A	A	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:3742942A>G	ENST00000378230.3	-	17	2571	c.2247T>C	c.(2245-2247)taT>taC	p.Y749Y		NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	749						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)			breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						ACTTATCTAGATAGTGCTCAT	0.463																																					p.Y749Y		Atlas-SNP	.											.	CEP104	79	.	0			c.T2247C						PASS	.						84.0	79.0	80.0					1																	3742942		2203	4300	6503	SO:0001819	synonymous_variant	9731	exon17			ATCTAGATAGTGC	AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"""glycine, glutamate, thienylcyclohexylpiperidine binding protein"""		"""KIAA0562"""	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.2247T>C	chr1.hg19:g.3742942A>G		114.0	0.0	.		113.0	48.0	.	NM_014704	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Silent	SNP	ENST00000378230.3	hg19	CCDS30571.1	.	.	.	.	.	.	.	.	.	.	A	0.033	-1.320509	0.01320	.	.	ENSG00000116198	ENST00000438539	.	.	.	4.52	-0.637	0.11504	.	.	.	.	.	T	0.31451	0.0797	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30822	-0.9965	4	.	.	.	.	7.5619	0.27855	0.5592:0.0:0.4408:0.0	.	.	.	.	T	46	.	.	I	-	2	0	CEP104	3732802	0.000000	0.05858	0.001000	0.08648	0.188000	0.23474	-0.889000	0.04144	-0.294000	0.08973	-0.408000	0.06270	ATC	.	.	.	none		0.463	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704	
SFPQ	6421	hgsc.bcm.edu	37	1	35650120	35650120	+	Silent	SNP	A	A	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:35650120A>T	ENST00000357214.5	-	10	2159	c.2061T>A	c.(2059-2061)acT>acA	p.T687T		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	687					alternative mRNA splicing, via spliceosome (GO:0000380)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H3 deacetylation (GO:0070932)|mRNA processing (GO:0006397)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|histone deacetylase binding (GO:0042826)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)		SFPQ/TFE3(6)	NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				ATCCTGCTGGAGTTCCAGGCC	0.488			T	TFE3	papillary renal cell																																p.T687T		Atlas-SNP	.		Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	.	SFPQ	51	.	0			c.T2061A						PASS	.						128.0	127.0	128.0					1																	35650120		2203	4300	6503	SO:0001819	synonymous_variant	6421	exon10			TGCTGGAGTTCCA	X70944	CCDS388.1	1p34.3	2014-06-13	2010-05-04		ENSG00000116560	ENSG00000116560		"""RNA binding motif (RRM) containing"""	10774	protein-coding gene	gene with protein product	"""polypyrimidine tract binding protein associated"", ""protein phosphatase 1, regulatory subunit 140"""	605199	"""splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated)"""			8449401	Standard	NM_005066		Approved	PSF, PPP1R140	uc001bys.3	P23246	OTTHUMG00000004157	ENST00000357214.5:c.2061T>A	chr1.hg19:g.35650120A>T		100.0	0.0	.		114.0	53.0	.	NM_005066	P30808|Q5SZ71	Silent	SNP	ENST00000357214.5	hg19	CCDS388.1																																																																																			.	.	.	none		0.488	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066	
ZMPSTE24	10269	hgsc.bcm.edu	37	1	40724001	40724001	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:40724001T>A	ENST00000372759.3	+	1	223	c.58T>A	c.(58-60)Ttc>Atc	p.F20I	RP1-39G22.7_ENST00000567508.1_RNA|ZMPSTE24_ENST00000479131.1_3'UTR	NM_005857.4	NP_005848.2	O75844	FACE1_HUMAN	zinc metallopeptidase STE24	20					CAAX-box protein processing (GO:0071586)|nuclear envelope organization (GO:0006998)|prenylated protein catabolic process (GO:0030327)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metalloexopeptidase activity (GO:0008235)			endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	16	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)			GAAGCGTATCTTCGGGGCCGT	0.627																																					p.F20I		Atlas-SNP	.											.	ZMPSTE24	50	.	0			c.T58A						PASS	.						123.0	106.0	112.0					1																	40724001		2203	4300	6503	SO:0001583	missense	10269	exon1			CGTATCTTCGGGG	Y13834	CCDS449.1	1p34	2014-09-17	2012-12-10		ENSG00000084073	ENSG00000084073	3.4.24.84		12877	protein-coding gene	gene with protein product	"""Hutchinson-Gilford progeria syndrome"", ""CAAX prenyl protease 1 homolog"""	606480	"""zinc metalloproteinase (STE24 homolog, yeast)"", ""zinc metallopeptidase (STE24 homolog, yeast)"", ""zinc metallopeptidase STE24 homolog (S. cerevisiae)"""			10373325, 9700155, 16671095	Standard	NM_005857		Approved	FACE-1, Ste24p, STE24, HGPS, PRO1	uc001cfg.4	O75844	OTTHUMG00000005762	ENST00000372759.3:c.58T>A	chr1.hg19:g.40724001T>A	ENSP00000361845:p.Phe20Ile	64.0	0.0	.		74.0	25.0	.	NM_005857	B3KQI7|D3DPU7|Q8NDZ8|Q9UBQ2	Missense_Mutation	SNP	ENST00000372759.3	hg19	CCDS449.1	.	.	.	.	.	.	.	.	.	.	T	36	5.971807	0.97162	.	.	ENSG00000084073	ENST00000372759	T	0.00902	5.56	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.04452	0.0122	M	0.71036	2.16	0.80722	D	1	D	0.69078	0.997	P	0.62560	0.904	T	0.36866	-0.9730	10	0.59425	D	0.04	-16.1505	15.3325	0.74226	0.0:0.0:0.0:1.0	.	20	O75844	FACE1_HUMAN	I	20	ENSP00000361845:F20I	ENSP00000361845:F20I	F	+	1	0	ZMPSTE24	40496588	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	7.016000	0.76393	2.026000	0.59711	0.533000	0.62120	TTC	.	.	.	none		0.627	ZMPSTE24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015766.1		
FOXD2	2306	hgsc.bcm.edu	37	1	47905188	47905188	+	Missense_Mutation	SNP	G	G	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:47905188G>C	ENST00000334793.5	+	1	3500	c.1381G>C	c.(1381-1383)Gct>Cct	p.A461P		NM_004474.3	NP_004465.3	O60548	FOXD2_HUMAN	forkhead box D2	461	Ala-rich.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(4)	4				READ - Rectum adenocarcinoma(2;0.0908)		TCCGGCCCTGGCTCCCGTTGC	0.721																																					p.A461P		Atlas-SNP	.											.	FOXD2	16	.	0			c.G1381C						PASS	.						5.0	6.0	5.0					1																	47905188		2041	4122	6163	SO:0001583	missense	2306	exon1			GCCCTGGCTCCCG	AF042832	CCDS30708.1	1p34-p32	2008-02-05			ENSG00000186564	ENSG00000186564		"""Forkhead boxes"""	3803	protein-coding gene	gene with protein product		602211		FKHL17		9403061, 12621056	Standard	NM_004474		Approved	FREAC9	uc001crm.3	O60548	OTTHUMG00000007950	ENST00000334793.5:c.1381G>C	chr1.hg19:g.47905188G>C	ENSP00000335493:p.Ala461Pro	53.0	0.0	.		78.0	6.0	.	NM_004474	Q5SVZ3	Missense_Mutation	SNP	ENST00000334793.5	hg19	CCDS30708.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.439685	0.43326	.	.	ENSG00000186564	ENST00000334793	T	0.57436	0.4	4.46	2.37	0.29283	.	1.733230	0.03641	U	0.239565	T	0.44850	0.1313	L	0.29908	0.895	0.32396	N	0.552538	B	0.09022	0.002	B	0.08055	0.003	T	0.46303	-0.9201	10	0.72032	D	0.01	.	9.3432	0.38093	0.2205:0.0:0.7795:0.0	.	461	O60548	FOXD2_HUMAN	P	461	ENSP00000335493:A461P	ENSP00000335493:A461P	A	+	1	0	FOXD2	47677775	1.000000	0.71417	0.993000	0.49108	0.782000	0.44232	2.417000	0.44653	1.039000	0.40074	0.561000	0.74099	GCT	.	.	.	none		0.721	FOXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021831.1	NM_004474	
BCAN	63827	hgsc.bcm.edu	37	1	156622136	156622136	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:156622136A>C	ENST00000329117.5	+	8	1730	c.1394A>C	c.(1393-1395)aAa>aCa	p.K465T	BCAN_ENST00000361588.5_Missense_Mutation_p.K465T|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	465	Glu-rich.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					gaagaagagaaagaggaggaa	0.542																																					p.K465T		Atlas-SNP	.											.	BCAN	174	.	0			c.A1394C						PASS	.						26.0	26.0	26.0					1																	156622136		2203	4300	6503	SO:0001583	missense	63827	exon8			AAGAGAAAGAGGA	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	23059	protein-coding gene	gene with protein product	"""chondroitin sulfate proteoglycan 7"", ""brevican proteoglycan"""	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.1394A>C	chr1.hg19:g.156622136A>C	ENSP00000331210:p.Lys465Thr	118.0	0.0	.		126.0	63.0	.	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	hg19	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	A	0.144	-1.098712	0.01843	.	.	ENSG00000132692	ENST00000255029;ENST00000329117;ENST00000361588	T;T	0.14766	2.48;3.22	3.69	-0.137	0.13469	.	3.115980	0.01588	N	0.021411	T	0.01765	0.0056	N	0.14661	0.345	0.09310	N	1	B;B	0.26400	0.148;0.0	B;B	0.24155	0.051;0.001	T	0.33548	-0.9864	10	0.11485	T	0.65	0.0752	3.617	0.08081	0.3722:0.3192:0.0:0.3087	.	465;465	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	T	404;465;465	ENSP00000331210:K465T;ENSP00000354925:K465T	ENSP00000255029:K404T	K	+	2	0	BCAN	154888760	0.005000	0.15991	0.003000	0.11579	0.429000	0.31625	0.189000	0.17037	-0.229000	0.09854	0.454000	0.30748	AAA	.	.	.	none		0.542	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948	
LAMC1	3915	hgsc.bcm.edu	37	1	183090998	183090998	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:183090998G>A	ENST00000258341.4	+	12	2388	c.2131G>A	c.(2131-2133)Gaa>Aaa	p.E711K		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	711	Laminin EGF-like 5; second part. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						TTACAGAAGAGAAACTCCTAA	0.532																																					p.E711K		Atlas-SNP	.											.	LAMC1	176	.	0			c.G2131A						PASS	.						171.0	152.0	159.0					1																	183090998		2203	4300	6503	SO:0001583	missense	3915	exon12			AGAAGAGAAACTC	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.2131G>A	chr1.hg19:g.183090998G>A	ENSP00000258341:p.Glu711Lys	53.0	0.0	.		69.0	33.0	.	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	hg19	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.731851	0.69189	.	.	ENSG00000135862	ENST00000258341	T	0.30182	1.54	5.17	5.17	0.71159	EGF-like, laminin (1);	0.309234	0.36444	N	0.002581	T	0.38931	0.1059	M	0.84846	2.72	0.48632	D	0.999681	P	0.44627	0.839	B	0.39379	0.298	T	0.48198	-0.9056	10	0.10636	T	0.68	.	18.6846	0.91559	0.0:0.0:1.0:0.0	.	711	P11047	LAMC1_HUMAN	K	711	ENSP00000258341:E711K	ENSP00000258341:E711K	E	+	1	0	LAMC1	181357621	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.571000	0.53841	2.402000	0.81655	0.655000	0.94253	GAA	.	.	.	none		0.532	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
PLXNA2	5362	hgsc.bcm.edu	37	1	208390905	208390905	+	Silent	SNP	G	G	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:208390905G>A	ENST00000367033.3	-	2	1120	c.363C>T	c.(361-363)taC>taT	p.Y121Y		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	121	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GGTTCTCAGAGTAGTCAATGA	0.572																																					p.Y121Y		Atlas-SNP	.											.	PLXNA2	178	.	0			c.C363T						PASS	.						102.0	105.0	104.0					1																	208390905		2203	4300	6503	SO:0001819	synonymous_variant	5362	exon2			CTCAGAGTAGTCA	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.363C>T	chr1.hg19:g.208390905G>A		125.0	0.0	.		144.0	69.0	.	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	hg19	CCDS31013.1																																																																																			.	.	.	none		0.572	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
KCNH1	3756	hgsc.bcm.edu	37	1	211093156	211093156	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:211093156A>T	ENST00000271751.4	-	7	1315	c.1288T>A	c.(1288-1290)Tac>Aac	p.Y430N	KCNH1_ENST00000367007.4_Missense_Mutation_p.Y403N			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	430					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		TTAAACTGGTAAGGGGTGCCA	0.507																																					p.Y430N		Atlas-SNP	.											.	KCNH1	199	.	0			c.T1288A						PASS	.						190.0	169.0	176.0					1																	211093156		2203	4300	6503	SO:0001583	missense	3756	exon7			ACTGGTAAGGGGT	AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.1288T>A	chr1.hg19:g.211093156A>T	ENSP00000271751:p.Tyr430Asn	224.0	0.0	.		214.0	108.0	.	NM_172362	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	hg19	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.521034	0.85495	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.99186	-5.44;-5.53	5.8	5.8	0.92144	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99130	0.9700	M	0.76574	2.34	0.80722	D	1	D;D	0.58970	0.984;0.984	D;D	0.68483	0.958;0.958	D	0.99651	1.0991	10	0.87932	D	0	.	15.3272	0.74176	1.0:0.0:0.0:0.0	.	403;430	Q14CL3;O95259	.;KCNH1_HUMAN	N	430;403	ENSP00000271751:Y430N;ENSP00000355974:Y403N	ENSP00000271751:Y430N	Y	-	1	0	KCNH1	209159779	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.999000	0.93557	2.219000	0.72066	0.533000	0.62120	TAC	.	.	.	none		0.507	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238	
TMEM63A	9725	hgsc.bcm.edu	37	1	226050526	226050526	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:226050526C>T	ENST00000366835.3	-	11	1042	c.772G>A	c.(772-774)Gtt>Att	p.V258I	TMEM63A_ENST00000474478.1_5'UTR|TMEM63A_ENST00000537914.1_5'UTR	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	258					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)			breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					TGCACATCAACCACCTCACAC	0.577																																					p.V258I		Atlas-SNP	.											.	TMEM63A	75	.	0			c.G772A						PASS	.						109.0	78.0	88.0					1																	226050526		2203	4300	6503	SO:0001583	missense	9725	exon11			CATCAACCACCTC		CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"""KIAA0792"""	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.772G>A	chr1.hg19:g.226050526C>T	ENSP00000355800:p.Val258Ile	134.0	0.0	.		187.0	67.0	.	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Missense_Mutation	SNP	ENST00000366835.3	hg19	CCDS31042.1	.	.	.	.	.	.	.	.	.	.	C	7.629	0.678465	0.14841	.	.	ENSG00000196187	ENST00000366835	T	0.44482	0.92	5.84	4.91	0.64330	Nucleotide-binding, alpha-beta plait (1);	0.632722	0.17914	N	0.157757	T	0.39009	0.1062	L	0.48362	1.52	0.80722	D	1	B	0.20550	0.046	B	0.17098	0.017	T	0.13710	-1.0499	10	0.38643	T	0.18	-16.8033	15.0439	0.71813	0.0:0.7315:0.2685:0.0	.	258	O94886	TM63A_HUMAN	I	258	ENSP00000355800:V258I	ENSP00000355800:V258I	V	-	1	0	TMEM63A	224117149	0.573000	0.26676	1.000000	0.80357	0.258000	0.26162	0.886000	0.28241	1.448000	0.47680	0.561000	0.74099	GTT	.	.	.	none		0.577	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
PLEKHH2	130271	hgsc.bcm.edu	37	2	43986044	43986044	+	Missense_Mutation	SNP	T	T	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:43986044T>G	ENST00000282406.4	+	27	4057	c.3947T>G	c.(3946-3948)cTt>cGt	p.L1316R		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	1316	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				tttAGGCAGCTTTGCCAGCGA	0.423																																					p.L1316R		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.T3947G						PASS	.						36.0	35.0	35.0					2																	43986044		2203	4300	6503	SO:0001583	missense	130271	exon27			GGCAGCTTTGCCA	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"""Pleckstrin homology (PH) domain containing"""	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.3947T>G	chr2.hg19:g.43986044T>G	ENSP00000282406:p.Leu1316Arg	55.0	0.0	.		50.0	26.0	.	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	hg19	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.580076	0.86645	.	.	ENSG00000152527	ENST00000282406	T	0.81415	-1.49	5.66	5.66	0.87406	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.85682	D	0.000000	D	0.89976	0.6871	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91227	0.5011	10	0.72032	D	0.01	-17.0245	15.8843	0.79232	0.0:0.0:0.0:1.0	.	1316	Q8IVE3	PKHH2_HUMAN	R	1316	ENSP00000282406:L1316R	ENSP00000282406:L1316R	L	+	2	0	PLEKHH2	43839548	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	7.698000	0.84413	2.164000	0.68074	0.533000	0.62120	CTT	.	.	.	none		0.423	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069	
EPAS1	2034	hgsc.bcm.edu	37	2	46605215	46605215	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:46605215A>T	ENST00000263734.3	+	10	1942	c.1432A>T	c.(1432-1434)Agc>Tgc	p.S478C		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	478	Poly-Ser.				angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			CAGCAGCAGCAGCTGCTCCAC	0.652																																					p.S478C		Atlas-SNP	.											.	EPAS1	83	.	0			c.A1432T						PASS	.						10.0	10.0	10.0					2																	46605215		2180	4275	6455	SO:0001583	missense	2034	exon10			AGCAGCAGCTGCT	U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"""Basic helix-loop-helix proteins"""	3374	protein-coding gene	gene with protein product	"""HIF-1 alpha-like factor"""	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.1432A>T	chr2.hg19:g.46605215A>T	ENSP00000263734:p.Ser478Cys	113.0	0.0	.		125.0	5.0	.	NM_001430	Q86VA2|Q99630	Missense_Mutation	SNP	ENST00000263734.3	hg19	CCDS1825.1	.	.	.	.	.	.	.	.	.	.	A	18.75	3.689835	0.68271	.	.	ENSG00000116016	ENST00000263734	T	0.56444	0.46	5.58	3.23	0.37069	.	0.981388	0.08371	N	0.956092	T	0.67287	0.2877	M	0.76574	2.34	0.37050	D	0.897573	D	0.62365	0.991	P	0.59288	0.855	T	0.59553	-0.7433	10	0.37606	T	0.19	.	9.6414	0.39842	0.8591:0.0:0.1409:0.0	.	478	Q99814	EPAS1_HUMAN	C	478	ENSP00000263734:S478C	ENSP00000263734:S478C	S	+	1	0	EPAS1	46458719	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	4.474000	0.60203	0.427000	0.26145	0.533000	0.62120	AGC	.	.	.	none		0.652	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250752.2	NM_001430	
KCMF1	56888	hgsc.bcm.edu	37	2	85276536	85276536	+	Missense_Mutation	SNP	C	C	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:85276536C>A	ENST00000409785.4	+	6	1008	c.649C>A	c.(649-651)Ctt>Att	p.L217I		NM_020122.4	NP_064507.3	Q9P0J7	KCMF1_HUMAN	potassium channel modulatory factor 1	217							ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						AGGAGGACAGCTTAATTCCTC	0.478																																					p.L217I		Atlas-SNP	.											.	KCMF1	38	.	0			c.C649A						PASS	.						111.0	117.0	115.0					2																	85276536		2131	4242	6373	SO:0001583	missense	56888	exon6			GGACAGCTTAATT	AF155652	CCDS46350.1	2p11.2	2010-11-23			ENSG00000176407	ENSG00000176407		"""Zinc fingers, ZZ-type"""	20589	protein-coding gene	gene with protein product		614719					Standard	NM_020122		Approved	DEBT91, PCMF, DKFZP434L1021, ZZZ1	uc002sox.4	Q9P0J7	OTTHUMG00000153004	ENST00000409785.4:c.649C>A	chr2.hg19:g.85276536C>A	ENSP00000386738:p.Leu217Ile	123.0	0.0	.		109.0	47.0	.	NM_020122	Q4ZG04|Q53SC7|Q9BWK2|Q9H8P5|Q9UFE8	Missense_Mutation	SNP	ENST00000409785.4	hg19	CCDS46350.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.844635	0.51164	.	.	ENSG00000176407	ENST00000409785	T	0.48522	0.81	5.96	5.96	0.96718	Drought induced 19/ RING finger protein 114 (1);	0.111308	0.64402	D	0.000008	T	0.32526	0.0832	N	0.08118	0	0.44966	D	0.997988	B	0.15930	0.015	B	0.21360	0.034	T	0.08513	-1.0718	10	0.37606	T	0.19	-15.8537	17.9158	0.88950	0.0:1.0:0.0:0.0	.	217	Q9P0J7	KCMF1_HUMAN	I	217	ENSP00000386738:L217I	ENSP00000386738:L217I	L	+	1	0	KCMF1	85130047	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.484000	0.53201	2.832000	0.97577	0.655000	0.94253	CTT	.	.	.	none		0.478	KCMF1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328942.4	NM_020122	
KDM3A	55818	hgsc.bcm.edu	37	2	86709141	86709141	+	Missense_Mutation	SNP	T	T	A	rs144469383	byFrequency	TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:86709141T>A	ENST00000409556.1	+	18	2966	c.2601T>A	c.(2599-2601)caT>caA	p.H867Q	KDM3A_ENST00000312912.5_Missense_Mutation_p.H867Q|KDM3A_ENST00000409064.1_Missense_Mutation_p.H867Q|KDM3A_ENST00000542128.1_Missense_Mutation_p.H815Q			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	867					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						CAGTCCTCCATACGTTTAACA	0.383																																					p.H867Q	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.T2601A						PASS	.						157.0	147.0	150.0					2																	86709141		2203	4300	6503	SO:0001583	missense	55818	exon17			CCTCCATACGTTT	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"""Chromatin-modifying enzymes / K-demethylases"""	20815	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 2A"""	611512	"""jumonji domain containing 1"", ""jumonji domain containing 1A"""	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.2601T>A	chr2.hg19:g.86709141T>A	ENSP00000386660:p.His867Gln	278.0	0.0	.		316.0	121.0	.	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	hg19	CCDS1990.1	.	.	.	.	.	.	.	.	.	.	T	0.181	-1.061940	0.01950	.	.	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.8	-4.8	0.03190	.	0.158851	0.45606	N	0.000360	T	0.21347	0.0514	N	0.11560	0.145	0.20489	N	0.999898	B;B	0.13145	0.007;0.004	B;B	0.20577	0.03;0.013	T	0.21861	-1.0233	10	0.12103	T	0.63	.	4.2025	0.10473	0.1625:0.1718:0.0861:0.5796	.	815;867	F5H070;Q9Y4C1	.;KDM3A_HUMAN	Q	867;867;867;867;815	ENSP00000386660:H867Q;ENSP00000323659:H867Q;ENSP00000386516:H867Q;ENSP00000438324:H815Q	ENSP00000323659:H867Q	H	+	3	2	KDM3A	86562652	0.737000	0.28175	0.337000	0.25536	0.581000	0.36288	-0.439000	0.06897	-2.060000	0.00893	-2.501000	0.00191	CAT	.	T|1.000;C|0.000	.	alt		0.383	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433	
CNNM3	26505	hgsc.bcm.edu	37	2	97494855	97494855	+	Missense_Mutation	SNP	G	G	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:97494855G>C	ENST00000305510.3	+	7	2071	c.2043G>C	c.(2041-2043)aaG>aaC	p.K681N	CNNM3_ENST00000480035.1_3'UTR|CNNM3_ENST00000377060.3_Missense_Mutation_p.K633N|ANKRD23_ENST00000476975.1_Intron	NM_017623.4	NP_060093.3	Q8NE01	CNNM3_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 3	681					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(2)|skin(1)|urinary_tract(2)	13						TTGGTGAGAAGACCACCACAG	0.612																																					p.K681N		Atlas-SNP	.											.	CNNM3	33	.	0			c.G2043C						PASS	.						69.0	70.0	70.0					2																	97494855		2203	4300	6503	SO:0001583	missense	26505	exon7			TGAGAAGACCACC	AF216965	CCDS2025.1, CCDS2026.1	2q11.2	2014-08-08	2014-08-07		ENSG00000168763	ENSG00000168763			104	protein-coding gene	gene with protein product		607804	"""cyclin M3"""	ACDP3		21393841, 24632616	Standard	XM_005263917		Approved		uc002swy.3	Q8NE01	OTTHUMG00000130531	ENST00000305510.3:c.2043G>C	chr2.hg19:g.97494855G>C	ENSP00000305449:p.Lys681Asn	119.0	0.0	.		123.0	67.0	.	NM_017623	B3KX67|Q8TBV4|Q96IW4|Q9NRK4|Q9NXW6	Missense_Mutation	SNP	ENST00000305510.3	hg19	CCDS2025.1	.	.	.	.	.	.	.	.	.	.	G	10.77	1.445374	0.25987	.	.	ENSG00000168763	ENST00000377060;ENST00000424641;ENST00000305510	D;D	0.91740	-2.58;-2.9	5.56	3.74	0.42951	.	0.845028	0.10091	N	0.717179	D	0.86981	0.6064	L	0.38531	1.155	0.58432	D	0.999996	B;B	0.27823	0.016;0.19	B;B	0.28709	0.015;0.093	T	0.76650	-0.2881	10	0.25106	T	0.35	-13.8197	8.2356	0.31625	0.2409:0.0:0.7591:0.0	.	633;681	Q8NE01-2;Q8NE01	.;CNNM3_HUMAN	N	633;633;681	ENSP00000366260:K633N;ENSP00000305449:K681N	ENSP00000305449:K681N	K	+	3	2	CNNM3	96858582	0.992000	0.36948	0.489000	0.27452	0.352000	0.29268	3.142000	0.50601	0.684000	0.31448	0.655000	0.94253	AAG	.	.	.	none		0.612	CNNM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252952.2	NM_017623	
ZC3H6	376940	hgsc.bcm.edu	37	2	113089842	113089843	+	Missense_Mutation	DNP	AC	AC	GG	rs371812950		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:113089842_113089843AC>GG	ENST00000409871.1	+	12	3748_3749	c.3347_3348AC>GG	c.(3346-3348)gAC>gGG	p.D1116G	ZC3H6_ENST00000343936.4_Missense_Mutation_p.D1116G|AC115115.2_ENST00000607612.1_RNA	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	1116							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						CCACAGGCGGACGTTCCCAGGA	0.535																																					p.D1116G|p.D1116E		Atlas-SNP	.											.	ZC3H6	93	.	0			c.A3347G|c.C3348G						PASS	.																																			SO:0001583	missense	376940	exon12			AGGCGGACGTTCC|GGCGGACGTTCCC	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"""Zinc fingers, CCCH-type domain containing"""	24762	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 6"""	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	Exception_encountered	chr2.hg19:g.113089842_113089843delinsGG	ENSP00000386764:p.Asp1116Gly	276.0|274.0	0.0	.		360.0|225.0	152.0|20.0	.	NM_198581	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	hg19	CCDS46393.1																																																																																			.	.	.	none|alt		0.535	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581	
GLI2	2736	hgsc.bcm.edu	37	2	121746958	121746958	+	Silent	SNP	C	C	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:121746958C>G	ENST00000452319.1	+	14	3528	c.3468C>G	c.(3466-3468)gcC>gcG	p.A1156A	GLI2_ENST00000314490.11_Intron|GLI2_ENST00000361492.4_Silent_p.A1156A					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				CCGTAGACGCCCTGGCCAGCC	0.617																																					p.A1156A		Atlas-SNP	.											.	GLI2	187	.	0			c.C3468G						PASS	.						27.0	25.0	26.0					2																	121746958		2177	4259	6436	SO:0001819	synonymous_variant	2736	exon13			AGACGCCCTGGCC		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.3468C>G	chr2.hg19:g.121746958C>G		94.0	0.0	.		104.0	42.0	.	NM_005270		Silent	SNP	ENST00000452319.1	hg19	CCDS33283.1																																																																																			.	.	.	none		0.617	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
TTN	7273	hgsc.bcm.edu	37	2	179478924	179478924	+	Missense_Mutation	SNP	C	C	G	rs539513077		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:179478924C>G	ENST00000591111.1	-	212	44501	c.44277G>C	c.(44275-44277)aaG>aaC	p.K14759N	TTN_ENST00000342992.6_Missense_Mutation_p.K13832N|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.K7527N|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.K16400N|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.K7460N|TTN_ENST00000460472.2_Missense_Mutation_p.K7335N|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14759	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGGATGAGAGCTTGTGCCACA	0.443																																					p.K16400N		Atlas-SNP	.											.	TTN	18412	.	0			c.G49200C						PASS	.						153.0	142.0	145.0					2																	179478924		2003	4177	6180	SO:0001583	missense	7273	exon262			TGAGAGCTTGTGC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.44277G>C	chr2.hg19:g.179478924C>G	ENSP00000465570:p.Lys14759Asn	152.0	0.0	.		162.0	56.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.16	1.557484	0.27827	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	5.77	3.99	0.46301	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.61912	0.2385	L	0.42581	1.335	0.41869	D	0.990264	D;D;D;D	0.71674	0.997;0.997;0.997;0.998	D;D;D;D	0.69824	0.918;0.918;0.918;0.966	T	0.63817	-0.6551	9	0.87932	D	0	.	10.5973	0.45345	0.0:0.7432:0.0:0.2568	.	7335;7460;7527;14759	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	13832;7335;7527;7460;7335	ENSP00000343764:K13832N;ENSP00000434586:K7335N;ENSP00000340554:K7527N;ENSP00000352154:K7460N	ENSP00000340554:K7527N	K	-	3	2	TTN	179187169	0.975000	0.34042	1.000000	0.80357	0.974000	0.67602	0.227000	0.17795	0.914000	0.36822	-0.136000	0.14681	AAG	.	.	.	none		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ARIH2OS	646450	hgsc.bcm.edu	37	3	48956576	48956576	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr3:48956576C>T	ENST00000408959.2	-	1	242	c.7G>A	c.(7-9)Gga>Aga	p.G3R	ARIH2_ENST00000356401.4_Intron|ARIH2_ENST00000449376.1_Intron|ARIH2_ENST00000490095.1_Intron	NM_001123040.1	NP_001116512.1	Q8N7S6	ARI2O_HUMAN	ariadne homolog 2 opposite strand	3						integral component of membrane (GO:0016021)											GCACGTTGTCCGAGCATTACC	0.751																																					p.G3R		Atlas-SNP	.											.	.	.	.	0			c.G7A						PASS	.						4.0	5.0	4.0					3																	48956576		961	2282	3243	SO:0001583	missense	646450	exon1			GTTGTCCGAGCAT	DA461567	CCDS43088.1	3p21.31	2012-10-08	2012-10-08	2012-10-08	ENSG00000221883	ENSG00000221883			34425	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 71"""	C3orf71			Standard	NM_001123040		Approved		uc010hkk.1	Q8N7S6	OTTHUMG00000156672	ENST00000408959.2:c.7G>A	chr3.hg19:g.48956576C>T	ENSP00000386193:p.Gly3Arg	39.0	0.0	.		52.0	20.0	.	NM_001123040		Missense_Mutation	SNP	ENST00000408959.2	hg19	CCDS43088.1	.	.	.	.	.	.	.	.	.	.	C	11.75	1.731212	0.30684	.	.	ENSG00000221883	ENST00000408959	.	.	.	3.3	-5.21	0.02815	.	.	.	.	.	T	0.14917	0.0360	N	0.08118	0	0.09310	N	0.999995	B	0.22604	0.072	B	0.19391	0.025	T	0.23084	-1.0198	8	0.87932	D	0	.	3.7894	0.08713	0.2267:0.3251:0.0:0.4482	.	3	Q8N7S6	CC071_HUMAN	R	3	.	ENSP00000386193:G3R	G	-	1	0	C3orf71	48931580	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.310000	0.08135	-1.121000	0.02949	0.561000	0.74099	GGA	.	.	.	none		0.751	ARIH2OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345247.1	NM_001123040	
PRKCD	5580	hgsc.bcm.edu	37	3	53221398	53221398	+	Missense_Mutation	SNP	C	C	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr3:53221398C>G	ENST00000394729.2	+	14	1723	c.1395C>G	c.(1393-1395)caC>caG	p.H465Q	PRKCD_ENST00000330452.3_Missense_Mutation_p.H465Q	NM_212539.1	NP_997704.1	Q05655	KPCD_HUMAN	protein kinase C, delta	465	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular senescence (GO:0090398)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-10 production (GO:0032613)|interleukin-12 production (GO:0032615)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|mRNA metabolic process (GO:0016071)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of filopodium assembly (GO:0051490)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil activation (GO:0042119)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of glucosylceramide catabolic process (GO:2000753)|positive regulation of phospholipid scramblase activity (GO:1900163)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of sphingomyelin catabolic process (GO:2000755)|positive regulation of superoxide anion generation (GO:0032930)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of receptor activity (GO:0010469)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|termination of signal transduction (GO:0023021)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|insulin receptor substrate binding (GO:0043560)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Ovarian(412;0.0728)		OV - Ovarian serous cystadenocarcinoma(275;3.58e-08)|BRCA - Breast invasive adenocarcinoma(193;0.000142)|Kidney(197;0.00153)|KIRC - Kidney renal clear cell carcinoma(197;0.00173)	Ingenol Mebutate(DB05013)|Tamoxifen(DB00675)	AGTTTCTACACAGCAAGGGCA	0.557																																					p.H465Q		Atlas-SNP	.											.	PRKCD	124	.	0			c.C1395G						PASS	.						120.0	117.0	118.0					3																	53221398		2203	4300	6503	SO:0001583	missense	5580	exon14			TCTACACAGCAAG		CCDS2870.1	3p21.31	2009-07-10			ENSG00000163932	ENSG00000163932	2.7.11.1		9399	protein-coding gene	gene with protein product		176977				8188219	Standard	NM_006254		Approved		uc003dgm.3	Q05655	OTTHUMG00000133659	ENST00000394729.2:c.1395C>G	chr3.hg19:g.53221398C>G	ENSP00000378217:p.His465Gln	67.0	0.0	.		58.0	23.0	.	NM_212539	B0KZ81|B2R834|Q15144|Q86XJ6	Missense_Mutation	SNP	ENST00000394729.2	hg19	CCDS2870.1	.	.	.	.	.	.	.	.	.	.	C	18.99	3.740330	0.69304	.	.	ENSG00000163932	ENST00000394729;ENST00000330452	D;D	0.84516	-1.86;-1.86	5.47	4.59	0.56863	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.92489	0.7615	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.92943	0.6374	10	0.87932	D	0	.	10.5386	0.45020	0.0:0.8413:0.0:0.1587	.	465	Q05655	KPCD_HUMAN	Q	465	ENSP00000378217:H465Q;ENSP00000331602:H465Q	ENSP00000331602:H465Q	H	+	3	2	PRKCD	53196438	1.000000	0.71417	0.974000	0.42286	0.968000	0.65278	1.343000	0.33930	1.285000	0.44548	0.591000	0.81541	CAC	.	.	.	none		0.557	PRKCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257818.1		
CADPS	8618	hgsc.bcm.edu	37	3	62423814	62423814	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr3:62423814C>T	ENST00000383710.4	-	28	4091	c.3742G>A	c.(3742-3744)Gtc>Atc	p.V1248I	CADPS_ENST00000283269.9_Missense_Mutation_p.V1209I|CADPS_ENST00000357948.3_Missense_Mutation_p.V1169I	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	1248	Mediates targeting and association with DCVs. {ECO:0000250}.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TCCTCATTGACCTTATCACGC	0.448																																					p.V1248I		Atlas-SNP	.											.	CADPS	387	.	0			c.G3742A						PASS	.						95.0	91.0	92.0					3																	62423814		2203	4300	6503	SO:0001583	missense	8618	exon28			CATTGACCTTATC	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.3742G>A	chr3.hg19:g.62423814C>T	ENSP00000373215:p.Val1248Ile	227.0	0.0	.		263.0	94.0	.	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.10|12.10	1.835491|1.835491	0.32421|0.32421	.|.	.|.	ENSG00000163618|ENSG00000163618	ENST00000466621|ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269	.|T;T;T	.|0.30448	.|1.53;1.53;1.53	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.30572|0.30572	0.0769|0.0769	L|L	0.40543|0.40543	1.245|1.245	0.80722|0.80722	D|D	1|1	.|B;B;B;B	.|0.23377	.|0.084;0.001;0.002;0.058	.|B;B;B;B	.|0.26614	.|0.071;0.007;0.004;0.065	T|T	0.04115|0.04115	-1.0976|-1.0976	5|10	.|0.24483	.|T	.|0.36	.|.	19.7806|19.7806	0.96414|0.96414	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1169;1209;1248;1253	.|Q9ULU8-2;Q9ULU8-3;Q9ULU8;Q9ULU8-4	.|.;.;CAPS1_HUMAN;.	D|I	148|1254;1248;1169;1209	.|ENSP00000373215:V1248I;ENSP00000350632:V1169I;ENSP00000283269:V1209I	.|ENSP00000283269:V1209I	G|V	-|-	2|1	0|0	CADPS|CADPS	62398854|62398854	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	5.978000|5.978000	0.70501|0.70501	2.668000|2.668000	0.90789|0.90789	0.644000|0.644000	0.83932|0.83932	GGT|GTC	.	.	.	none		0.448	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394	
FNDC3B	64778	hgsc.bcm.edu	37	3	172065011	172065011	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr3:172065011A>T	ENST00000336824.4	+	21	2473	c.2374A>T	c.(2374-2376)Agt>Tgt	p.S792C	FNDC3B_ENST00000416957.1_Missense_Mutation_p.S792C|FNDC3B_ENST00000415807.2_Missense_Mutation_p.S792C	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	792	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		GAGTCCTGATAGTTCTGGTGC	0.403																																					p.S792C		Atlas-SNP	.											.	FNDC3B	118	.	0			c.A2374T						PASS	.						125.0	125.0	125.0					3																	172065011		2203	4300	6503	SO:0001583	missense	64778	exon21			CCTGATAGTTCTG	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"""Fibronectin type III domain containing"""	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.2374A>T	chr3.hg19:g.172065011A>T	ENSP00000338523:p.Ser792Cys	89.0	0.0	.		97.0	47.0	.	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	hg19	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	A	9.703	1.154942	0.21371	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957	T;T;T	0.59224	0.28;0.28;0.28	6.03	3.61	0.41365	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.383662	0.37348	N	0.002126	T	0.34571	0.0902	N	0.13168	0.305	0.80722	D	1	B	0.06786	0.001	B	0.15484	0.013	T	0.06391	-1.0829	10	0.24483	T	0.36	-7.0432	5.9877	0.19444	0.5632:0.0:0.0696:0.3671	.	792	Q53EP0	FND3B_HUMAN	C	792	ENSP00000411242:S792C;ENSP00000338523:S792C;ENSP00000389094:S792C	ENSP00000338523:S792C	S	+	1	0	FNDC3B	173547705	1.000000	0.71417	0.140000	0.22221	0.895000	0.52256	1.823000	0.39062	0.499000	0.27970	0.533000	0.62120	AGT	.	.	.	none		0.403	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763	
RNF168	165918	hgsc.bcm.edu	37	3	196215554	196215554	+	Splice_Site	SNP	G	G	T	rs144091604		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr3:196215554G>T	ENST00000318037.3	-	2	896	c.302C>A	c.(301-303)gCt>gAt	p.A101D		NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	101					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		ATAGTCATCAGCTATTTCATA	0.308																																					p.A101D		Atlas-SNP	.											.	RNF168	49	.	0			c.C302A						PASS	.						64.0	67.0	66.0					3																	196215554		2203	4300	6503	SO:0001630	splice_region_variant	165918	exon2			TCATCAGCTATTT	AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"""RING-type (C3HC4) zinc fingers"""	26661	protein-coding gene	gene with protein product		612688	"""ring finger protein 168"""			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.302-1C>A	chr3.hg19:g.196215554G>T		223.0	0.0	.		249.0	106.0	.	NM_152617	Q8NA67|Q96NS4	Missense_Mutation	SNP	ENST00000318037.3	hg19	CCDS3317.1	.	.	.	.	.	.	.	.	.	.	G	6.047	0.377061	0.11466	.	.	ENSG00000163961	ENST00000318037	T	0.08102	3.13	5.75	-1.81	0.07882	.	0.268702	0.26130	N	0.026166	T	0.05364	0.0142	L	0.40543	1.245	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39961	-0.9588	10	0.20046	T	0.44	.	5.8089	0.18456	0.3866:0.3711:0.2423:0.0	.	101	Q8IYW5	RN168_HUMAN	D	101	ENSP00000320898:A101D	ENSP00000320898:A101D	A	-	2	0	RNF168	197699951	1.000000	0.71417	0.021000	0.16686	0.172000	0.22775	0.859000	0.27858	-0.536000	0.06298	-0.225000	0.12378	GCT	.	G|1.000;A|0.000	.	alt		0.308	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617	Missense_Mutation
WDFY3	23001	hgsc.bcm.edu	37	4	85598373	85598374	+	Missense_Mutation	DNP	CA	CA	AG			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr4:85598373_85598374CA>AG	ENST00000295888.4	-	67	10842_10843	c.10435_10436TG>CT	c.(10435-10437)TGt>CTt	p.C3479L	WDFY3_ENST00000322366.6_Missense_Mutation_p.C3462L	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	3479	Interaction with ATG5.|Interaction with SQSTM1.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GAGCTGACCACAGTTCCTGCAA	0.45																																					p.C3479F|p.C3479R		Atlas-SNP	.											.	WDFY3	314	.	0			c.G10436T|c.T10435C						PASS	.																																			SO:0001583	missense	23001	exon67			TGACCACAGTTCC|GACCACAGTTCCT	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.10435_10436delinsAG	chr4.hg19:g.85598373_85598374delinsAG	ENSP00000295888:p.Cys3479Leu	127.0	0.0	.		154.0|155.0	69.0|71.0	.	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1																																																																																			.	.	.	none		0.450	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
ADH6	130	hgsc.bcm.edu	37	4	100128709	100128709	+	Missense_Mutation	SNP	G	G	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr4:100128709G>T	ENST00000237653.7	-	7	1242	c.858C>A	c.(856-858)agC>agA	p.S286R	ADH6_ENST00000394897.1_Intron|RP11-696N14.1_ENST00000500358.2_RNA|ADH6_ENST00000394899.2_Missense_Mutation_p.S286R|ADH6_ENST00000407820.2_Missense_Mutation_p.S77R|ADH6_ENST00000504257.1_5'Flank|RP11-696N14.1_ENST00000506160.1_RNA|RP11-696N14.1_ENST00000506454.1_RNA	NM_000672.3	NP_000663	P28332	ADH6_HUMAN	alcohol dehydrogenase 6 (class V)	286					ethanol oxidation (GO:0006069)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|ethanol binding (GO:0035276)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)	20				OV - Ovarian serous cystadenocarcinoma(123;3.58e-08)	Abacavir(DB01048)	AGACCCCATAGCTCTCATTGC	0.463																																					p.S286R		Atlas-SNP	.											.	ADH6	74	.	0			c.C858A						PASS	.						108.0	103.0	105.0					4																	100128709		2203	4300	6503	SO:0001583	missense	130	exon7			CCCATAGCTCTCA	AK092768	CCDS3647.1, CCDS43255.1	4q23	2008-02-05			ENSG00000172955	ENSG00000172955	1.1.1.1	"""Alcohol dehydrogenases"""	255	protein-coding gene	gene with protein product		103735				1881901	Standard	NM_000672		Approved	ADH-5	uc003huo.2	P28332	OTTHUMG00000131024	ENST00000237653.7:c.858C>A	chr4.hg19:g.100128709G>T	ENSP00000237653:p.Ser286Arg	127.0	0.0	.		150.0	61.0	.	NM_000672	B3KS45|Q58F53	Missense_Mutation	SNP	ENST00000237653.7	hg19	CCDS3647.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.328806	0.24167	.	.	ENSG00000172955	ENST00000394899;ENST00000407820;ENST00000237653;ENST00000508558	T;T;T;T	0.06528	3.29;3.29;3.29;3.29	3.8	0.95	0.19572	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.328356	0.36703	N	0.002444	T	0.08802	0.0218	L	0.28740	0.885	0.09310	N	1	P;P;D	0.56746	0.908;0.94;0.977	P;P;P	0.58873	0.752;0.656;0.847	T	0.14117	-1.0484	10	0.87932	D	0	-9.2534	4.2097	0.10505	0.1775:0.0:0.5047:0.3178	.	163;286;286	B4DPD8;P28332;P28332-2	.;ADH6_HUMAN;.	R	286;77;286;222	ENSP00000378359:S286R;ENSP00000384997:S77R;ENSP00000237653:S286R;ENSP00000426187:S222R	ENSP00000237653:S286R	S	-	3	2	ADH6	100347732	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.031000	0.12287	0.201000	0.20466	-0.251000	0.11542	AGC	.	.	.	none		0.463	ADH6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253665.1	NM_000672	
SLC12A7	10723	hgsc.bcm.edu	37	5	1087135	1087135	+	Silent	SNP	G	G	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:1087135G>A	ENST00000264930.5	-	6	601	c.558C>T	c.(556-558)taC>taT	p.Y186Y		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	186					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	ATATCATGTAGTAGGACCCGC	0.637																																					p.Y186Y		Atlas-SNP	.											.	SLC12A7	97	.	0			c.C558T						PASS	.						23.0	24.0	24.0					5																	1087135		2199	4298	6497	SO:0001819	synonymous_variant	10723	exon6			CATGTAGTAGGAC	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.558C>T	chr5.hg19:g.1087135G>A		144.0	0.0	.		180.0	88.0	.	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	hg19	CCDS34129.1																																																																																			.	.	.	none		0.637	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
C5orf49	134121	hgsc.bcm.edu	37	5	7831994	7831994	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:7831994T>A	ENST00000399810.2	-	3	881	c.413A>T	c.(412-414)gAa>gTa	p.E138V	C5orf49_ENST00000509627.1_Missense_Mutation_p.E136V	NM_001089584.2	NP_001083053.1	A4QMS7	CE049_HUMAN	chromosome 5 open reading frame 49	138										large_intestine(3)|lung(5)|skin(1)	9						AAAGCCGGGTTCCTTGAGGCT	0.587																																					p.E138V		Atlas-SNP	.											.	C5orf49	27	.	0			c.A413T						PASS	.						109.0	117.0	115.0					5																	7831994		2013	4171	6184	SO:0001583	missense	134121	exon3			CCGGGTTCCTTGA		CCDS43300.1	5p15.31	2008-07-16			ENSG00000215217	ENSG00000215217			27028	protein-coding gene	gene with protein product						12477932	Standard	NM_001089584		Approved	LOC134121	uc003jea.5	A4QMS7	OTTHUMG00000161897	ENST00000399810.2:c.413A>T	chr5.hg19:g.7831994T>A	ENSP00000382708:p.Glu138Val	83.0	0.0	.		87.0	32.0	.	NM_001089584		Missense_Mutation	SNP	ENST00000399810.2	hg19	CCDS43300.1	.	.	.	.	.	.	.	.	.	.	T	3.625	-0.076646	0.07184	.	.	ENSG00000215217	ENST00000399810;ENST00000509627	T;T	0.26067	1.76;1.76	5.0	-9.72	0.00515	.	.	.	.	.	T	0.14787	0.0357	L	0.29908	0.895	0.09310	N	1	B	0.15473	0.013	B	0.13407	0.009	T	0.28364	-1.0046	9	0.36615	T	0.2	-10.2664	11.0233	0.47730	0.0:0.237:0.1945:0.5685	.	138	A4QMS7	CE049_HUMAN	V	138;136	ENSP00000382708:E138V;ENSP00000426019:E136V	ENSP00000382708:E138V	E	-	2	0	C5orf49	7884994	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-2.342000	0.01099	-1.768000	0.01298	-1.349000	0.01238	GAA	.	.	.	none		0.587	C5orf49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366322.1	NM_001089584	
RAI14	26064	hgsc.bcm.edu	37	5	34688329	34688329	+	Intron	SNP	G	G	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:34688329G>A	ENST00000265109.3	+	2	323				RAI14_ENST00000503673.1_Intron|RAI14_ENST00000428746.2_Intron|RAI14_ENST00000506376.1_Intron|RAI14_ENST00000515799.1_Silent_p.P7P|RAI14_ENST00000512629.1_Intron	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					CATATCTCCCGTGGCTTTCAG	0.448																																					p.P7P		Atlas-SNP	.											.	RAI14	100	.	0			c.G21A						PASS	.						98.0	85.0	89.0					5																	34688329		692	1591	2283	SO:0001627	intron_variant	26064	exon4			TCTCCCGTGGCTT	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"""Ankyrin repeat domain containing"""	14873	protein-coding gene	gene with protein product	"""novel retinal pigment epithelial"""	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.36+1269G>A	chr5.hg19:g.34688329G>A		139.0	0.0	.		155.0	54.0	.	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Silent	SNP	ENST00000265109.3	hg19	CCDS34142.1																																																																																			.	.	.	none		0.448	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
WDR41	55255	hgsc.bcm.edu	37	5	76732151	76732151	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:76732151C>T	ENST00000296679.4	-	12	1537	c.1162G>A	c.(1162-1164)Gaa>Aaa	p.E388K	WDR41_ENST00000512033.1_5'Flank|WDR41_ENST00000414719.2_Missense_Mutation_p.E134K|WDR41_ENST00000507029.1_Missense_Mutation_p.E333K	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	388						lysosomal membrane (GO:0005765)				NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)	14		all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40)		GTAGCATTTTCTTGCTGCTTT	0.393																																					p.E388K		Atlas-SNP	.											.	WDR41	29	.	0			c.G1162A						PASS	.						174.0	149.0	158.0					5																	76732151		2203	4300	6503	SO:0001583	missense	55255	exon12			CATTTTCTTGCTG	AF115511	CCDS4038.1	5q14	2013-01-09			ENSG00000164253	ENSG00000164253		"""WD repeat domain containing"""	25601	protein-coding gene	gene with protein product						12477932	Standard	NM_018268		Approved	FLJ10904	uc003kff.1	Q9HAD4	OTTHUMG00000102169	ENST00000296679.4:c.1162G>A	chr5.hg19:g.76732151C>T	ENSP00000296679:p.Glu388Lys	127.0	0.0	.		114.0	55.0	.	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Missense_Mutation	SNP	ENST00000296679.4	hg19	CCDS4038.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.049649	0.55218	.	.	ENSG00000164253	ENST00000296679;ENST00000414719;ENST00000515253;ENST00000507029	T;T;T;T	0.51071	0.73;1.54;0.72;1.98	5.65	5.65	0.86999	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.224635	0.45606	D	0.000357	T	0.52224	0.1721	L	0.32530	0.975	0.58432	D	0.999996	D;D;D	0.58268	0.982;0.982;0.982	P;P;P	0.53760	0.664;0.664;0.734	T	0.41520	-0.9504	9	.	.	.	-26.7881	19.7233	0.96151	0.0:1.0:0.0:0.0	.	333;134;388	B4DT55;B4E2L4;Q9HAD4	.;.;WDR41_HUMAN	K	388;134;323;333	ENSP00000296679:E388K;ENSP00000392931:E134K;ENSP00000426499:E323K;ENSP00000424287:E333K	.	E	-	1	0	WDR41	76767907	1.000000	0.71417	0.994000	0.49952	0.210000	0.24377	6.532000	0.73825	2.653000	0.90120	0.563000	0.77884	GAA	.	.	.	none		0.393	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268	
MSH3	4437	hgsc.bcm.edu	37	5	79950745	79950745	+	Missense_Mutation	SNP	C	C	G	rs144629981|rs3045983|rs557874766	byFrequency	TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:79950745C>G	ENST00000265081.6	+	1	279	c.199C>G	c.(199-201)Cca>Gca	p.P67A	DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000504396.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	67					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		CCCAGCGCCCCCAGCTCCCGC	0.731								Mismatch excision repair (MMR)					C|||	1091	0.217851	0.2678	0.1916	5008	,	,		6483	0.0476		0.2356	False		,,,				2504	0.3262				p.P67A	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											MSH3,NS,carcinoma,0,1	MSH3	129	.	0			c.C199G						PASS	.						3.0	4.0	3.0					5																	79950745		1702	3410	5112	SO:0001583	missense	4437	exon1			GCGCCCCCAGCTC	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.199C>G	chr5.hg19:g.79950745C>G	ENSP00000265081:p.Pro67Ala	51.0	0.0	.		79.0	12.0	.	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	hg19	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	C	6.333	0.429466	0.11987	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.85484	-1.99	.	.	.	.	.	.	.	.	T	0.70150	0.3191	N	0.19112	0.55	0.19945	N	0.999946	B	0.18741	0.03	B	0.17098	0.017	T	0.53507	-0.8429	6	.	.	.	0.6693	.	.	.	.	67	P20585	MSH3_HUMAN	A	67;58	ENSP00000265081:P67A	.	P	+	1	0	MSH3	79986501	0.560000	0.26570	0.857000	0.33713	0.119000	0.20118	0.055000	0.14229	0.064000	0.16427	0.064000	0.15345	CCA	.	.	.	none		0.731	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	
PCDHA12	56137	hgsc.bcm.edu	37	5	140256290	140256290	+	Silent	SNP	C	C	T	rs369536692		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:140256290C>T	ENST00000398631.2	+	1	1233	c.1233C>T	c.(1231-1233)agC>agT	p.S411S	PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	411	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S411S(1)		NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTGGACAGCGCCCTGGACC	0.607													.|||	1	0.000199681	0.0008	0.0	5008	,	,		19945	0.0		0.0	False		,,,				2504	0.0				p.S411S	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,NS,NS,0,1	PCDHA12	196	.	1	Substitution - coding silent(1)	NS(1)	c.C1233T						PASS	.	C	,,,,,,,,,,,,,,,	5,4401	9.9+/-24.2	0,5,2198	196.0	189.0	192.0		,,,1233,,,,,,,,,,,,1233	0.6	0.0	5		192	0,8600		0,0,4300	no	intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031864.1	,,,,,,,,,,,,,,,	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	,,,,,,,,,,,,,,,	,,,411/942,,,,,,,,,,,,411/793	140256290	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	56137	exon1			GGACAGCGCCCTG	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"""Cadherins / Protocadherins : Clustered"""	8666	other	complex locus constituent	"""KIAA0345-like 2"""	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1233C>T	chr5.hg19:g.140256290C>T		163.0	0.0	.		153.0	72.0	.	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	hg19	CCDS47285.1																																																																																			.	.	.	weak		0.607	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
NDST1	3340	hgsc.bcm.edu	37	5	149927825	149927825	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:149927825C>T	ENST00000261797.6	+	12	2693	c.2191C>T	c.(2191-2193)Cat>Tat	p.H731Y	NDST1_ENST00000523767.1_Intron	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	731	Heparan sulfate N-sulfotransferase 1.				carbohydrate metabolic process (GO:0005975)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|midbrain development (GO:0030901)|polysaccharide biosynthetic process (GO:0000271)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	34		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTACACCTTCCATGAGGTGAT	0.617																																					p.H731Y		Atlas-SNP	.											.	NDST1	79	.	0			c.C2191T						PASS	.						88.0	61.0	70.0					5																	149927825		2203	4300	6503	SO:0001583	missense	3340	exon12			ACCTTCCATGAGG	U18918	CCDS34277.1, CCDS75358.1	5q33.1	2008-02-05				ENSG00000070614		"""Sulfotransferases, membrane-bound"""	7680	protein-coding gene	gene with protein product		600853		HSST		7601448, 9230113	Standard	NM_001543		Approved	NST1	uc003lsk.4	P52848		ENST00000261797.6:c.2191C>T	chr5.hg19:g.149927825C>T	ENSP00000261797:p.His731Tyr	85.0	0.0	.		92.0	47.0	.	NM_001543	Q96E57	Missense_Mutation	SNP	ENST00000261797.6	hg19	CCDS34277.1	.	.	.	.	.	.	.	.	.	.	C	9.808	1.182455	0.21870	.	.	ENSG00000070614	ENST00000261797	D	0.81579	-1.51	4.91	4.91	0.64330	Sulfotransferase domain (1);	0.136269	0.64402	D	0.000002	T	0.56381	0.1981	N	0.01789	-0.72	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.60125	-0.7324	10	0.02654	T	1	.	18.4857	0.90828	0.0:1.0:0.0:0.0	.	731	P52848	NDST1_HUMAN	Y	731	ENSP00000261797:H731Y	ENSP00000261797:H731Y	H	+	1	0	NDST1	149908018	1.000000	0.71417	0.998000	0.56505	0.929000	0.56500	2.653000	0.46691	2.434000	0.82447	0.655000	0.94253	CAT	.	.	.	none		0.617	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543	
TNIP1	10318	hgsc.bcm.edu	37	5	150443286	150443286	+	Silent	SNP	C	C	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:150443286C>T	ENST00000389378.2	-	3	747	c.159G>A	c.(157-159)caG>caA	p.Q53Q	TNIP1_ENST00000523338.1_Silent_p.Q53Q|TNIP1_ENST00000315050.7_Silent_p.Q53Q|TNIP1_ENST00000522226.1_Silent_p.Q53Q|TNIP1_ENST00000521591.1_Silent_p.Q53Q|TNIP1_ENST00000523200.1_Silent_p.Q53Q|TNIP1_ENST00000524280.1_Silent_p.Q53Q|TNIP1_ENST00000518977.1_Silent_p.Q53Q|TNIP1_ENST00000520931.1_5'UTR	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1	53					defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCGCTTCCATCTGGGACTCTT	0.587																																					p.Q53Q		Atlas-SNP	.											.	TNIP1	51	.	0			c.G159A						PASS	.						71.0	74.0	73.0					5																	150443286		2203	4300	6503	SO:0001819	synonymous_variant	10318	exon3			TTCCATCTGGGAC	AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"""virion-associated nuclear-shuttling protein"", ""Nef-associated factor 1 SNP"""	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025		ENST00000389378.2:c.159G>A	chr5.hg19:g.150443286C>T		75.0	0.0	.		64.0	20.0	.	NM_001252385	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Silent	SNP	ENST00000389378.2	hg19	CCDS34280.1																																																																																			.	.	.	none		0.587	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058	
PKHD1	5314	hgsc.bcm.edu	37	6	51613145	51613145	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr6:51613145T>A	ENST00000371117.3	-	58	9544	c.9269A>T	c.(9268-9270)aAc>aTc	p.N3090I	PKHD1_ENST00000340994.4_Missense_Mutation_p.N3090I	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3090					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GCCATGGAGGTTGATGTCCTT	0.512																																					p.N3090I		Atlas-SNP	.											.	PKHD1	927	.	0			c.A9269T						PASS	.						217.0	188.0	198.0					6																	51613145		2203	4300	6503	SO:0001583	missense	5314	exon58			TGGAGGTTGATGT	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.9269A>T	chr6.hg19:g.51613145T>A	ENSP00000360158:p.Asn3090Ile	95.0	0.0	.		106.0	47.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	0.870	-0.732173	0.03135	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.79653	-1.29;-1.19	5.72	-11.4	0.00090	Pectin lyase fold/virulence factor (1);	1.979650	0.02080	N	0.052295	T	0.33206	0.0855	N	0.17723	0.515	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.12156	0.004;0.001;0.007	T	0.35176	-0.9799	10	0.18710	T	0.47	.	2.4497	0.04515	0.2549:0.1962:0.4045:0.1445	.	3090;3090;3090	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	I	3090	ENSP00000360158:N3090I;ENSP00000341097:N3090I	ENSP00000341097:N3090I	N	-	2	0	PKHD1	51721104	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.765000	0.01799	-1.898000	0.01100	-0.313000	0.08912	AAC	.	.	.	none		0.512	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
EIF2AK1	27102	hgsc.bcm.edu	37	7	6068606	6068606	+	Missense_Mutation	SNP	G	G	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:6068606G>C	ENST00000199389.6	-	12	1536	c.1390C>G	c.(1390-1392)Ctg>Gtg	p.L464V	EIF2AK1_ENST00000536084.1_Missense_Mutation_p.L340V|ANKRD61_ENST00000409061.1_5'Flank	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	464	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		GTGCAGGCCAGACCAAAGTCT	0.383																																					p.L464V		Atlas-SNP	.											.	EIF2AK1	76	.	0			c.C1390G						PASS	.						100.0	96.0	97.0					7																	6068606		2203	4300	6503	SO:0001583	missense	27102	exon12			AGGCCAGACCAAA	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"""heme regulated initiation factor 2 alpha kinase"""	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.1390C>G	chr7.hg19:g.6068606G>C	ENSP00000199389:p.Leu464Val	107.0	0.0	.		108.0	43.0	.	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Missense_Mutation	SNP	ENST00000199389.6	hg19	CCDS5345.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.067812	0.55539	.	.	ENSG00000086232	ENST00000199389;ENST00000536084;ENST00000426957	T;T	0.33438	1.54;1.41	4.85	3.06	0.35304	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000005	T	0.51312	0.1667	M	0.75777	2.31	0.47511	D	0.999445	D;D;P	0.89917	1.0;0.998;0.937	D;D;P	0.80764	0.994;0.924;0.85	T	0.50440	-0.8828	10	0.87932	D	0	-13.4813	9.2919	0.37791	0.2527:0.0:0.7473:0.0	.	340;463;464	B4DIP4;Q9BQI3-2;Q9BQI3	.;.;E2AK1_HUMAN	V	464;340;91	ENSP00000199389:L464V;ENSP00000445784:L340V	ENSP00000199389:L464V	L	-	1	2	EIF2AK1	6035132	0.991000	0.36638	0.999000	0.59377	0.991000	0.79684	2.311000	0.43717	0.486000	0.27676	-0.266000	0.10368	CTG	.	.	.	none		0.383	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413	
HOXA11	3207	hgsc.bcm.edu	37	7	27224287	27224287	+	Silent	SNP	G	G	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:27224287G>A	ENST00000006015.3	-	1	548	c.477C>T	c.(475-477)taC>taT	p.Y159Y	RP1-170O19.14_ENST00000523331.1_lincRNA|HOXA11-AS_ENST00000522674.1_RNA|HOXA11-AS_ENST00000522863.1_RNA|HOXA11-AS_ENST00000520395.1_RNA|HOXA11-AS_ENST00000520360.1_RNA	NM_005523.5	NP_005514.1	P31270	HXA11_HUMAN	homeobox A11	159					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|developmental growth (GO:0048589)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal joint morphogenesis (GO:0060272)|male gonad development (GO:0008584)|mesodermal cell fate specification (GO:0007501)|metanephros development (GO:0001656)|multicellular organismal development (GO:0007275)|organ induction (GO:0001759)|positive regulation of cell development (GO:0010720)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)	nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	16						TGTCCCCGGGGTAGTCGGAGG	0.697			T	NUP98	CML																																p.Y159Y		Atlas-SNP	.		Dom	yes		7	7p15-p14.2	3207	homeo box A11		L	.	HOXA11	29	.	0			c.C477T						PASS	.						13.0	15.0	14.0					7																	27224287		2177	4275	6452	SO:0001819	synonymous_variant	3207	exon1			CCCGGGGTAGTCG		CCDS5411.1	7p15.2	2014-09-17	2005-12-22		ENSG00000005073	ENSG00000005073		"""Homeoboxes / ANTP class : HOXL subclass"""	5101	protein-coding gene	gene with protein product		142958	"""homeo box A11"""	HOX1I, HOX1		1973146, 1358459	Standard	NM_005523		Approved		uc003syx.3	P31270	OTTHUMG00000023437	ENST00000006015.3:c.477C>T	chr7.hg19:g.27224287G>A		132.0	0.0	.		139.0	53.0	.	NM_005523	A4D190	Silent	SNP	ENST00000006015.3	hg19	CCDS5411.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.135477	0.37728	.	.	ENSG00000005073	ENST00000517402	.	.	.	5.25	4.36	0.52297	.	.	.	.	.	T	0.56381	0.1981	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53899	-0.8373	4	.	.	.	.	6.6845	0.23138	0.2056:0.1362:0.6583:0.0	.	.	.	.	I	129	.	.	T	-	2	0	HOXA11	27190812	0.993000	0.37304	1.000000	0.80357	0.990000	0.78478	1.028000	0.30128	2.436000	0.82500	0.655000	0.94253	ACC	.	.	.	none		0.697	HOXA11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358754.1		
CALCR	799	hgsc.bcm.edu	37	7	93055856	93055856	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:93055856A>T	ENST00000394441.1	-	13	1552	c.1237T>A	c.(1237-1239)Tgg>Agg	p.W413R	CALCR_ENST00000359558.2_Missense_Mutation_p.W447R|CALCR_ENST00000360249.4_Missense_Mutation_p.W429R|CALCR_ENST00000421592.1_Missense_Mutation_p.W429R|CALCR_ENST00000426151.1_Missense_Mutation_p.W413R	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	447					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	CGCTGGTTCCACTGAATTTTG	0.542																																					p.W447R		Atlas-SNP	.											.	CALCR	200	.	0			c.T1339A						PASS	.						46.0	51.0	50.0					7																	93055856		2203	4300	6503	SO:0001583	missense	799	exon16			GGTTCCACTGAAT	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"""GPCR / Class B : Calcitonin receptors"""	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.1237T>A	chr7.hg19:g.93055856A>T	ENSP00000377959:p.Trp413Arg	97.0	0.0	.		124.0	55.0	.	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Missense_Mutation	SNP	ENST00000394441.1	hg19	CCDS5631.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.937626	0.73557	.	.	ENSG00000004948	ENST00000359558;ENST00000360249;ENST00000421592;ENST00000394441;ENST00000426151	T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02	4.57	4.57	0.56435	.	.	.	.	.	T	0.68659	0.3025	L	0.45228	1.405	0.51482	D	0.999925	D;P	0.71674	0.998;0.613	D;B	0.72075	0.976;0.248	T	0.66106	-0.6006	9	0.33141	T	0.24	.	10.4932	0.44762	1.0:0.0:0.0:0.0	.	447;413	F5H605;A4D1G6	.;.	R	447;429;429;413;413	ENSP00000352561:W447R;ENSP00000353385:W429R;ENSP00000399552:W429R;ENSP00000377959:W413R;ENSP00000389295:W413R	ENSP00000352561:W447R	W	-	1	0	CALCR	92893792	1.000000	0.71417	0.495000	0.27527	0.014000	0.08584	6.514000	0.73746	2.055000	0.61198	0.477000	0.44152	TGG	.	.	.	none		0.542	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742	
AP1S1	1174	hgsc.bcm.edu	37	7	100802348	100802349	+	Missense_Mutation	DNP	GC	GC	CT			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:100802348_100802349GC>CT	ENST00000337619.5	+	4	418_419	c.300_301GC>CT	c.(298-303)gaGCtg>gaCTtg	p.E100D	MIR4653_ENST00000585107.1_RNA	NM_001283.3	NP_001274.1	P61966	AP1S1_HUMAN	adaptor-related protein complex 1, sigma 1 subunit	100					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor-mediated endocytosis (GO:0006898)|regulation of defense response to virus by virus (GO:0050690)|response to virus (GO:0009615)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|coated pit (GO:0005905)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)	protein transporter activity (GO:0008565)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)	8	Lung NSC(181;0.168)|all_lung(186;0.215)					AGGTGTGCGAGCTGGACATCAT	0.559																																					p.E100D|p.L101L		Atlas-SNP	.											.	AP1S1	22	.	0			c.G300C|c.C301T						PASS	.																																			SO:0001583	missense	1174	exon4			GTGCGAGCTGGAC|TGCGAGCTGGACA	AB015319	CCDS47669.1	7q22.1	2014-02-04			ENSG00000106367	ENSG00000106367			559	protein-coding gene	gene with protein product	"""clathrin-associated/assembly/adaptor protein, small 1 (19kD)"", ""clathrin coat assembly protein AP19"", ""sigma1A subunit of AP-1 clathrin adaptor complex"", ""AP-1 complex subunit sigma-1A"", ""sigma1A-adaptin"", ""golgi adaptor HA1/AP1 adaptin sigma-1A subunit"", ""clathrin assembly protein complex 1 sigma-1A small chain"", ""HA1 19 kDa subunit"""	603531	"""erythrokeratodermia variabilis 3 (Kamouraska type)"""	CLAPS1, EKV3		9653655, 9733768, 19057675	Standard	NM_001283		Approved	AP19, SIGMA1A, WUGSC:H_DJ0747G18.2	uc003uxv.4	P61966	OTTHUMG00000157103	Exception_encountered	chr7.hg19:g.100802348_100802349delinsCT	ENSP00000336666:p.Glu100Asp	31.0	0.0	.		46.0|48.0	15.0|16.0	.	NM_001283	B2R5D8|P82267|Q00382|Q53YA7|Q9BTN4|Q9UDW9	Missense_Mutation|Silent	SNP	ENST00000337619.5	hg19	CCDS47669.1																																																																																			.	.	.	none		0.559	AP1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347439.1	NM_001283	
DOCK4	9732	hgsc.bcm.edu	37	7	111535707	111535707	+	Missense_Mutation	SNP	C	C	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:111535707C>A	ENST00000437633.1	-	16	1804	c.1548G>T	c.(1546-1548)agG>agT	p.R516S	DOCK4_ENST00000476846.1_5'UTR|DOCK4_ENST00000428084.1_Missense_Mutation_p.R516S	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	516	DHR-1.				cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				CTGGAAGAGTCCTACCATCTT	0.413																																					p.R516S		Atlas-SNP	.											.	DOCK4	365	.	0			c.G1548T						PASS	.						228.0	209.0	215.0					7																	111535707		2001	4180	6181	SO:0001583	missense	9732	exon16			AAGAGTCCTACCA		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.1548G>T	chr7.hg19:g.111535707C>A	ENSP00000404179:p.Arg516Ser	112.0	0.0	.		173.0	74.0	.	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	hg19	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.45|19.45	3.830388|3.830388	0.71258|0.71258	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000445943|ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250	.|T;T	.|0.14266	.|2.52;2.52	5.88|5.88	4.99|4.99	0.66335|0.66335	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.15955|0.15955	0.0384|0.0384	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.37548	.|0.599;0.599;0.599	.|B;P;B	.|0.45167	.|0.356;0.472;0.356	T|T	0.01065|0.01065	-1.1463|-1.1463	5|10	.|0.44086	.|T	.|0.13	.|.	10.7911|10.7911	0.46434|0.46434	0.0:0.8056:0.0:0.1944|0.0:0.8056:0.0:0.1944	.|.	.|516;516;516	.|Q149N2;Q149N5;Q8N1I0	.|.;.;DOCK4_HUMAN	V|S	504|504;516;516;504;515	.|ENSP00000410746:R516S;ENSP00000404179:R516S	.|ENSP00000345432:R504S	G|R	-|-	2|3	0|2	DOCK4|DOCK4	111322943|111322943	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	1.605000|1.605000	0.36815|0.36815	2.781000|2.781000	0.95711|0.95711	0.591000|0.591000	0.81541|0.81541	GGA|AGG	.	.	.	none		0.413	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	
PRKAG2	51422	hgsc.bcm.edu	37	7	151478467	151478467	+	Missense_Mutation	SNP	T	T	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:151478467T>G	ENST00000287878.4	-	3	741	c.237A>C	c.(235-237)agA>agC	p.R79S	PRKAG2_ENST00000461529.1_5'UTR|PRKAG2_ENST00000392801.2_Missense_Mutation_p.R35S	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	79					ATP biosynthetic process (GO:0006754)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|glycogen metabolic process (GO:0005977)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase activity (GO:0045860)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid metabolic process (GO:0019217)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose import (GO:0046324)|regulation of glycolytic process (GO:0006110)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|phosphorylase kinase regulator activity (GO:0008607)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|upper_aerodigestive_tract(1)	26	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)	Acetylsalicylic acid(DB00945)	GCTGGGGGCCTCTGGAGAAGA	0.642																																					p.R79S		Atlas-SNP	.											.	PRKAG2	86	.	0			c.A237C						PASS	.						13.0	16.0	15.0					7																	151478467		2202	4297	6499	SO:0001583	missense	51422	exon3			GGGGCCTCTGGAG	AF087875	CCDS5928.1, CCDS43683.1, CCDS47752.1	7q35-q36	2014-09-17			ENSG00000106617	ENSG00000106617			9386	protein-coding gene	gene with protein product	"""AMPK gamma2"""	602743				8557660, 8621499	Standard	NM_024429		Approved	AAKG, AAKG2, H91620p, WPWS, CMH6	uc003wkk.3	Q9UGJ0	OTTHUMG00000157324	ENST00000287878.4:c.237A>C	chr7.hg19:g.151478467T>G	ENSP00000287878:p.Arg79Ser	92.0	0.0	.		130.0	54.0	.	NM_016203	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Missense_Mutation	SNP	ENST00000287878.4	hg19	CCDS5928.1	.	.	.	.	.	.	.	.	.	.	T	14.23	2.472139	0.43942	.	.	ENSG00000106617	ENST00000287878;ENST00000392801	D;D	0.90069	-2.29;-2.61	4.6	-0.604	0.11626	.	0.174068	0.43579	D	0.000545	T	0.80513	0.4637	L	0.27053	0.805	0.80722	D	1	P;B	0.46142	0.873;0.099	B;B	0.42361	0.385;0.027	T	0.75668	-0.3238	10	0.59425	D	0.04	.	9.7457	0.40446	0.0:0.3953:0.0:0.6047	.	79;79	Q8NCK6;Q9UGJ0	.;AAKG2_HUMAN	S	79;35	ENSP00000287878:R79S;ENSP00000376549:R35S	ENSP00000287878:R79S	R	-	3	2	PRKAG2	151109400	0.952000	0.32445	0.998000	0.56505	0.938000	0.57974	0.152000	0.16302	-0.121000	0.11787	-0.464000	0.05259	AGA	.	.	.	none		0.642	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203	
CSMD1	64478	hgsc.bcm.edu	37	8	3063031	3063031	+	Missense_Mutation	SNP	T	T	G	rs548826533		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr8:3063031T>G	ENST00000520002.1	-	32	5537	c.4982A>C	c.(4981-4983)gAa>gCa	p.E1661A	CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602723.1_Missense_Mutation_p.E1661A|CSMD1_ENST00000539096.1_Missense_Mutation_p.E1660A|CSMD1_ENST00000400186.3_Missense_Mutation_p.E1661A|CSMD1_ENST00000542608.1_Missense_Mutation_p.E1660A|CSMD1_ENST00000537824.1_Missense_Mutation_p.E1660A|CSMD1_ENST00000602557.1_Missense_Mutation_p.E1661A			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1661	CUB 10. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CTTACCGAATTCCTTTGGTAC	0.383																																					p.E1660A		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A4979C						PASS	.						69.0	66.0	67.0					8																	3063031		1842	4093	5935	SO:0001583	missense	64478	exon31			CCGAATTCCTTTG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.4982A>C	chr8.hg19:g.3063031T>G	ENSP00000430733:p.Glu1661Ala	54.0	0.0	.		67.0	22.0	.	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.03	2.713104	0.48517	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.60171	0.21;0.21;0.21;0.21;0.21	5.28	5.28	0.74379	CUB (5);	0.071868	0.56097	D	0.000031	T	0.66218	0.2767	L	0.31845	0.965	0.58432	D	0.999992	D;P;P	0.69078	0.997;0.537;0.84	D;B;P	0.80764	0.994;0.309;0.557	T	0.66204	-0.5982	10	0.41790	T	0.15	.	15.5029	0.75713	0.0:0.0:0.0:1.0	.	1661;1661;1661	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	A	1661;1661;1523;1660;1660;1660	ENSP00000383047:E1661A;ENSP00000430733:E1661A;ENSP00000441462:E1660A;ENSP00000446243:E1660A;ENSP00000441675:E1660A	ENSP00000320445:E1523A	E	-	2	0	CSMD1	3050438	1.000000	0.71417	0.990000	0.47175	0.474000	0.32979	7.809000	0.86057	2.115000	0.64714	0.533000	0.62120	GAA	.	.	.	none		0.383	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
SPIDR	23514	hgsc.bcm.edu	37	8	48647877	48647877	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr8:48647877A>T	ENST00000297423.4	+	20	2997	c.2613A>T	c.(2611-2613)gaA>gaT	p.E871D	SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000541342.1_Missense_Mutation_p.E801D|SPIDR_ENST00000518060.1_Missense_Mutation_p.K95M|SPIDR_ENST00000518074.1_Missense_Mutation_p.S812C|SPIDR_ENST00000517693.1_Missense_Mutation_p.E346D	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	871					cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)											AGAGCTACGAAGTGAAGAGTG	0.517																																					p.E871D		Atlas-SNP	.											.	KIAA0146	64	.	0			c.A2613T						PASS	.						184.0	195.0	191.0					8																	48647877		1971	4147	6118	SO:0001583	missense	23514	exon20			CTACGAAGTGAAG	AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808			28971	protein-coding gene	gene with protein product		615384	"""KIAA0146"""	KIAA0146		8590280, 23509288	Standard	XM_005251189		Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000297423.4:c.2613A>T	chr8.hg19:g.48647877A>T	ENSP00000297423:p.Glu871Asp	193.0	0.0	.		214.0	90.0	.	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Missense_Mutation	SNP	ENST00000297423.4	hg19	CCDS43737.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	12.91|12.91|12.91	2.078043|2.078043|2.078043	0.36662|0.36662|0.36662	.|.|.	.|.|.	ENSG00000164808|ENSG00000164808|ENSG00000164808	ENST00000297423;ENST00000541342;ENST00000519141;ENST00000517693;ENST00000519362;ENST00000517619|ENST00000518060|ENST00000518074;ENST00000519401	.|.|.	.|.|.	.|.|.	5.73|5.73|5.73	1.97|1.97|1.97	0.26223|0.26223|0.26223	.|.|.	0.109030|.|.	0.64402|.|.	D|.|.	0.000010|.|.	T|T|T	0.58991|0.58991|0.58991	0.2161|0.2161|0.2161	L|L|L	0.40543|0.40543|0.40543	1.245|1.245|1.245	0.35176|0.35176|0.35176	D|D|D	0.771997|0.771997|0.771997	D;D;D;D|.|D	0.89917|.|0.89917	1.0;0.986;1.0;1.0|.|1.0	D;P;D;D|.|D	0.85130|.|0.73380	0.997;0.706;0.997;0.997|.|0.98	T|T|T	0.63310|0.63310|0.63310	-0.6666|-0.6666|-0.6666	9|6|8	0.38643|0.87932|0.40728	T|D|T	0.18|0|0.16	.|.|.	9.6477|9.6477|9.6477	0.39877|0.39877|0.39877	0.6588:0.0:0.3412:0.0|0.6588:0.0:0.3412:0.0|0.6588:0.0:0.3412:0.0	.|.|.	361;376;801;871|.|812	B4DZY2;B4DWT8;B4DFV2;Q14159|.|B4E0Y6	.;.;.;K0146_HUMAN|.|.	D|M|C	871;801;376;346;346;73|95|812;497	.|.|.	ENSP00000297423:E871D|ENSP00000429448:K95M|ENSP00000429487:S812C	E|K|S	+|+|+	3|2|1	2|0|0	KIAA0146|KIAA0146|KIAA0146	48810430|48810430|48810430	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.066000|0.066000|0.066000	0.16364|0.16364|0.16364	0.996000|0.996000|0.996000	0.29719|0.29719|0.29719	0.432000|0.432000|0.432000	0.26286|0.26286|0.26286	-0.558000|-0.558000|-0.558000	0.04189|0.04189|0.04189	GAA|AAG|AGT	.	.	.	none		0.517	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394	
KLHL38	340359	hgsc.bcm.edu	37	8	124659249	124659249	+	Silent	SNP	A	A	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr8:124659249A>G	ENST00000325995.7	-	2	1379	c.1356T>C	c.(1354-1356)taT>taC	p.Y452Y	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	452										breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						TGGAAATGTGATAAACCTGAG	0.438																																					p.Y452Y		Atlas-SNP	.											.	KLHL38	81	.	0			c.T1356C						PASS	.						160.0	154.0	156.0					8																	124659249		1937	4136	6073	SO:0001819	synonymous_variant	340359	exon2			AATGTGATAAACC		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"""Kelch-like"", ""BTB/POZ domain containing"""	34435	protein-coding gene	gene with protein product			"""kelch-like 38 (Drosophila)"""				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.1356T>C	chr8.hg19:g.124659249A>G		118.0	0.0	.		124.0	52.0	.	NM_001081675	A0PK12	Silent	SNP	ENST00000325995.7	hg19	CCDS43766.1																																																																																			.	.	.	none		0.438	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
BICC1	80114	hgsc.bcm.edu	37	10	60560753	60560753	+	Silent	SNP	T	T	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr10:60560753T>C	ENST00000373886.3	+	14	1966	c.1962T>C	c.(1960-1962)tgT>tgC	p.C654C	BICC1_ENST00000263103.1_Silent_p.C280C	NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	654					multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)	cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	44						AGGTTTCCTGTGCCAAAAGGC	0.408																																					p.C654C		Atlas-SNP	.											.	BICC1	121	.	0			c.T1962C						PASS	.						130.0	118.0	122.0					10																	60560753		2203	4300	6503	SO:0001819	synonymous_variant	80114	exon14			TTCCTGTGCCAAA	AK026129	CCDS31206.1	10q21.3	2014-09-17	2014-02-03		ENSG00000122870	ENSG00000122870		"""Sterile alpha motif (SAM) domain containing"""	19351	protein-coding gene	gene with protein product		614295	"""bicaudal C homolog 1 (Drosophila)"""				Standard	XM_005270166		Approved		uc001jki.1	Q9H694	OTTHUMG00000018271	ENST00000373886.3:c.1962T>C	chr10.hg19:g.60560753T>C		115.0	0.0	.		114.0	41.0	.	NM_001080512		Silent	SNP	ENST00000373886.3	hg19	CCDS31206.1																																																																																			.	.	.	none		0.408	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044	
TMEM254	80195	hgsc.bcm.edu	37	10	81838872	81838872	+	Intron	SNP	A	A	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr10:81838872A>T	ENST00000372281.3	+	1	117				TMEM254-AS1_ENST00000432070.2_RNA|TMEM254-AS1_ENST00000448729.2_RNA|TMEM254_ENST00000372274.1_Intron|TMEM254-AS1_ENST00000412298.1_RNA|TMEM254_ENST00000372277.3_Intron|TMEM254_ENST00000372275.1_Intron	NM_001270372.1|NM_025125.3	NP_001257301.1|NP_079401.2	Q8TBM7	TM254_HUMAN	transmembrane protein 254							integral component of membrane (GO:0016021)											CAATGCGGCTACCGCCTATTT	0.632																																					p.T31S		Atlas-SNP	.											.	TMEM254	1	.	0			c.A91T						PASS	.																																			SO:0001627	intron_variant	80195	exon1			GCGGCTACCGCCT	BC022252	CCDS7363.1, CCDS58086.1, CCDS58087.1, CCDS73157.1	10q23.1	2012-11-06	2012-11-06	2012-11-06	ENSG00000133678	ENSG00000133678			25804	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 57"""	C10orf57		14702039	Standard	NM_025125		Approved	FLJ13263, bA369J21.6	uc010qlw.3	Q8TBM7	OTTHUMG00000018602	ENST00000372281.3:c.87+330A>T	chr10.hg19:g.81838872A>T		271.0	0.0	.		308.0	121.0	.	NM_001270368	D3DWC8|Q53HP4|Q5JTC0|Q5JTC1|Q6IA45|Q9H8S6	Missense_Mutation	SNP	ENST00000372281.3	hg19	CCDS7363.1																																																																																			.	.	.	none		0.632	TMEM254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049030.1	NM_025125	
CC2D2B	387707	hgsc.bcm.edu	37	10	97784670	97784670	+	Intron	SNP	T	T	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr10:97784670T>A	ENST00000344386.3	+	8	944				ENTPD1-AS1_ENST00000458228.1_RNA|RP11-690P14.4_ENST00000475252.2_Intron|ENTPD1-AS1_ENST00000452728.1_RNA|CC2D2B_ENST00000410012.2_Splice_Site|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1-AS1_ENST00000454638.1_RNA|ENTPD1-AS1_ENST00000451364.1_RNA|CC2D2B_ENST00000371198.2_Intron|ENTPD1-AS1_ENST00000449197.1_RNA	NM_001001732.3	NP_001001732.2	Q6DHV5	C2D2B_HUMAN	coiled-coil and C2 domain containing 2B											large_intestine(1)|lung(7)|ovary(1)|urinary_tract(1)	10		Colorectal(252;0.158)		Epithelial(162;7.08e-08)|all cancers(201;2.71e-06)		AAGGAATAGGTACTGTGTTTT	0.363																																					.		Atlas-SNP	.											.	CC2D2B	46	.	0			c.839+2T>A						PASS	.						312.0	273.0	285.0					10																	97784670		692	1591	2283	SO:0001627	intron_variant	387707	exon10			AATAGGTACTGTG	BC075861	CCDS41555.1, CCDS53560.1	10q23.33	2008-11-06	2007-10-19	2007-10-19	ENSG00000188649	ENSG00000188649			31666	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 130"""	C10orf130			Standard	NM_001001732		Approved	bA248J23.4	uc010qop.2	Q6DHV5	OTTHUMG00000018820	ENST00000344386.3:c.780+5089T>A	chr10.hg19:g.97784670T>A		153.0	0.0	.		155.0	77.0	.	NM_001159747	A2A3E9|B4DYD4|E9PCC3|Q5VUS0	Splice_Site	SNP	ENST00000344386.3	hg19	CCDS41555.1	.	.	.	.	.	.	.	.	.	.	T	15.03	2.713349	0.48517	.	.	ENSG00000188649	ENST00000451649;ENST00000410012	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3455	0.66658	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CC2D2B	97774660	1.000000	0.71417	0.958000	0.39756	0.348000	0.29142	4.719000	0.61937	2.371000	0.80710	0.533000	0.62120	.	.	.	.	none		0.363	CC2D2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049573.3	NM_001001732	
RRP12	23223	hgsc.bcm.edu	37	10	99141485	99141485	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr10:99141485G>A	ENST00000370992.4	-	11	1418	c.1307C>T	c.(1306-1308)aCg>aTg	p.T436M	RRP12_ENST00000536831.1_Missense_Mutation_p.T154M|RRP12_ENST00000315563.6_Missense_Mutation_p.T336M|RRP12_ENST00000414986.1_Missense_Mutation_p.T375M	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	436						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.T436M(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		GAGGCTCTGCGTAGCAGCAGT	0.597																																					p.T436M		Atlas-SNP	.											RRP12,colon,carcinoma,+1,1	RRP12	97	.	1	Substitution - Missense(1)	ovary(1)	c.C1307T						PASS	.						69.0	58.0	62.0					10																	99141485		2203	4300	6503	SO:0001583	missense	23223	exon11			CTCTGCGTAGCAG		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.1307C>T	chr10.hg19:g.99141485G>A	ENSP00000360031:p.Thr436Met	293.0	0.0	.		363.0	173.0	.	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	hg19	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	G	19.78	3.891743	0.72524	.	.	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986;ENST00000536831	T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13	5.7	5.7	0.88788	Armadillo-like helical (1);Armadillo-type fold (1);	0.223488	0.48767	D	0.000171	T	0.73337	0.3574	L	0.56769	1.78	0.42336	D	0.992316	D;B;D;D	0.76494	0.999;0.139;0.998;0.998	P;B;P;P	0.59424	0.8;0.052;0.857;0.724	T	0.67699	-0.5603	10	0.22706	T	0.39	-17.4342	19.8221	0.96602	0.0:0.0:1.0:0.0	.	375;336;154;436	E9PCK7;Q5JTH9-2;F5H456;Q5JTH9	.;.;.;RRP12_HUMAN	M	436;336;375;154	ENSP00000360031:T436M;ENSP00000324315:T336M;ENSP00000414863:T375M;ENSP00000446184:T154M	ENSP00000324315:T336M	T	-	2	0	RRP12	99131475	1.000000	0.71417	0.998000	0.56505	0.242000	0.25591	9.563000	0.98148	2.684000	0.91462	0.563000	0.77884	ACG	.	.	.	none		0.597	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
PSTK	118672	hgsc.bcm.edu	37	10	124740027	124740027	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr10:124740027G>A	ENST00000368887.3	+	1	472	c.32G>A	c.(31-33)gGc>gAc	p.G11D	PSTK_ENST00000405485.1_Missense_Mutation_p.G11D	NM_153336.2	NP_699167.2	Q8IV42	PSTK_HUMAN	phosphoseryl-tRNA kinase	11					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|tRNA binding (GO:0000049)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|skin(1)|stomach(2)	13		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0725)		AGAGGAACCGGCAGCGACGGG	0.701											OREG0020597	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G11D		Atlas-SNP	.											.	PSTK	34	.	0			c.G32A						PASS	.						18.0	21.0	20.0					10																	124740027		2194	4282	6476	SO:0001583	missense	118672	exon1			GAACCGGCAGCGA	AK127173	CCDS7633.1	10q26.13	2007-04-17	2007-04-17	2007-04-17	ENSG00000179988	ENSG00000179988			28578	protein-coding gene	gene with protein product		611310	"""chromosome 10 open reading frame 89"""	C10orf89		15317934	Standard	NM_153336		Approved	MGC35392	uc001lgy.1	Q8IV42	OTTHUMG00000019191	ENST00000368887.3:c.32G>A	chr10.hg19:g.124740027G>A	ENSP00000357882:p.Gly11Asp	142.0	0.0	.	1536	165.0	80.0	.	NM_153336	Q6ZSS9	Missense_Mutation	SNP	ENST00000368887.3	hg19	CCDS7633.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.314|8.314	0.822752|0.822752	0.16678|0.16678	.|.	.|.	ENSG00000179988|ENSG00000179988	ENST00000406217|ENST00000368887;ENST00000405485	.|T;T	.|0.43688	.|0.94;0.98	3.99|3.99	-3.11|-3.11	0.05299|0.05299	.|.	.|1.236170	.|0.06046	.|N	.|0.655665	T|T	0.27169|0.27169	0.0666|0.0666	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	.|B	.|0.06786	.|0.001	.|B	.|0.08055	.|0.003	T|T	0.17715|0.17715	-1.0360|-1.0360	5|10	.|0.22109	.|T	.|0.4	-0.0124|-0.0124	5.4915|5.4915	0.16779|0.16779	0.5242:0.1624:0.3135:0.0|0.5242:0.1624:0.3135:0.0	.|.	.|11	.|Q8IV42	.|PSTK_HUMAN	T|D	12|11	.|ENSP00000357882:G11D;ENSP00000384764:G11D	.|ENSP00000357882:G11D	A|G	+|+	1|2	0|0	PSTK|PSTK	124730017|124730017	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.038000|0.038000	0.13279|0.13279	-0.052000|-0.052000	0.11865|0.11865	-1.010000|-1.010000	0.03396|0.03396	0.655000|0.655000	0.94253|0.94253	GCA|GGC	.	.	.	none		0.701	PSTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050811.1	NM_153336	
OR51S1	119692	hgsc.bcm.edu	37	11	4869827	4869827	+	Silent	SNP	G	G	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:4869827G>A	ENST00000322101.2	-	1	687	c.612C>T	c.(610-612)gcC>gcT	p.A204A	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	204						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		ATAGGCTGTAGGCTGCACCCC	0.532																																					p.A204A		Atlas-SNP	.											.	OR51S1	83	.	0			c.C612T						PASS	.						77.0	83.0	81.0					11																	4869827		2201	4298	6499	SO:0001819	synonymous_variant	119692	exon1			GCTGTAGGCTGCA	AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"""GPCR / Class A : Olfactory receptors"""	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.612C>T	chr11.hg19:g.4869827G>A		140.0	0.0	.		176.0	64.0	.	NM_001004758	B9EGZ1|Q6IFI2	Silent	SNP	ENST00000322101.2	hg19	CCDS31362.1																																																																																			.	.	.	none		0.532	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758	
USP47	55031	hgsc.bcm.edu	37	11	11924349	11924349	+	Silent	SNP	A	A	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:11924349A>G	ENST00000399455.2	+	7	861	c.741A>G	c.(739-741)aaA>aaG	p.K247K	USP47_ENST00000339865.5_Silent_p.K159K|USP47_ENST00000527733.1_Silent_p.K227K|USP47_ENST00000539466.1_5'UTR	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	247	USP.				base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		AAACCAGCAAAAAGAGAGCAA	0.348																																					p.K159K		Atlas-SNP	.											.	USP47	91	.	0			c.A477G						PASS	.						125.0	118.0	120.0					11																	11924349		1818	4070	5888	SO:0001819	synonymous_variant	55031	exon5			CAGCAAAAAGAGA	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"""Ubiquitin-specific peptidases"""	20076	protein-coding gene	gene with protein product		614460	"""Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)"", ""ubiquitin specific protease 47"""			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.741A>G	chr11.hg19:g.11924349A>G		484.0	0.0	.		594.0	252.0	.	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Silent	SNP	ENST00000399455.2	hg19																																																																																				.	.	.	none		0.348	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944	
GLYATL1	92292	hgsc.bcm.edu	37	11	58722267	58722267	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:58722267T>C	ENST00000317391.4	+	6	551	c.211T>C	c.(211-213)Tac>Cac	p.Y71H	GLYATL1_ENST00000300079.5_Missense_Mutation_p.Y102H|RP11-142C4.6_ENST00000533954.1_RNA	NM_001220494.1	NP_001207423.1	Q969I3	GLYL1_HUMAN	glycine-N-acyltransferase-like 1	71						mitochondrion (GO:0005739)	glutamine N-acyltransferase activity (GO:0047946)|glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|skin(4)|urinary_tract(1)	34					Glycine(DB00145)	CATGGATTCATACACAAACGT	0.368																																					p.Y102H		Atlas-SNP	.											.	GLYATL1	89	.	0			c.T304C						PASS	.						94.0	88.0	90.0					11																	58722267		2201	4295	6496	SO:0001583	missense	92292	exon5			GATTCATACACAA	AK091965	CCDS31556.1, CCDS55768.1	11q12.1	2014-08-12			ENSG00000166840	ENSG00000166840			30519	protein-coding gene	gene with protein product		614761				12477932	Standard	NM_080661		Approved	MGC15397, FLJ34646	uc001nnh.2	Q969I3	OTTHUMG00000167221	ENST00000317391.4:c.211T>C	chr11.hg19:g.58722267T>C	ENSP00000322223:p.Tyr71His	283.0	0.0	.		294.0	119.0	.	NM_080661	A6NDT0|Q7Z510|Q8NAW8	Missense_Mutation	SNP	ENST00000317391.4	hg19	CCDS55768.1	.	.	.	.	.	.	.	.	.	.	.	11.71	1.719568	0.30503	.	.	ENSG00000166840	ENST00000526351;ENST00000317391;ENST00000532726;ENST00000300079	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	2.37	1.19	0.21007	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	0.782658	0.10400	U	0.679322	T	0.39489	0.1080	M	0.67397	2.05	0.09310	N	0.999999	D;D	0.67145	0.995;0.996	P;P	0.61722	0.829;0.893	T	0.16778	-1.0391	9	.	.	.	.	4.1384	0.10181	0.0:0.1862:0.0:0.8138	.	102;71	Q969I3-2;Q969I3	.;GLYL1_HUMAN	H	94;71;71;102	ENSP00000434652:Y94H;ENSP00000322223:Y71H;ENSP00000436116:Y71H;ENSP00000300079:Y102H	.	Y	+	1	0	GLYATL1	58478843	0.166000	0.22962	0.001000	0.08648	0.037000	0.13140	1.220000	0.32491	0.172000	0.19760	0.164000	0.16699	TAC	.	.	.	none		0.368	GLYATL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393783.1	NM_080661	
WDR74	54663	hgsc.bcm.edu	37	11	62600570	62600570	+	Missense_Mutation	SNP	C	C	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:62600570C>A	ENST00000525239.1	-	12	1549	c.1012G>T	c.(1012-1014)Gtg>Ttg	p.V338L	WDR74_ENST00000529106.1_Missense_Mutation_p.V338L|WDR74_ENST00000311713.7_Missense_Mutation_p.V319L|RP11-727F15.9_ENST00000535867.1_RNA|STX5_ENST00000294179.3_5'Flank|WDR74_ENST00000525752.1_Missense_Mutation_p.V281L|WDR74_ENST00000540620.1_5'Flank|STX5_ENST00000377897.4_5'Flank|WDR74_ENST00000278856.4_Missense_Mutation_p.V338L|RP11-727F15.9_ENST00000535817.1_RNA|STX5_ENST00000394690.1_5'Flank|STX5_ENST00000541317.1_5'Flank			Q6RFH5	WDR74_HUMAN	WD repeat domain 74	338					blastocyst formation (GO:0001825)|RNA metabolic process (GO:0016070)	nucleolus (GO:0005730)|nucleus (GO:0005634)				kidney(2)|large_intestine(1)|liver(1)|lung(3)|ovary(1)	8						TCTAGGGGCACCTTGTTGGGT	0.587																																					p.V338L		Atlas-SNP	.											.	WDR74	36	.	0			c.G1012T						PASS	.						70.0	69.0	69.0					11																	62600570		1871	4104	5975	SO:0001583	missense	54663	exon12			GGGGCACCTTGTT		CCDS44630.1	11q12.3	2013-01-09				ENSG00000133316		"""WD repeat domain containing"""	25529	protein-coding gene	gene with protein product							Standard	NM_018093		Approved	FLJ10439	uc001nvm.2	Q6RFH5		ENST00000525239.1:c.1012G>T	chr11.hg19:g.62600570C>A	ENSP00000432119:p.Val338Leu	95.0	0.0	.		83.0	35.0	.	NM_018093	A8K8G5|Q9BRC9|Q9H6X8|Q9NVY2	Missense_Mutation	SNP	ENST00000525239.1	hg19	CCDS44630.1	.	.	.	.	.	.	.	.	.	.	C	2.862	-0.235939	0.05944	.	.	ENSG00000133316	ENST00000311713;ENST00000529106;ENST00000525239;ENST00000278856;ENST00000535048;ENST00000525752	T	0.43294	0.95	4.97	0.918	0.19386	.	0.666571	0.13764	N	0.364341	T	0.25382	0.0617	L	0.36672	1.1	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.18209	-1.0344	10	0.27785	T	0.31	-0.0311	1.6117	0.02695	0.1606:0.4701:0.1821:0.1872	.	281;338;319	E9PS41;Q6RFH5;Q6RFH5-2	.;WDR74_HUMAN;.	L	319;338;338;338;134;281	ENSP00000432113:V281L	ENSP00000278856:V338L	V	-	1	0	WDR74	62357146	0.000000	0.05858	0.000000	0.03702	0.337000	0.28794	0.091000	0.15046	0.011000	0.14865	0.655000	0.94253	GTG	.	.	.	none		0.587	WDR74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395678.1	NM_018093	
DDX10	1662	hgsc.bcm.edu	37	11	108593893	108593893	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:108593893T>A	ENST00000322536.3	+	13	1798	c.1669T>A	c.(1669-1671)Tcc>Acc	p.S557T	DDX10_ENST00000526794.1_Missense_Mutation_p.S557T	NM_004398.2	NP_004389.2	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	557					metabolic process (GO:0008152)		ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2)	27		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		TGAGAAAATGTCCATCCTTCA	0.433			T	NUP98	AML*																																p.S557T		Atlas-SNP	.		Dom	yes		11	11q22-q23	1662	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10		L	.	DDX10	70	.	0			c.T1669A						PASS	.						68.0	67.0	67.0					11																	108593893		2201	4298	6499	SO:0001583	missense	1662	exon13			AAAATGTCCATCC	U28042	CCDS8342.1	11q22-q23	2005-10-11	2003-06-13		ENSG00000178105	ENSG00000178105		"""DEAD-boxes"""	2735	protein-coding gene	gene with protein product		601235	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)"""			8660968	Standard	NM_004398		Approved	HRH-J8	uc001pkm.3	Q13206	OTTHUMG00000166540	ENST00000322536.3:c.1669T>A	chr11.hg19:g.108593893T>A	ENSP00000314348:p.Ser557Thr	131.0	0.0	.		127.0	58.0	.	NM_004398	B2RCQ3|Q5BJD8	Missense_Mutation	SNP	ENST00000322536.3	hg19	CCDS8342.1	.	.	.	.	.	.	.	.	.	.	T	10.97	1.501157	0.26861	.	.	ENSG00000178105	ENST00000322536;ENST00000456020;ENST00000526794	T;T	0.41065	1.01;1.02	4.9	3.68	0.42216	.	0.222920	0.38959	N	0.001508	T	0.17492	0.0420	N	0.08118	0	0.26714	N	0.970905	B;B	0.19583	0.013;0.037	B;B	0.16289	0.01;0.015	T	0.13548	-1.0505	10	0.13853	T	0.58	-9.0985	5.0685	0.14594	0.1615:0.0897:0.0:0.7488	.	557;557	Q13206;E9PIF2	DDX10_HUMAN;.	T	557;463;557	ENSP00000314348:S557T;ENSP00000432032:S557T	ENSP00000314348:S557T	S	+	1	0	DDX10	108099103	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	2.025000	0.41059	1.954000	0.56735	0.397000	0.26171	TCC	.	.	.	none		0.433	DDX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390343.1	NM_004398	
DDX25	29118	hgsc.bcm.edu	37	11	125791201	125791201	+	Silent	SNP	G	G	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:125791201G>C	ENST00000263576.6	+	11	1472	c.1317G>C	c.(1315-1317)ggG>ggC	p.G439G	DDX25_ENST00000525943.1_3'UTR|RP11-680F20.9_ENST00000533033.2_RNA	NM_013264.4	NP_037396.3	Q9UHL0	DDX25_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 25	439	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)	10	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0203)|Lung NSC(97;0.0203)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.14e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.046)		GGCGCTTTGGGAAAAAAGGCC	0.493																																					p.G439G		Atlas-SNP	.											.	DDX25	65	.	0			c.G1317C						PASS	.						46.0	45.0	46.0					11																	125791201		1922	4128	6050	SO:0001819	synonymous_variant	29118	exon11			CTTTGGGAAAAAA	AF155140	CCDS44766.1	11q24	2012-02-23	2012-02-23		ENSG00000109832	ENSG00000109832		"""DEAD-boxes"""	18698	protein-coding gene	gene with protein product	"""gonadotropin-regulated testicular RNA helicase"""	607663	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 25"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 25"""			10608860, 15096601	Standard	NM_013264		Approved	GRTH	uc001qcz.5	Q9UHL0	OTTHUMG00000165859	ENST00000263576.6:c.1317G>C	chr11.hg19:g.125791201G>C		98.0	0.0	.		129.0	61.0	.	NM_013264	B2R6Z0|Q5XVN2|Q86W81|Q8IYP1	Silent	SNP	ENST00000263576.6	hg19	CCDS44766.1																																																																																			.	.	.	none		0.493	DDX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386736.3	NM_013264	
SRPR	6734	hgsc.bcm.edu	37	11	126134972	126134972	+	Silent	SNP	G	G	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:126134972G>T	ENST00000332118.6	-	11	1561	c.1407C>A	c.(1405-1407)acC>acA	p.T469T	SRPR_ENST00000530680.1_5'Flank|SRPR_ENST00000532259.1_Silent_p.T441T	NM_003139.3	NP_003130.2	P08240	SRPR_HUMAN	signal recognition particle receptor (docking protein)	469					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|signal recognition particle receptor complex (GO:0005785)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			endometrium(7)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)	21	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)		TCAAACGCCGGGTGTGTGTAC	0.547																																					p.T469T		Atlas-SNP	.											.	SRPR	60	.	0			c.C1407A						PASS	.						67.0	61.0	63.0					11																	126134972		2201	4299	6500	SO:0001819	synonymous_variant	6734	exon11			ACGCCGGGTGTGT	BC001162	CCDS31717.1, CCDS53722.1	11q24-q25	2012-10-02	2008-10-29		ENSG00000182934	ENSG00000182934			11307	protein-coding gene	gene with protein product		182180	"""signal recognition particle receptor ('docking protein')"""			3340536, 1312991	Standard	NM_001177842		Approved	SRP-alpha, Sralpha	uc001qdh.3	P08240	OTTHUMG00000165826	ENST00000332118.6:c.1407C>A	chr11.hg19:g.126134972G>T		103.0	0.0	.		88.0	35.0	.	NM_003139	A6NIB3|B2R5Z8|B4E0H3|E9PJS4|Q9BVJ4	Silent	SNP	ENST00000332118.6	hg19	CCDS31717.1																																																																																			.	.	.	none		0.547	SRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386425.2	NM_003139	
ACSM4	341392	hgsc.bcm.edu	37	12	7459269	7459269	+	Silent	SNP	A	A	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:7459269A>T	ENST00000399422.4	+	2	390	c.342A>T	c.(340-342)ggA>ggT	p.G114G		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	114					acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty-acyl-CoA synthase activity (GO:0004321)|metal ion binding (GO:0046872)			endometrium(6)|kidney(1)|lung(14)	21						TGCAGAGAGGAGACCGTTTGG	0.522																																					p.G114G		Atlas-SNP	.											.	ACSM4	98	.	0			c.A342T						PASS	.						77.0	85.0	83.0					12																	7459269		2093	4251	6344	SO:0001819	synonymous_variant	341392	exon2			GAGAGGAGACCGT		CCDS44825.1	12p13.31	2008-06-12			ENSG00000215009	ENSG00000215009		"""Acyl-CoA synthetase family"""	32016	protein-coding gene	gene with protein product	"""similar to olfactory specific medium-chain acyl CoA synthetase"""	614360				17762044	Standard	NM_001080454		Approved		uc001qsx.1	P0C7M7	OTTHUMG00000154975	ENST00000399422.4:c.342A>T	chr12.hg19:g.7459269A>T		128.0	0.0	.		240.0	161.0	.	NM_001080454	A8MTI6	Silent	SNP	ENST00000399422.4	hg19	CCDS44825.1																																																																																			.	.	.	none		0.522	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	NM_001080454	
CAPZA3	93661	hgsc.bcm.edu	37	12	18891585	18891585	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:18891585A>C	ENST00000317658.3	+	1	541	c.383A>C	c.(382-384)tAt>tCt	p.Y128S	PLCZ1_ENST00000266505.7_5'Flank|PLCZ1_ENST00000539875.1_5'Flank|PLCZ1_ENST00000435379.1_5'Flank|RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000447925.2_5'Flank	NM_033328.2	NP_201585.1	Q96KX2	CAZA3_HUMAN	capping protein (actin filament) muscle Z-line, alpha 3	128					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cortical cytoskeleton (GO:0030863)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|nucleus (GO:0005634)|WASH complex (GO:0071203)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)	19	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)	Hepatocellular(102;0.194)				TTAAAACTGTATGTGAATGAC	0.388																																					p.Y128S		Atlas-SNP	.											.	CAPZA3	51	.	0			c.A383C						PASS	.						90.0	82.0	84.0					12																	18891585		2203	4300	6503	SO:0001583	missense	93661	exon1			AACTGTATGTGAA	AB053259	CCDS8681.1	12p12.3	2008-02-05			ENSG00000177938	ENSG00000177938			24205	protein-coding gene	gene with protein product		608722				12029070	Standard	NM_033328		Approved	Gsg3, CAPPA3	uc001rdy.3	Q96KX2	OTTHUMG00000169001	ENST00000317658.3:c.383A>C	chr12.hg19:g.18891585A>C	ENSP00000326238:p.Tyr128Ser	166.0	0.0	.		239.0	144.0	.	NM_033328	Q969J0	Missense_Mutation	SNP	ENST00000317658.3	hg19	CCDS8681.1	.	.	.	.	.	.	.	.	.	.	A	12.78	2.040528	0.35989	.	.	ENSG00000177938	ENST00000317658	.	.	.	4.43	4.43	0.53597	.	0.000000	0.64402	D	0.000001	T	0.77412	0.4126	M	0.78049	2.395	0.52099	D	0.999946	D	0.76494	0.999	D	0.87578	0.998	T	0.80264	-0.1455	9	0.87932	D	0	-1.4926	11.1782	0.48612	1.0:0.0:0.0:0.0	.	128	Q96KX2	CAZA3_HUMAN	S	128	.	ENSP00000326238:Y128S	Y	+	2	0	CAPZA3	18782852	0.995000	0.38212	0.801000	0.32222	0.378000	0.30076	5.493000	0.66899	1.876000	0.54355	0.379000	0.24179	TAT	.	.	.	none		0.388	CAPZA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401902.1	NM_033328	
GOLT1B	51026	hgsc.bcm.edu	37	12	21661461	21661461	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:21661461A>T	ENST00000229314.5	+	3	371	c.262A>T	c.(262-264)Atc>Ttc	p.I88F	GOLT1B_ENST00000540141.1_Missense_Mutation_p.I88F|GOLT1B_ENST00000535593.1_Intron|GOLT1B_ENST00000542038.1_Missense_Mutation_p.I24F	NM_016072.4	NP_057156.1	Q9Y3E0	GOT1B_HUMAN	golgi transport 1B	88	Phe-rich.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein transport (GO:0015031)|signal transduction (GO:0007165)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	signal transducer activity (GO:0004871)			large_intestine(2)|lung(3)	5						GATAGGCATGATCTTCGAAAT	0.333																																					p.I88F		Atlas-SNP	.											.	GOLT1B	13	.	0			c.A262T						PASS	.						112.0	111.0	111.0					12																	21661461		2203	4298	6501	SO:0001583	missense	51026	exon3			GGCATGATCTTCG	AB097020	CCDS8689.1	12p13.1	2010-06-24	2010-06-24		ENSG00000111711	ENSG00000111711			20175	protein-coding gene	gene with protein product		615078	"""golgi transport 1 homolog B (S. cerevisiae)"""			12414650, 10810093	Standard	NM_016072		Approved	CGI-141, YMR292W, GOT1	uc001rez.2	Q9Y3E0	OTTHUMG00000169133	ENST00000229314.5:c.262A>T	chr12.hg19:g.21661461A>T	ENSP00000229314:p.Ile88Phe	104.0	0.0	.		183.0	105.0	.	NM_016072	B2R4R4|Q54A40|Q6I9W6|Q9P1R9	Missense_Mutation	SNP	ENST00000229314.5	hg19	CCDS8689.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.800809	0.50315	.	.	ENSG00000111711	ENST00000542038;ENST00000540141;ENST00000229314	T;T;T	0.47869	0.83;0.83;0.83	5.9	5.9	0.94986	.	0.055804	0.64402	D	0.000001	T	0.44746	0.1308	M	0.64170	1.965	0.58432	D	0.999993	B	0.10296	0.003	B	0.20767	0.031	T	0.42716	-0.9435	10	0.46703	T	0.11	-9.0019	8.6254	0.33886	0.8585:0.0:0.1415:0.0	.	88	Q9Y3E0	GOT1B_HUMAN	F	24;88;88	ENSP00000446231:I24F;ENSP00000437351:I88F;ENSP00000229314:I88F	ENSP00000229314:I88F	I	+	1	0	GOLT1B	21552728	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.462000	0.53042	2.251000	0.74343	0.528000	0.53228	ATC	.	.	.	none		0.333	GOLT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402384.2	NM_016072	
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS_ENST00000256078,NS,adenocarcinoma,0,66	KRAS	30930	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35A						PASS	.						91.0	81.0	85.0					12																	25398284		2203	4300	6503	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ACGCCACCAGCTC	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	chr12.hg19:g.25398284C>T	ENSP00000256078:p.Gly12Asp	177.0	0.0	.		272.0	141.0	.	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	.	.	.	weak		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
MYF6	4618	hgsc.bcm.edu	37	12	81101509	81101509	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:81101509A>C	ENST00000228641.3	+	1	233	c.11A>C	c.(10-12)gAc>gCc	p.D4A		NM_002469.2	NP_002460.1	P23409	MYF6_HUMAN	myogenic factor 6 (herculin)	4					muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|skin(1)	26						ATGATGATGGACCTTTTTGAA	0.468																																					p.D4A		Atlas-SNP	.											.	MYF6	74	.	0			c.A11C						PASS	.						115.0	122.0	120.0					12																	81101509		2203	4300	6503	SO:0001583	missense	4618	exon1			TGATGGACCTTTT		CCDS9019.1	12q21	2013-05-21				ENSG00000111046		"""Basic helix-loop-helix proteins"""	7566	protein-coding gene	gene with protein product	"""muscle-specific regulatory factor 4"""	159991				8978788	Standard	NM_002469		Approved	MRF4, bHLHc4	uc001szf.2	P23409		ENST00000228641.3:c.11A>C	chr12.hg19:g.81101509A>C	ENSP00000228641:p.Asp4Ala	71.0	0.0	.		137.0	77.0	.	NM_002469	B2R898|Q53X80|Q6FHI9	Missense_Mutation	SNP	ENST00000228641.3	hg19	CCDS9019.1	.	.	.	.	.	.	.	.	.	.	A	19.76	3.887817	0.72410	.	.	ENSG00000111046	ENST00000228641	T	0.79352	-1.26	5.46	5.46	0.80206	Myogenic basic muscle-specific protein (2);	0.000000	0.85682	D	0.000000	D	0.84074	0.5392	L	0.51422	1.61	0.80722	D	1	D	0.71674	0.998	D	0.64877	0.93	D	0.85751	0.1343	10	0.72032	D	0.01	.	15.5368	0.76011	1.0:0.0:0.0:0.0	.	4	P23409	MYF6_HUMAN	A	4	ENSP00000228641:D4A	ENSP00000228641:D4A	D	+	2	0	MYF6	79625640	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.730000	0.91510	2.090000	0.63153	0.533000	0.62120	GAC	.	.	.	none		0.468	MYF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407756.1	NM_002469	
PLXNC1	10154	hgsc.bcm.edu	37	12	94543226	94543226	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:94543226G>A	ENST00000258526.4	+	1	728	c.479G>A	c.(478-480)gGc>gAc	p.G160D		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	160	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CACCCGCAGGGCTCGACGGCC	0.741																																					p.G160D		Atlas-SNP	.											.	PLXNC1	135	.	0			c.G479A						PASS	.						2.0	2.0	2.0					12																	94543226		1355	2986	4341	SO:0001583	missense	10154	exon1			CGCAGGGCTCGAC	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"""CD molecules"", ""Plexins"""	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.479G>A	chr12.hg19:g.94543226G>A	ENSP00000258526:p.Gly160Asp	16.0	0.0	.		38.0	7.0	.	NM_005761	Q59H25	Missense_Mutation	SNP	ENST00000258526.4	hg19	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.404871	0.62288	.	.	ENSG00000136040	ENST00000258526	T	0.04551	3.6	4.87	4.87	0.63330	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (2);	0.352781	0.24001	N	0.042462	T	0.16300	0.0392	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00503	-1.1701	10	0.39692	T	0.17	.	12.2042	0.54342	0.0:0.0:0.8298:0.1702	.	160	O60486	PLXC1_HUMAN	D	160	ENSP00000258526:G160D	ENSP00000258526:G160D	G	+	2	0	PLXNC1	93067357	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.442000	0.52900	2.233000	0.73108	0.561000	0.74099	GGC	.	.	.	none		0.741	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
ATP2A2	488	hgsc.bcm.edu	37	12	110760813	110760813	+	Silent	SNP	T	T	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:110760813T>C	ENST00000539276.2	+	6	589	c.480T>C	c.(478-480)ccT>ccC	p.P160P	ATP2A2_ENST00000395494.2_Intron|ATP2A2_ENST00000550248.2_3'UTR|ATP2A2_ENST00000308664.6_Silent_p.P160P			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	160			P -> L (in DD).		blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						ACAAAGTTCCTGCTGATATAA	0.323																																					p.P160P		Atlas-SNP	.											.	ATP2A2	78	.	0			c.T480C						PASS	.						82.0	84.0	83.0					12																	110760813		2203	4300	6503	SO:0001819	synonymous_variant	488	exon6			AGTTCCTGCTGAT		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"""ATPases / P-type"""	812	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 2"", ""calcium pump 2"""	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.480T>C	chr12.hg19:g.110760813T>C		104.0	0.0	.		171.0	55.0	.	NM_001681	A6NDN7|B4DF05|P16614|Q86VJ2	Silent	SNP	ENST00000539276.2	hg19	CCDS9144.1																																																																																			.	.	.	none		0.323	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681	
TAOK3	51347	hgsc.bcm.edu	37	12	118681252	118681252	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:118681252T>C	ENST00000392533.3	-	5	752	c.262A>G	c.(262-264)Aaa>Gaa	p.K88E	TAOK3_ENST00000419821.2_Missense_Mutation_p.K88E	NM_016281.3	NP_057365.3	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	88	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|MAPK cascade (GO:0000165)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of JNK cascade (GO:0046329)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			central_nervous_system(1)|lung(5)|skin(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TAACAGCCTTTGTACTCAATA	0.289																																					p.K88E		Atlas-SNP	.											.	TAOK3	151	.	0			c.A262G						PASS	.						72.0	70.0	71.0					12																	118681252		2202	4294	6496	SO:0001583	missense	51347	exon5			AGCCTTTGTACTC	AF135158	CCDS9188.1	12q	2007-08-03				ENSG00000135090			18133	protein-coding gene	gene with protein product						10559204, 10924369	Standard	NM_016281		Approved	JIK, DPK, MAP3K18	uc001twy.4	Q9H2K8		ENST00000392533.3:c.262A>G	chr12.hg19:g.118681252T>C	ENSP00000376317:p.Lys88Glu	103.0	0.0	.		183.0	110.0	.	NM_016281	Q658N1|Q8IUM4|Q9HC79|Q9NZM9|Q9UHG7	Missense_Mutation	SNP	ENST00000392533.3	hg19	CCDS9188.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.38|14.38	2.517362|2.517362	0.44763|0.44763	.|.	.|.	ENSG00000135090|ENSG00000135090	ENST00000419821;ENST00000392533;ENST00000535570;ENST00000541186|ENST00000538601	T;T;T;T|T	0.24908|0.74315	1.83;1.83;1.83;1.83|-0.83	5.05|5.05	5.05|5.05	0.67936|0.67936	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.68504|0.68504	0.3008|0.3008	N|N	0.13235|0.13235	0.315|0.315	0.80722|0.80722	D|D	1|1	B|.	0.28636|.	0.218|.	P|.	0.44990|.	0.466|.	T|T	0.74472|0.74472	-0.3654|-0.3654	10|7	0.87932|0.87932	D|D	0|0	.|.	14.9553|14.9553	0.71107|0.71107	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	88|.	Q9H2K8|.	TAOK3_HUMAN|.	E|R	88|1	ENSP00000416374:K88E;ENSP00000376317:K88E;ENSP00000443465:K88E;ENSP00000438820:K88E|ENSP00000437389:Q1R	ENSP00000376317:K88E|ENSP00000437389:Q1R	K|Q	-|-	1|2	0|0	TAOK3|TAOK3	117165635|117165635	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	7.719000|7.719000	0.84751|0.84751	2.119000|2.119000	0.64992|0.64992	0.533000|0.533000	0.62120|0.62120	AAA|CAA	.	.	.	none		0.289	TAOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401456.2	NM_016281	
EP400	57634	hgsc.bcm.edu	37	12	132547081	132547081	+	Silent	SNP	G	G	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:132547081G>A	ENST00000333577.4	+	48	8386	c.8277G>A	c.(8275-8277)caG>caA	p.Q2759Q	EP400_ENST00000330386.6_Silent_p.Q2642Q|EP400_ENST00000332482.4_Silent_p.Q2686Q|EP400_ENST00000389561.2_Silent_p.Q2723Q|EP400_ENST00000389562.2_Silent_p.Q2722Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2759	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcagcagcagcagcaac	0.562																																					p.Q2723Q		Atlas-SNP	.											.	EP400	370	.	0			c.G8169A						PASS	.						33.0	35.0	34.0					12																	132547081		2203	4300	6503	SO:0001819	synonymous_variant	57634	exon47			GCAGCAGCAGCAG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8277G>A	chr12.hg19:g.132547081G>A		91.0	0.0	.		157.0	7.0	.	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	hg19																																																																																				.	.	.	none		0.562	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
EP400	57634	hgsc.bcm.edu	37	12	132547084	132547084	+	Silent	SNP	G	G	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:132547084G>A	ENST00000333577.4	+	48	8389	c.8280G>A	c.(8278-8280)caG>caA	p.Q2760Q	EP400_ENST00000330386.6_Silent_p.Q2643Q|EP400_ENST00000332482.4_Silent_p.Q2687Q|EP400_ENST00000389561.2_Silent_p.Q2724Q|EP400_ENST00000389562.2_Silent_p.Q2723Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2760	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcagcagcagcaacaac	0.557																																					p.Q2724Q		Atlas-SNP	.											.	EP400	370	.	0			c.G8172A						PASS	.						30.0	33.0	32.0					12																	132547084		2203	4298	6501	SO:0001819	synonymous_variant	57634	exon47			GCAGCAGCAGCAA	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8280G>A	chr12.hg19:g.132547084G>A		93.0	0.0	.		162.0	9.0	.	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	hg19																																																																																				.	.	.	none		0.557	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
FOXO1	2308	hgsc.bcm.edu	37	13	41134273	41134273	+	Missense_Mutation	SNP	A	A	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr13:41134273A>G	ENST00000379561.5	-	2	1739	c.1355T>C	c.(1354-1356)aTg>aCg	p.M452T	FOXO1_ENST00000473775.1_5'Flank	NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	452	Required for interaction with RUNX2. {ECO:0000250}.|Sufficient for interaction with NLK. {ECO:0000250}.				apoptotic process (GO:0006915)|autophagy (GO:0006914)|blood vessel development (GO:0001568)|cellular glucose homeostasis (GO:0001678)|cellular response to cold (GO:0070417)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hyperoxia (GO:0071455)|cellular response to insulin stimulus (GO:0032869)|cellular response to nitric oxide (GO:0071732)|cellular response to oxidative stress (GO:0034599)|cellular response to starvation (GO:0009267)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|regulation of cell proliferation (GO:0042127)|regulation of energy homeostasis (GO:2000505)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|protein phosphatase 2A binding (GO:0051721)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)		PAX7/FOXO1(197)|PAX3/FOXO1(749)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	20		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		ATACTGACTCATACCTCCATA	0.463																																					p.M452T		Atlas-SNP	.											.	FOXO1	110	.	0			c.T1355C						PASS	.						102.0	87.0	92.0					13																	41134273		2203	4300	6503	SO:0001583	missense	2308	exon2			TGACTCATACCTC		CCDS9371.1	13q14.1	2011-08-01	2007-05-02	2007-05-02	ENSG00000150907	ENSG00000150907		"""Forkhead boxes"""	3819	protein-coding gene	gene with protein product		136533	"""forkhead homolog in rhabdomyosarcoma"""	FKHR, FOXO1A		8275086, 15057823	Standard	NM_002015		Approved	FKH1	uc001uxl.4	Q12778	OTTHUMG00000016775	ENST00000379561.5:c.1355T>C	chr13.hg19:g.41134273A>G	ENSP00000368880:p.Met452Thr	69.0	0.0	.		91.0	42.0	.	NM_002015	O43523|Q5VYC7|Q6NSK6	Missense_Mutation	SNP	ENST00000379561.5	hg19	CCDS9371.1	.	.	.	.	.	.	.	.	.	.	A	10.99	1.508445	0.27036	.	.	ENSG00000150907	ENST00000379561	D	0.93906	-3.31	5.78	5.78	0.91487	.	0.369149	0.30742	N	0.008980	D	0.91412	0.7290	L	0.61218	1.895	0.39378	D	0.966211	B	0.14805	0.011	B	0.12837	0.008	D	0.88343	0.2976	10	0.20519	T	0.43	-0.5556	15.295	0.73898	1.0:0.0:0.0:0.0	.	452	Q12778	FOXO1_HUMAN	T	452	ENSP00000368880:M452T	ENSP00000368880:M452T	M	-	2	0	FOXO1	40032273	0.998000	0.40836	0.321000	0.25320	0.301000	0.27625	7.027000	0.76463	2.220000	0.72140	0.533000	0.62120	ATG	.	.	.	none		0.463	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015	
ALG11	440138	hgsc.bcm.edu	37	13	52598354	52598354	+	Missense_Mutation	SNP	C	C	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr13:52598354C>G	ENST00000521508.1	+	3	493	c.488C>G	c.(487-489)gCt>gGt	p.A163G	ALG11_ENST00000523764.1_Intron|ALG11_ENST00000519151.1_3'UTR|UTP14C_ENST00000521776.2_5'Flank	NM_001004127.2	NP_001004127.2	Q2TAA5	ALG11_HUMAN	ALG11, alpha-1,2-mannosyltransferase	163					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GDP-Man:Man3GlcNAc2-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0004377)			endometrium(1)|large_intestine(6)|lung(4)|ovary(2)	13		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.44e-08)		GGCTGGGAAGCTCTAATGCAG	0.413																																					p.A163G		Atlas-SNP	.											.	ALG11	39	.	0			c.C488G						PASS	.						182.0	169.0	173.0					13																	52598354		2203	4300	6503	SO:0001583	missense	440138	exon3			GGGAAGCTCTAAT	AK025456	CCDS31977.1	13q14.3	2013-02-22	2013-02-22		ENSG00000253710	ENSG00000253710	2.4.1.131	"""Glycosyltransferase group 1 domain containing"""	32456	protein-coding gene	gene with protein product	"""GDP-Man:Man(3)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"""	613666	"""asparagine-linked glycosylation 11 homolog (S. cerevisiae, alpha-1,2-mannosyltransferase)"", ""asparagine-linked glycosylation 11, alpha-1,2-mannosyltransferase homolog (yeast)"""			20080937	Standard	NM_001004127		Approved	KIAA0266		Q2TAA5	OTTHUMG00000016959	ENST00000521508.1:c.488C>G	chr13.hg19:g.52598354C>G	ENSP00000430236:p.Ala163Gly	100.0	0.0	.		100.0	43.0	.	NM_001004127	A5PLP3|B4DKW9|Q5TAN9|Q6DKI6|Q96FI7	Missense_Mutation	SNP	ENST00000521508.1	hg19	CCDS31977.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719490	0.68844	.	.	ENSG00000253710	ENST00000521508	T	0.69685	-0.42	5.94	5.94	0.96194	.	0.000000	0.85682	U	0.000000	T	0.74612	0.3739	M	0.82630	2.6	0.80722	D	1	P	0.49090	0.919	B	0.43331	0.416	T	0.78947	-0.2003	10	0.62326	D	0.03	.	20.3736	0.98901	0.0:1.0:0.0:0.0	.	163	Q2TAA5	ALG11_HUMAN	G	163	ENSP00000430236:A163G	ENSP00000430236:A163G	A	+	2	0	ALG11	51496355	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	7.438000	0.80431	2.820000	0.97059	0.650000	0.86243	GCT	.	.	.	none		0.413	ALG11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045050.1	NM_001004127	
FERMT2	10979	hgsc.bcm.edu	37	14	53386039	53386039	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr14:53386039A>C	ENST00000395631.2	-	3	409	c.193T>G	c.(193-195)Tgg>Ggg	p.W65G	FERMT2_ENST00000343279.4_Missense_Mutation_p.W65G|FERMT2_ENST00000399304.3_Missense_Mutation_p.W65G|FERMT2_ENST00000341590.3_Missense_Mutation_p.W65G|FERMT2_ENST00000553373.1_Missense_Mutation_p.W65G			Q96AC1	FERM2_HUMAN	fermitin family member 2	65	Interaction with membranes containing phosphatidylinositol phosphate.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|focal adhesion assembly (GO:0048041)|integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|protein localization to membrane (GO:0072657)|regulation of cell shape (GO:0008360)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)		ERO1L/FERMT2(2)	NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Breast(41;0.0342)					TTCTTTTCCCACCAGAGAGCA	0.363																																					p.W65G		Atlas-SNP	.											.	FERMT2	59	.	0			c.T193G						PASS	.						119.0	111.0	114.0					14																	53386039		2203	4300	6503	SO:0001583	missense	10979	exon3			TTTCCCACCAGAG	Z24725	CCDS9713.1, CCDS45107.1, CCDS45108.1	14q22.1	2013-01-10	2010-06-24	2007-12-14	ENSG00000073712	ENSG00000073712		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15767	protein-coding gene	gene with protein product	"""kindlin-2"""	607746	"""pleckstrin homology domain containing, family C (with FERM domain) member 1"", ""fermitin family homolog 2 (Drosophila)"""	PLEKHC1		8175911, 12697302	Standard	NM_006832		Approved	mig-2, KIND2, UNC112B	uc001xac.3	Q96AC1	OTTHUMG00000140309	ENST00000395631.2:c.193T>G	chr14.hg19:g.53386039A>C	ENSP00000378993:p.Trp65Gly	150.0	0.0	.		168.0	60.0	.	NM_001135000	B5TJY2|Q14840|Q86TY7	Missense_Mutation	SNP	ENST00000395631.2	hg19	CCDS9713.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.140592	0.77775	.	.	ENSG00000073712	ENST00000395631;ENST00000341590;ENST00000554152;ENST00000343279;ENST00000553373;ENST00000399304;ENST00000555692;ENST00000554712	T;T;T;T;T;T;T;T	0.14893	2.47;2.47;2.47;2.47;2.47;2.47;2.47;2.47	5.82	5.82	0.92795	.	0.063724	0.64402	D	0.000002	T	0.47303	0.1438	M	0.86268	2.805	0.80722	D	1	P;P;P	0.50710	0.938;0.791;0.897	D;P;P	0.67725	0.953;0.812;0.898	T	0.52434	-0.8576	10	0.87932	D	0	.	16.1966	0.82029	1.0:0.0:0.0:0.0	.	65;65;65	Q96AC1-2;Q96AC1;B5TJY2	.;FERM2_HUMAN;.	G	65;65;7;65;65;65;21;65	ENSP00000378993:W65G;ENSP00000340391:W65G;ENSP00000450741:W7G;ENSP00000342858:W65G;ENSP00000451084:W65G;ENSP00000382243:W65G;ENSP00000452472:W21G;ENSP00000450506:W65G	ENSP00000340391:W65G	W	-	1	0	FERMT2	52455789	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.232000	0.73038	0.528000	0.53228	TGG	.	.	.	none		0.363	FERMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276907.2	NM_006832	
C15orf53	400359	hgsc.bcm.edu	37	15	38988810	38988810	+	Start_Codon_SNP	SNP	T	T	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr15:38988810T>C	ENST00000318792.1	+	1	12	c.2T>C	c.(1-3)aTg>aCg	p.M1T		NM_207444.2	NP_997327.1	Q8NAA6	CO053_HUMAN	chromosome 15 open reading frame 53	1										endometrium(1)|large_intestine(1)|lung(2)|skin(1)|stomach(1)	6		all_cancers(109;1.75e-13)|all_epithelial(112;1.02e-11)|Lung NSC(122;1.9e-09)|all_lung(180;4.04e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)		GBM - Glioblastoma multiforme(113;8.39e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0321)		TGTTCTGATATGGAGCTACAA	0.557																																					p.M1T		Atlas-SNP	.											.	C15orf53	12	.	0			c.T2C						PASS	.						86.0	81.0	83.0					15																	38988810		2200	4297	6497	SO:0001582	initiator_codon_variant	400359	exon1			CTGATATGGAGCT		CCDS10048.1	15q14	2007-11-21			ENSG00000175779	ENSG00000175779			33796	protein-coding gene	gene with protein product							Standard	NM_207444		Approved	FLJ35695	uc001zkf.1	Q8NAA6	OTTHUMG00000129841	ENST00000318792.1:c.2T>C	chr15.hg19:g.38988810T>C	ENSP00000325144:p.Met1Thr	113.0	0.0	.		116.0	56.0	.	NM_207444		Missense_Mutation	SNP	ENST00000318792.1	hg19	CCDS10048.1	.	.	.	.	.	.	.	.	.	.	T	1.475	-0.558766	0.03967	.	.	ENSG00000175779	ENST00000318792	T	0.35236	1.32	3.36	2.2	0.27929	.	.	.	.	.	T	0.26304	0.0642	.	.	.	0.80722	D	1	P	0.37955	0.612	B	0.34385	0.181	T	0.06917	-1.0800	8	0.87932	D	0	.	6.6129	0.22761	0.0:0.0:0.2466:0.7534	.	1	Q8NAA6	CO053_HUMAN	T	1	ENSP00000325144:M1T	ENSP00000325144:M1T	M	+	2	0	C15orf53	36776102	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	0.095000	0.15127	0.652000	0.30806	0.459000	0.35465	ATG	.	.	.	none		0.557	C15orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252081.1	NM_207444	Missense_Mutation
GTF2A2	2958	hgsc.bcm.edu	37	15	59942867	59942867	+	Splice_Site	SNP	C	C	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr15:59942867C>A	ENST00000396060.2	-	3	359		c.e3+1		GTF2A2_ENST00000396061.1_Splice_Site|AC092755.4_ENST00000441746.1_RNA|GTF2A2_ENST00000396064.3_Splice_Site|GTF2A2_ENST00000396063.1_Splice_Site|GTF2A2_ENST00000267869.4_Intron|GTF2A2_ENST00000484743.1_Intron	NM_004492.2	NP_004483.1	P52657	T2AG_HUMAN	general transcription factor IIA, 2, 12kDa						gene expression (GO:0010467)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIA complex (GO:0005672)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			central_nervous_system(2)|kidney(2)|lung(1)	5						AATATCCTTACCCTGAAATTG	0.398																																					.		Atlas-SNP	.											.	GTF2A2	9	.	0			c.177+1G>T						PASS	.						76.0	71.0	73.0					15																	59942867		2190	4290	6480	SO:0001630	splice_region_variant	2958	exon4			TCCTTACCCTGAA	BC001919	CCDS10173.1	15q21.3	2010-03-23	2002-08-29		ENSG00000140307	ENSG00000140307		"""General transcription factors"""	4647	protein-coding gene	gene with protein product		600519	"""general transcription factor IIA, 2 (12kD subunit)"""			7958899	Standard	NM_004492		Approved	TFIIA, HsT18745	uc002agg.3	P52657	OTTHUMG00000132725	ENST00000396060.2:c.177+1G>T	chr15.hg19:g.59942867C>A		75.0	0.0	.		87.0	26.0	.	NM_004492	A8MYQ7|Q6FGB5	Splice_Site	SNP	ENST00000396060.2	hg19	CCDS10173.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.498010	0.85069	.	.	ENSG00000140307	ENST00000396060;ENST00000396064;ENST00000396063;ENST00000396061	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1601	0.93527	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GTF2A2	57730159	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.172000	0.77604	2.523000	0.85059	0.555000	0.69702	.	.	.	.	none		0.398	GTF2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256067.2	NM_004492	Intron
CRAMP1L	57585	hgsc.bcm.edu	37	16	1691167	1691167	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr16:1691167T>C	ENST00000397412.3	+	6	905	c.806T>C	c.(805-807)cTg>cCg	p.L269P	CRAMP1L_ENST00000436138.3_Missense_Mutation_p.L266P|LA16c-431H6.6_ENST00000454337.1_Silent_p.A73A|CRAMP1L_ENST00000293925.5_Missense_Mutation_p.L269P			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	269						nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						GCAACAAAGCTGAATGAACTC	0.368																																					p.L269P		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.T806C						PASS	.						137.0	136.0	137.0					16																	1691167		1865	4115	5980	SO:0001583	missense	57585	exon5			CAAAGCTGAATGA	AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"""Crm (Cramped Drosophila)-like"""				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.806T>C	chr16.hg19:g.1691167T>C	ENSP00000380559:p.Leu269Pro	82.0	0.0	.		110.0	39.0	.	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Missense_Mutation	SNP	ENST00000397412.3	hg19	CCDS10440.2	.	.	.	.	.	.	.	.	.	.	T	16.10	3.026242	0.54683	.	.	ENSG00000007545	ENST00000397412;ENST00000293925;ENST00000436138	.	.	.	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000020	T	0.77585	0.4152	M	0.67700	2.07	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79680	-0.1702	9	0.62326	D	0.03	-8.9801	15.5282	0.75928	0.0:0.0:0.0:1.0	.	269	Q96RY5	CRML_HUMAN	P	269;269;266	.	ENSP00000293925:L269P	L	+	2	0	CRAMP1L	1631168	1.000000	0.71417	0.997000	0.53966	0.667000	0.39255	7.618000	0.83043	2.076000	0.62316	0.459000	0.35465	CTG	.	.	.	none		0.368	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4		
ELP5	23587	hgsc.bcm.edu	37	17	7162047	7162047	+	Intron	SNP	A	A	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr17:7162047A>G	ENST00000396628.2	+	6	952				RP1-4G17.5_ENST00000577138.1_Intron|ELP5_ENST00000396627.2_Intron|ELP5_ENST00000354429.2_Intron|ELP5_ENST00000356683.2_Silent_p.V260V|ELP5_ENST00000574993.1_Silent_p.V260V	NM_203414.1	NP_981959.1	Q8TE02	ELP5_HUMAN	elongator acetyltransferase complex subunit 5						chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Elongator holoenzyme complex (GO:0033588)|nucleus (GO:0005634)											GTAGTTTAGTATCTGGTCACG	0.527																																					p.V260V		Atlas-SNP	.											.	.	.	.	0			c.A780G						PASS	.						92.0	100.0	98.0					17																	7162047		2203	4300	6503	SO:0001627	intron_variant	23587	exon7			TTTAGTATCTGGT	BC002762	CCDS11094.1, CCDS11095.1	17p13.1	2012-08-14	2012-08-08	2012-08-08	ENSG00000170291	ENSG00000170291		"""Elongator acetyltransferase complex subunits"""	30617	protein-coding gene	gene with protein product	"""dermal papilla derived protein 6"", ""S-phase 2 protein"""	615019	"""chromosome 17 open reading frame 81"""	C17orf81		22854966	Standard	NM_203415		Approved	DERP6	uc002gfi.1	Q8TE02	OTTHUMG00000177974	ENST00000396628.2:c.735+45A>G	chr17.hg19:g.7162047A>G		119.0	0.0	.		176.0	95.0	.	NM_203413	A8K1M5|D3DTN9|Q659B6|Q7Z2T4|Q8TDR9|Q9BUB2|Q9Y2Q4	Silent	SNP	ENST00000396628.2	hg19	CCDS11094.1																																																																																			.	.	.	none		0.527	ELP5-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440111.1	NM_015362	
SLC47A1	55244	hgsc.bcm.edu	37	17	19480761	19480761	+	Silent	SNP	A	A	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr17:19480761A>G	ENST00000270570.4	+	17	1694	c.1608A>G	c.(1606-1608)aaA>aaG	p.K536K	RP11-1113L8.1_ENST00000574267.1_RNA|AC025627.7_ENST00000420951.1_RNA|SLC47A1_ENST00000436810.2_3'UTR|SLC47A1_ENST00000457293.1_Silent_p.K536K|SLC47A1_ENST00000571335.1_Silent_p.K282K|SLC47A1_ENST00000575023.1_Silent_p.K234K|SLC47A1_ENST00000395585.1_Silent_p.K536K	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	536					organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|monovalent cation:proton antiporter activity (GO:0005451)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(5)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)				Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	ACGGCGCTAAATTGTCCAGGA	0.507																																					p.K536K		Atlas-SNP	.											.	SLC47A1	55	.	0			c.A1608G						PASS	.						144.0	148.0	147.0					17																	19480761		2203	4300	6503	SO:0001819	synonymous_variant	55244	exon17			CGCTAAATTGTCC		CCDS11209.1	17p11.2	2013-07-17	2013-07-17		ENSG00000142494	ENSG00000142494		"""Solute carriers"""	25588	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 1"""	609832				16330770, 16996621, 16928787	Standard	NM_018242		Approved	FLJ10847, MATE1	uc002gvy.1	Q96FL8	OTTHUMG00000059466	ENST00000270570.4:c.1608A>G	chr17.hg19:g.19480761A>G		133.0	0.0	.		226.0	124.0	.	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Silent	SNP	ENST00000270570.4	hg19	CCDS11209.1																																																																																			.	.	.	none		0.507	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242	
MED13	9969	hgsc.bcm.edu	37	17	60061702	60061702	+	Missense_Mutation	SNP	T	T	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr17:60061702T>G	ENST00000397786.2	-	15	2794	c.2718A>C	c.(2716-2718)gaA>gaC	p.E906D		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	906					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TTTGACAATTTTCAGGCTTAT	0.353																																					p.E906D		Atlas-SNP	.											.	MED13	181	.	0			c.A2718C						PASS	.						59.0	55.0	56.0					17																	60061702		1797	4068	5865	SO:0001583	missense	9969	exon15			ACAATTTTCAGGC	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.2718A>C	chr17.hg19:g.60061702T>G	ENSP00000380888:p.Glu906Asp	137.0	0.0	.		200.0	63.0	.	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	T	18.17	3.563848	0.65651	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.74632	-0.86	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.82907	0.5139	M	0.65975	2.015	0.54753	D	0.999982	D	0.64830	0.994	D	0.70716	0.97	D	0.83879	0.0278	10	0.56958	D	0.05	-17.933	10.3148	0.43729	0.0:0.1158:0.0:0.8842	.	906	Q9UHV7	MED13_HUMAN	D	906;905	ENSP00000380888:E906D	ENSP00000262436:E905D	E	-	3	2	MED13	57416484	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.904000	0.39868	2.225000	0.72522	0.528000	0.53228	GAA	.	.	.	none		0.353	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
FAM20A	54757	hgsc.bcm.edu	37	17	66533874	66533874	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr17:66533874T>C	ENST00000592554.1	-	11	2092	c.1370A>G	c.(1369-1371)aAg>aGg	p.K457R	FAM20A_ENST00000226094.5_5'UTR|PRKAR1A_ENST00000588188.2_Intron	NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	457					calcium ion homeostasis (GO:0055074)|enamel mineralization (GO:0070166)|tooth eruption (GO:0044691)	cell (GO:0005623)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(1)	9	Breast(10;1.64e-13)					AAGTGTTTTCTTTTTTATCCT	0.448																																					p.K457R		Atlas-SNP	.											.	FAM20A	35	.	0			c.A1370G						PASS	.						48.0	45.0	46.0					17																	66533874		2203	4300	6503	SO:0001583	missense	54757	exon11			GTTTTCTTTTTTA	AK056789	CCDS11679.1	17q24.2	2014-02-07			ENSG00000108950	ENSG00000108950			23015	protein-coding gene	gene with protein product		611062					Standard	NM_017565		Approved	DKFZp434F2322	uc002jho.3	Q96MK3	OTTHUMG00000180152	ENST00000592554.1:c.1370A>G	chr17.hg19:g.66533874T>C	ENSP00000468308:p.Lys457Arg	76.0	0.0	.		116.0	28.0	.	NM_017565	B2RN47|B2RN49|Q9UF95	Missense_Mutation	SNP	ENST00000592554.1	hg19	CCDS11679.1	.	.	.	.	.	.	.	.	.	.	T	8.231	0.804584	0.16467	.	.	ENSG00000108950	ENST00000226094;ENST00000375556	.	.	.	5.81	-2.2	0.06994	.	0.468058	0.27831	N	0.017669	T	0.19046	0.0457	N	0.04686	-0.185	0.26802	N	0.969185	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.14117	-1.0484	9	0.19147	T	0.46	-13.7073	14.1661	0.65477	0.0:0.5689:0.0:0.4311	.	457;319	Q96MK3;B7Z4Y3	FA20A_HUMAN;.	R	457;61	.	ENSP00000226094:K457R	K	-	2	0	FAM20A	64045469	0.995000	0.38212	0.890000	0.34922	0.794000	0.44872	0.337000	0.19841	-0.737000	0.04824	-0.375000	0.07067	AAG	.	.	.	none		0.448	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565	
LGALS3BP	3959	hgsc.bcm.edu	37	17	76969173	76969173	+	Missense_Mutation	SNP	A	A	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr17:76969173A>G	ENST00000262776.3	-	5	816	c.508T>C	c.(508-510)Tgt>Cgt	p.C170R	LGALS3BP_ENST00000585407.1_Missense_Mutation_p.C170R|LGALS3BP_ENST00000591778.1_Intron	NM_005567.3	NP_005558.1	Q08380	LG3BP_HUMAN	lectin, galactoside-binding, soluble, 3 binding protein	170	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(5)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(99;0.0677)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			GTGTGGCCACAGAAGCCCAGG	0.642																																					p.C170R	GBM(89;1105 1755 18102 21513)	Atlas-SNP	.											.	LGALS3BP	47	.	0			c.T508C						PASS	.						54.0	41.0	46.0					17																	76969173		2203	4300	6503	SO:0001583	missense	3959	exon5			GGCCACAGAAGCC	L13210	CCDS11759.1	17q25	2014-07-09				ENSG00000108679		"""BTB/POZ domain containing"", ""Endogenous ligands"""	6564	protein-coding gene	gene with protein product	"""L3 antigen"", ""Mac-2-binding protein"", ""serum protein 90K"", ""transport and golgi organization 10 homolog B (Drosophila)"""	600626				7698018, 8034587, 8390986	Standard	NM_005567		Approved	MAC-2-BP, 90K, BTBD17B, TANGO10B, M2BP, gp90, CyCAP	uc002jwh.3	Q08380		ENST00000262776.3:c.508T>C	chr17.hg19:g.76969173A>G	ENSP00000262776:p.Cys170Arg	63.0	0.0	.		119.0	29.0	.	NM_005567	Q7M4S0|Q9UCH8|Q9UCH9|Q9UCI0	Missense_Mutation	SNP	ENST00000262776.3	hg19	CCDS11759.1	.	.	.	.	.	.	.	.	.	.	A	13.38	2.219105	0.39201	.	.	ENSG00000108679	ENST00000262776;ENST00000536190	T	0.19938	2.11	3.04	3.04	0.35103	BTB/POZ-like (1);BTB/POZ fold (2);	0.000000	0.38778	N	0.001580	T	0.30603	0.0770	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.02115	-1.1211	10	0.44086	T	0.13	.	7.8817	0.29627	1.0:0.0:0.0:0.0	.	170	Q08380	LG3BP_HUMAN	R	170;158	ENSP00000262776:C170R	ENSP00000262776:C170R	C	-	1	0	LGALS3BP	74480768	0.986000	0.35501	0.287000	0.24848	0.283000	0.27025	5.780000	0.68956	1.661000	0.50771	0.459000	0.35465	TGT	.	.	.	none		0.642	LGALS3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437785.3	NM_005567	
FSCN2	25794	hgsc.bcm.edu	37	17	79495707	79495707	+	Silent	SNP	C	C	T	rs184519759	byFrequency	TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr17:79495707C>T	ENST00000417245.2	+	1	286	c.150C>T	c.(148-150)ccC>ccT	p.P50P	RP13-766D20.2_ENST00000442532.1_RNA|RP13-766D20.2_ENST00000430912.1_RNA|FSCN2_ENST00000334850.7_Silent_p.P50P	NM_001077182.2|NM_012418.3	NP_001070650.1|NP_036550.1	O14926	FSCN2_HUMAN	fascin actin-bundling protein 2, retinal	50					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|anatomical structure morphogenesis (GO:0009653)|eye photoreceptor cell development (GO:0042462)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|stereocilium (GO:0032420)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			endometrium(1)|lung(1)|prostate(1)|urinary_tract(1)	4	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			TGCTGGAACCCGACCCAGGAC	0.647																																					p.P50P		Atlas-SNP	.											.	FSCN2	35	.	0			c.C150T						PASS	.						18.0	19.0	18.0					17																	79495707		1985	4159	6144	SO:0001819	synonymous_variant	25794	exon1			GGAACCCGACCCA	AF030165	CCDS45810.1, CCDS45811.1	17q25	2014-02-03	2014-02-03		ENSG00000186765	ENSG00000186765		"""Fascins"""	3960	protein-coding gene	gene with protein product		607643	"""fascin (Strongylocentrotus purpuratus) homolog 2 (actin-bundling protein, retinal)"", ""fascin homolog 2, actin-bundling protein, retinal (Strongylocentrotus purpuratus)"""			10234509	Standard	NM_012418		Approved	RP30, RFSN	uc010wuo.2	O14926	OTTHUMG00000167477	ENST00000417245.2:c.150C>T	chr17.hg19:g.79495707C>T		122.0	0.0	.		191.0	61.0	.	NM_001077182	A0AVC4|A8MRA6	Silent	SNP	ENST00000417245.2	hg19	CCDS45811.1																																																																																			.	C|0.997;G|0.003	.	alt		0.647	FSCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394746.1	NM_012418	
SIRT7	51547	hgsc.bcm.edu	37	17	79875730	79875730	+	Missense_Mutation	SNP	C	C	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr17:79875730C>G	ENST00000328666.6	-	2	269	c.207G>C	c.(205-207)gaG>gaC	p.E69D		NM_016538.2	NP_057622.1	Q9NRC8	SIR7_HUMAN	sirtuin 7	69	Arg-rich.				histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription on exit from mitosis (GO:0007072)|rRNA transcription (GO:0009303)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleolus organizer region (GO:0005731)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			GCTTCAGGCCCTCGCGCCGCC	0.796																																					p.E69D		Atlas-SNP	.											.	SIRT7	37	.	0			c.G207C						PASS	.						1.0	1.0	1.0					17																	79875730		661	1650	2311	SO:0001583	missense	51547	exon2			CAGGCCCTCGCGC	AF233395	CCDS11792.1	17q25.3	2010-06-25	2010-06-25			ENSG00000187531			14935	protein-coding gene	gene with protein product		606212	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 7"", ""sirtuin (silent mating type information regulation 2 homolog) 7 (S. cerevisiae)"""			10873683, 16618798	Standard	NM_016538		Approved		uc002kcj.2	Q9NRC8		ENST00000328666.6:c.207G>C	chr17.hg19:g.79875730C>G	ENSP00000329466:p.Glu69Asp	21.0	0.0	.		30.0	18.0	.	NM_016538	A8K2K0|B3KSU8|Q3MIK4|Q9NSZ6|Q9NUS6	Missense_Mutation	SNP	ENST00000328666.6	hg19	CCDS11792.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.069771	0.36566	.	.	ENSG00000187531	ENST00000328666;ENST00000536038	T	0.16897	2.31	3.6	3.6	0.41247	.	0.545275	0.19339	N	0.116697	T	0.09949	0.0244	N	0.20685	0.6	0.80722	D	1	B	0.14012	0.009	B	0.12156	0.007	T	0.12682	-1.0538	10	0.12766	T	0.61	-22.0401	10.329	0.43812	0.0:0.8966:0.0:0.1034	.	69	Q9NRC8	SIRT7_HUMAN	D	69;52	ENSP00000329466:E69D	ENSP00000329466:E69D	E	-	3	2	SIRT7	77469022	0.998000	0.40836	1.000000	0.80357	0.311000	0.27955	0.921000	0.28718	1.826000	0.53198	0.195000	0.17529	GAG	.	.	.	none		0.796	SIRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439961.1	NM_016538	
PIAS2	9063	hgsc.bcm.edu	37	18	44416418	44416418	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr18:44416418A>T	ENST00000585916.1	-	9	1103	c.1104T>A	c.(1102-1104)ttT>ttA	p.F368L	PIAS2_ENST00000545673.1_Missense_Mutation_p.F78L|PIAS2_ENST00000324794.7_Missense_Mutation_p.F368L	NM_004671.3	NP_004662.2	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT, 2	368					androgen receptor signaling pathway (GO:0030521)|negative regulation of androgen receptor signaling pathway (GO:0060766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|regulation of osteoblast differentiation (GO:0045667)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	22						GGGCAGCATCAAAACACTGCA	0.413																																					p.F368L		Atlas-SNP	.											.	PIAS2	85	.	0			c.T1104A						PASS	.						125.0	111.0	116.0					18																	44416418		2203	4300	6503	SO:0001583	missense	9063	exon9			AGCATCAAAACAC	AF077953	CCDS32824.1, CCDS32825.1	18q12.1-q12.3	2011-10-11				ENSG00000078043		"""Zinc fingers, MIZ-type"""	17311	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 4"""	603567				9724754, 9256341	Standard	NM_004671		Approved	PIASX-BETA, miz, PIASX-ALPHA, ZMIZ4	uc002lck.3	O75928		ENST00000585916.1:c.1104T>A	chr18.hg19:g.44416418A>T	ENSP00000465676:p.Phe368Leu	181.0	0.0	.		205.0	15.0	.	NM_173206	O75927|Q96BT5|Q96KE3	Missense_Mutation	SNP	ENST00000585916.1	hg19	CCDS32824.1	.	.	.	.	.	.	.	.	.	.	A	19.77	3.889121	0.72524	.	.	ENSG00000078043	ENST00000398654;ENST00000262161;ENST00000398651;ENST00000545673;ENST00000324794	T;T	0.78595	-1.18;-1.19	5.52	3.17	0.36434	Zinc finger, MIZ-type (2);	0.000000	0.85682	D	0.000000	D	0.91317	0.7262	H	0.98314	4.2	0.80722	D	1	D;D;D;D;D	0.89917	0.997;1.0;0.999;1.0;0.999	D;D;D;D;D	0.91635	0.98;0.999;0.997;0.988;0.996	D	0.91010	0.4849	10	0.87932	D	0	-18.4406	8.3757	0.32442	0.7133:0.0:0.2867:0.0	.	78;372;368;368;368	B4DGW0;O75928-3;Q2TA77;O75928-2;O75928	.;.;.;.;PIAS2_HUMAN	L	368;368;364;78;368	ENSP00000443238:F78L;ENSP00000317163:F368L	ENSP00000262161:F368L	F	-	3	2	PIAS2	42670416	0.993000	0.37304	1.000000	0.80357	0.937000	0.57800	0.637000	0.24659	0.925000	0.37094	-0.467000	0.05162	TTT	.	.	.	none		0.413	PIAS2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445656.2	NM_004671	
DIRAS1	148252	hgsc.bcm.edu	37	19	2717307	2717307	+	Silent	SNP	C	C	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:2717307C>T	ENST00000323469.4	-	2	681	c.498G>A	c.(496-498)acG>acA	p.T166T	DIRAS1_ENST00000585334.1_Silent_p.T166T	NM_145173.3	NP_660156.1	O95057	DIRA1_HUMAN	DIRAS family, GTP-binding RAS-like 1	166					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(1)|lung(2)|ovary(2)|prostate(1)	6				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)		GCGTCTCCAGCGTCAGCAGCT	0.612																																					p.T166T		Atlas-SNP	.											.	DIRAS1	26	.	0			c.G498A						PASS	.						122.0	113.0	116.0					19																	2717307		2203	4300	6503	SO:0001819	synonymous_variant	148252	exon2			CTCCAGCGTCAGC	BC030660	CCDS12092.1	19p13.3	2014-05-09				ENSG00000176490			19127	protein-coding gene	gene with protein product		607862				12107278	Standard	NM_145173		Approved	Di-Ras1, GBTS1, RIG	uc002lwf.3	O95057		ENST00000323469.4:c.498G>A	chr19.hg19:g.2717307C>T		30.0	0.0	.		26.0	11.0	.	NM_145173		Silent	SNP	ENST00000323469.4	hg19	CCDS12092.1																																																																																			.	.	.	none		0.612	DIRAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451350.1		
PRKCSH	5589	hgsc.bcm.edu	37	19	11558367	11558367	+	Silent	SNP	G	G	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:11558367G>A	ENST00000589838.1	+	10	963	c.963G>A	c.(961-963)gaG>gaA	p.E321E	PRKCSH_ENST00000591462.1_Silent_p.E321E|PRKCSH_ENST00000252455.2_Silent_p.E321E|PRKCSH_ENST00000592741.1_Silent_p.E321E|PRKCSH_ENST00000587327.1_Silent_p.E321E|PRKCSH_ENST00000412601.1_Silent_p.E321E			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	321	Glu-rich (acidic).				cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)	p.E321_E322delEE(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						aggaggaggaggaggaagaag	0.632																																					p.E321E		Atlas-SNP	.											.	PRKCSH	55	.	1	Deletion - In frame(1)	central_nervous_system(1)	c.G963A						PASS	.						28.0	28.0	28.0					19																	11558367		2200	4298	6498	SO:0001819	synonymous_variant	5589	exon11			GGAGGAGGAGGAA		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"""EF-hand domain containing"""	9411	protein-coding gene	gene with protein product		177060	"""polycystic liver disease"""	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.963G>A	chr19.hg19:g.11558367G>A		101.0	0.0	.		114.0	10.0	.	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	hg19	CCDS32911.1																																																																																			.	.	.	none		0.632	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1		
ZNF823	55552	hgsc.bcm.edu	37	19	11833785	11833785	+	Silent	SNP	T	T	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:11833785T>G	ENST00000341191.6	-	4	717	c.564A>C	c.(562-564)ggA>ggC	p.G188G	ZNF823_ENST00000545749.1_Silent_p.G6G|CTC-499B15.6_ENST00000586983.1_RNA	NM_001080493.2	NP_001073962.1	P16415	ZN823_HUMAN	zinc finger protein 823	188					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)	26						AAGGTCCATCTCCATGGTGTG	0.443										HNSCC(68;0.2)																											p.G188G		Atlas-SNP	.											.	ZNF823	104	.	0			c.A564C						PASS	.						93.0	99.0	97.0					19																	11833785		2199	4298	6497	SO:0001819	synonymous_variant	55552	exon4			TCCATCTCCATGG	X51760	CCDS45981.1	19p13.2	2013-01-08			ENSG00000197933	ENSG00000197933		"""Zinc fingers, C2H2-type"", ""-"""	30936	protein-coding gene	gene with protein product	"""ZFP 36 for a zinc finger protein"""						Standard	XM_006722789		Approved	HSZFP36	uc002msm.2	P16415	OTTHUMG00000156528	ENST00000341191.6:c.564A>C	chr19.hg19:g.11833785T>G		146.0	0.0	.		152.0	69.0	.	NM_001080493	A0PJL4|B7Z8D4|Q6P4A9	Silent	SNP	ENST00000341191.6	hg19	CCDS45981.1																																																																																			.	.	.	none		0.443	ZNF823-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344516.2	NM_001080493	
SPHK2	56848	hgsc.bcm.edu	37	19	49132774	49132774	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:49132774G>A	ENST00000245222.4	+	7	2075	c.1709G>A	c.(1708-1710)tGg>tAg	p.W570*	SPHK2_ENST00000599029.1_Nonsense_Mutation_p.W534*|SPHK2_ENST00000600537.1_Nonsense_Mutation_p.W511*|SPHK2_ENST00000599748.1_Nonsense_Mutation_p.W534*|SPHK2_ENST00000443164.1_Nonsense_Mutation_p.W632*|SPHK2_ENST00000598088.1_Nonsense_Mutation_p.W570*|SPHK2_ENST00000340932.3_Nonsense_Mutation_p.W532*	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	570					blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		CACCTGTGCTGGGTGCGTAGC	0.667																																					p.W570X		Atlas-SNP	.											.	SPHK2	62	.	0			c.G1709A						PASS	.						27.0	24.0	25.0					19																	49132774		2200	4297	6497	SO:0001587	stop_gained	56848	exon7			TGTGCTGGGTGCG	AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.1709G>A	chr19.hg19:g.49132774G>A	ENSP00000245222:p.Trp570*	56.0	0.0	.		60.0	22.0	.	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Nonsense_Mutation	SNP	ENST00000245222.4	hg19	CCDS12727.1	.	.	.	.	.	.	.	.	.	.	G	39	7.795158	0.98495	.	.	ENSG00000063176	ENST00000245222;ENST00000406269;ENST00000340932;ENST00000443164	.	.	.	4.49	4.49	0.54785	.	0.199237	0.44285	D	0.000466	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-5.8616	10.1564	0.42825	0.0:0.0:0.8006:0.1993	.	.	.	.	X	570;543;532;632	.	ENSP00000245222:W570X	W	+	2	0	SPHK2	53824586	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	1.194000	0.32174	2.492000	0.84095	0.555000	0.69702	TGG	.	.	.	none		0.667	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
HRC	3270	hgsc.bcm.edu	37	19	49657747	49657747	+	Missense_Mutation	SNP	C	C	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:49657747C>A	ENST00000252825.4	-	1	934	c.748G>T	c.(748-750)Gat>Tat	p.D250Y	HRC_ENST00000595625.1_Missense_Mutation_p.D250Y	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	250	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Asp-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		tcatcatcatcatcatcgtca	0.498																																					p.D250Y	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.G748T						PASS	.						138.0	100.0	113.0					19																	49657747		2203	4300	6503	SO:0001583	missense	3270	exon1			CATCATCATCATC		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.748G>T	chr19.hg19:g.49657747C>A	ENSP00000252825:p.Asp250Tyr	22.0	0.0	.		25.0	11.0	.	NM_002152	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	hg19	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	N	12.91	2.079771	0.36662	.	.	ENSG00000130528	ENST00000252825;ENST00000434964	T	0.39787	1.06	2.35	1.24	0.21308	.	.	.	.	.	T	0.51873	0.1700	L	0.55990	1.75	0.34621	D	0.718578	D	0.56968	0.978	D	0.64144	0.922	T	0.60188	-0.7312	9	0.51188	T	0.08	.	8.641	0.33976	0.0:0.761:0.239:0.0	.	250	P23327	SRCH_HUMAN	Y	250;220	ENSP00000252825:D250Y	ENSP00000252825:D250Y	D	-	1	0	HRC	54349559	0.014000	0.17966	0.052000	0.19188	0.167000	0.22549	1.033000	0.30191	0.309000	0.22966	0.394000	0.25966	GAT	.	.	.	none		0.498	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
POLD1	5424	hgsc.bcm.edu	37	19	50918121	50918121	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:50918121T>A	ENST00000440232.2	+	20	2491	c.2438T>A	c.(2437-2439)cTc>cAc	p.L813H	POLD1_ENST00000599857.1_Missense_Mutation_p.L813H|POLD1_ENST00000595904.1_Missense_Mutation_p.L839H|CTD-2545M3.6_ENST00000599632.1_5'Flank	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	813					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		GCGGGCCTGCTCTTCTCCTCC	0.662								DNA polymerases (catalytic subunits)			OREG0025635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L813H		Atlas-SNP	.											.	POLD1	174	.	0			c.T2438A						PASS	.						55.0	53.0	54.0					19																	50918121		2203	4300	6503	SO:0001583	missense	5424	exon20			GCCTGCTCTTCTC		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.2438T>A	chr19.hg19:g.50918121T>A	ENSP00000406046:p.Leu813His	73.0	0.0	.	973	99.0	44.0	.	NM_002691	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	hg19	CCDS12795.1	.	.	.	.	.	.	.	.	.	.	T	12.00	1.806200	0.31961	.	.	ENSG00000062822	ENST00000440232;ENST00000376930	T	0.18502	2.21	4.84	4.84	0.62591	DNA polymerase, palm domain (1);DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.219677	0.39909	N	0.001224	T	0.30008	0.0751	M	0.80847	2.515	0.37207	D	0.90462	B;P	0.37731	0.407;0.607	B;P	0.46208	0.309;0.507	T	0.34304	-0.9834	10	0.87932	D	0	-38.3143	8.1304	0.31024	0.2888:0.0:0.0:0.7112	.	839;813	E7EVW0;P28340	.;DPOD1_HUMAN	H	813;814	ENSP00000406046:L813H	ENSP00000366129:L814H	L	+	2	0	POLD1	55609933	1.000000	0.71417	0.998000	0.56505	0.006000	0.05464	4.017000	0.57167	1.970000	0.57323	0.449000	0.29647	CTC	.	.	.	none		0.662	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1		
ZNF331	55422	hgsc.bcm.edu	37	19	54080924	54080924	+	Silent	SNP	C	C	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:54080924C>T	ENST00000253144.9	+	7	2443	c.1110C>T	c.(1108-1110)ctC>ctT	p.L370L	ZNF331_ENST00000512387.1_Silent_p.L370L|ZNF331_ENST00000513265.1_3'UTR|ZNF331_ENST00000411977.2_Silent_p.L370L|ZNF331_ENST00000449416.1_Silent_p.L370L|ZNF331_ENST00000513999.1_Silent_p.L370L|ZNF331_ENST00000511154.1_Silent_p.L370L|ZNF331_ENST00000511593.2_Silent_p.L370L	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	370					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		GCTATCACCTCACTCAGCACG	0.507			T	?	follicular thyroid adenoma																																p.L370L		Atlas-SNP	.		Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	.	ZNF331	66	.	0			c.C1110T						PASS	.						100.0	88.0	92.0					19																	54080924		2203	4300	6503	SO:0001819	synonymous_variant	55422	exon5			TCACCTCACTCAG	AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"""Zinc fingers, C2H2-type"", ""-"""	15489	protein-coding gene	gene with protein product	"""rearranged in thyroid adenomas"""	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.1110C>T	chr19.hg19:g.54080924C>T		212.0	0.0	.		254.0	115.0	.	NM_001253801	Q96GJ4	Silent	SNP	ENST00000253144.9	hg19	CCDS33102.1																																																																																			.	.	.	none		0.507	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1	NM_018555	
PPP6R1	22870	hgsc.bcm.edu	37	19	55748303	55748303	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:55748303G>A	ENST00000412770.2	-	16	2353	c.1787C>T	c.(1786-1788)tCc>tTc	p.S596F	AC010327.1_ENST00000581390.1_RNA|PPP6R1_ENST00000587283.1_Missense_Mutation_p.S596F	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	596					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						AGCATTGAGGGAGAAGGTGAT	0.622																																					p.S596F		Atlas-SNP	.											.	PPP6R1	63	.	0			c.C1787T						PASS	.						91.0	94.0	93.0					19																	55748303		2113	4217	6330	SO:0001583	missense	22870	exon16			TTGAGGGAGAAGG	AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	29195	protein-coding gene	gene with protein product		610875	"""KIAA1115"", ""SAPS domain family, member 1"""	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.1787C>T	chr19.hg19:g.55748303G>A	ENSP00000414202:p.Ser596Phe	167.0	0.0	.		165.0	67.0	.	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Missense_Mutation	SNP	ENST00000412770.2	hg19	CCDS46186.1	.	.	.	.	.	.	.	.	.	.	G	18.96	3.733755	0.69189	.	.	ENSG00000105063	ENST00000412770	T	0.49432	0.78	4.7	4.7	0.59300	.	0.000000	0.56097	D	0.000023	T	0.60051	0.2239	L	0.46157	1.445	0.38613	D	0.950959	D	0.64830	0.994	P	0.61328	0.887	T	0.65940	-0.6046	10	0.87932	D	0	-37.8255	16.9293	0.86186	0.0:0.0:1.0:0.0	.	596	Q9UPN7	PP6R1_HUMAN	F	596	ENSP00000414202:S596F	ENSP00000414202:S596F	S	-	2	0	PPP6R1	60440115	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	1.831000	0.39141	2.613000	0.88420	0.467000	0.42956	TCC	.	.	.	none		0.622	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931	
AAR2	25980	hgsc.bcm.edu	37	20	34832729	34832729	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr20:34832729A>C	ENST00000373932.3	+	3	1214	c.868A>C	c.(868-870)Aag>Cag	p.K290Q	AAR2_ENST00000320849.4_Missense_Mutation_p.K290Q|AAR2_ENST00000397286.3_Missense_Mutation_p.K290Q	NM_015511.3	NP_056326.2	Q9Y312	AAR2_HUMAN	AAR2 splicing factor homolog (S. cerevisiae)	290																	AGCCATGATGAAGCACCACAC	0.522																																					p.K290Q		Atlas-SNP	.											.	.	.	.	0			c.A868C						PASS	.						237.0	189.0	206.0					20																	34832729		2203	4300	6503	SO:0001583	missense	25980	exon3			ATGATGAAGCACC		CCDS13273.1	20q11.23	2012-07-20	2012-07-20	2012-07-20	ENSG00000131043	ENSG00000131043			15886	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 4"""	C20orf4			Standard	NM_015511		Approved	bA234K24.2	uc002xfc.3	Q9Y312	OTTHUMG00000032380	ENST00000373932.3:c.868A>C	chr20.hg19:g.34832729A>C	ENSP00000363043:p.Lys290Gln	122.0	0.0	.		133.0	56.0	.	NM_001271874	E1P5S7|Q9H4F9|Q9P1P3|Q9UFK9	Missense_Mutation	SNP	ENST00000373932.3	hg19	CCDS13273.1	.	.	.	.	.	.	.	.	.	.	A	12.67	2.007091	0.35415	.	.	ENSG00000131043	ENST00000397286;ENST00000320849;ENST00000373932	T;T;T	0.46819	0.86;0.86;0.86	6.03	4.94	0.65067	.	0.280019	0.46442	D	0.000292	T	0.29749	0.0743	N	0.25245	0.725	0.35498	D	0.79959	B;B	0.26902	0.163;0.029	B;B	0.30029	0.11;0.029	T	0.31971	-0.9924	10	0.14656	T	0.56	.	6.9997	0.24803	0.7752:0.1505:0.0743:0.0	.	290;290	A2A2Q9;Q9Y312	.;CT004_HUMAN	Q	290	ENSP00000380455:K290Q;ENSP00000313674:K290Q;ENSP00000363043:K290Q	ENSP00000313674:K290Q	K	+	1	0	C20orf4	34296143	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.832000	0.55783	2.308000	0.77769	0.533000	0.62120	AAG	.	.	.	none		0.522	AAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079001.2	NM_015511	
CSF2RB	1439	hgsc.bcm.edu	37	22	37333782	37333782	+	Missense_Mutation	SNP	G	G	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr22:37333782G>T	ENST00000403662.3	+	14	2154	c.1932G>T	c.(1930-1932)caG>caT	p.Q644H	CSF2RB_ENST00000536485.1_Missense_Mutation_p.Q591H|CSF2RB_ENST00000262825.5_Missense_Mutation_p.Q650H|CSF2RB_ENST00000406230.1_Missense_Mutation_p.Q650H			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	644					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	CTCTGGCCCAGGCGATGGGAC	0.701																																					p.Q644H		Atlas-SNP	.											.	CSF2RB	104	.	0			c.G1932T						PASS	.						8.0	9.0	9.0					22																	37333782		2169	4247	6416	SO:0001583	missense	1439	exon14			GGCCCAGGCGATG	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"""CD molecules"", ""Fibronectin type III domain containing"""	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.1932G>T	chr22.hg19:g.37333782G>T	ENSP00000384053:p.Gln644His	74.0	0.0	.		105.0	38.0	.	NM_000395	Q5JZI1|Q6ICE0	Missense_Mutation	SNP	ENST00000403662.3	hg19	CCDS13936.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.503380	0.44558	.	.	ENSG00000100368	ENST00000403662;ENST00000539104;ENST00000262825;ENST00000406230;ENST00000536485	D;D;D;D	0.93426	-2.71;-3.22;-3.22;-3.22	5.12	3.0	0.34707	.	0.556068	0.15041	N	0.283883	D	0.94984	0.8377	M	0.71581	2.175	0.27457	N	0.953266	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.978	D	0.87687	0.2551	10	0.22706	T	0.39	-24.6502	8.2995	0.32006	0.1892:0.0:0.8108:0.0	.	650;644	P32927-2;P32927	.;IL3RB_HUMAN	H	644;644;650;650;591	ENSP00000384053:Q644H;ENSP00000262825:Q650H;ENSP00000385271:Q650H;ENSP00000440003:Q591H	ENSP00000262825:Q650H	Q	+	3	2	CSF2RB	35663728	0.988000	0.35896	0.966000	0.40874	0.362000	0.29581	0.976000	0.29462	1.161000	0.42604	0.557000	0.71058	CAG	.	.	.	none		0.701	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395	
SREBF2	6721	hgsc.bcm.edu	37	22	42280845	42280846	+	Splice_Site	DNP	GG	GG	AT			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr22:42280845_42280846GG>AT	ENST00000361204.4	+	11	2204_2205	c.2038_2039GG>AT	c.(2038-2040)GGg>ATg	p.G680M		NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	680					cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						GCCCACCCTAGGGAAGCTTCCT	0.535																																					.|p.G680V		Atlas-SNP	.											.	SREBF2	99	.	0			c.2039-1G>A|c.G2039T						PASS	.																																			SO:0001630	splice_region_variant	6721	exon11			ACCCTAGGGAAGC|CCCTAGGGAAGCT	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"""Basic helix-loop-helix proteins"""	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	Exception_encountered	chr22.hg19:g.42280845_42280846delinsAT		126.0|124.0	0.0	.		132.0	64.0|62.0	.	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Splice_Site|Missense_Mutation	SNP	ENST00000361204.4	hg19	CCDS14023.1																																																																																			.	.	.	none		0.535	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599	Missense_Mutation
KDM5C	8242	hgsc.bcm.edu	37	X	53223343	53223343	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chrX:53223343C>T	ENST00000375401.3	-	23	4548	c.4016G>A	c.(4015-4017)gGc>gAc	p.G1339D	KDM5C_ENST00000375379.3_Missense_Mutation_p.G1339D|KDM5C_ENST00000404049.3_Missense_Mutation_p.G1338D|KDM5C_ENST00000375383.3_Missense_Mutation_p.G1298D|KDM5C_ENST00000452825.3_Missense_Mutation_p.G1272D	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	1339					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						CTTGCCACTGCCCTCTCTGAG	0.612			"""N, F, S"""		clear cell renal carcinoma																																p.G1339D		Atlas-SNP	.		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C	385	.	0			c.G4016A						PASS	.						22.0	20.0	21.0					X																	53223343		2201	4299	6500	SO:0001583	missense	8242	exon23			CCACTGCCCTCTC	Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	11114	protein-coding gene	gene with protein product		314690	"""Jumonji, AT rich interactive domain 1C (RBP2-like)"", ""Smcy homolog, X-linked (mouse)"", ""jumonji, AT rich interactive domain 1C"", ""mental retardation, X-linked 13"""	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.4016G>A	chrX.hg19:g.53223343C>T	ENSP00000364550:p.Gly1339Asp	201.0	0.0	.		237.0	108.0	.	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Missense_Mutation	SNP	ENST00000375401.3	hg19	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	c	0.196	-1.048772	0.01981	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	D;D;D;D;D	0.85773	-2.03;-1.71;-1.71;-1.73;-1.86	4.76	3.9	0.45041	.	0.400598	0.27631	N	0.018501	T	0.72087	0.3417	L	0.34521	1.04	0.26500	N	0.974785	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.13407	0.009;0.003;0.003	T	0.53933	-0.8368	10	0.02654	T	1	-4.4102	8.1117	0.30917	0.0:0.8839:0.0:0.1161	.	1272;1338;1339	F5H3T1;B0QZ44;P41229	.;.;KDM5C_HUMAN	D	1272;1339;1338;1339;1298	ENSP00000445176:G1272D;ENSP00000364550:G1339D;ENSP00000385394:G1338D;ENSP00000364528:G1339D;ENSP00000364532:G1298D	ENSP00000364528:G1339D	G	-	2	0	KDM5C	53240068	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	1.338000	0.33873	0.825000	0.34637	0.507000	0.49892	GGC	.	.	.	none		0.612	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187	
AR	367	hgsc.bcm.edu	37	X	66765164	66765164	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chrX:66765164A>T	ENST00000374690.3	+	1	700	c.176A>T	c.(175-177)cAg>cTg	p.Q59L	AR_ENST00000504326.1_Missense_Mutation_p.Q59L|AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q59L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	59	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	CTGCTgcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q59L		Atlas-SNP	.											.	AR	249	.	0			c.A176T						PASS	.						7.0	10.0	9.0					X																	66765164		2055	4063	6118	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	TGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"""Nuclear hormone receptors"""	644	protein-coding gene	gene with protein product	"""testicular feminization"", ""Kennedy disease"""	313700	"""dihydrotestosterone receptor"", ""spinal and bulbar muscular atrophy"""	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.176A>T	chrX.hg19:g.66765164A>T	ENSP00000363822:p.Gln59Leu	181.0	0.0	.		263.0	18.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	12.32	1.901651	0.33535	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.69175	-0.38;-0.38;-0.38	.	.	.	.	1.117170	0.06949	N	0.814177	T	0.47060	0.1425	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.34313	0.448;0.448	B;B	0.36534	0.227;0.227	T	0.31724	-0.9933	8	0.13108	T	0.6	.	.	.	.	.	59;59	E7EVX6;D3YPQ2	.;.	L	59	ENSP00000363822:Q59L;ENSP00000421155:Q59L;ENSP00000379359:Q59L	ENSP00000363822:Q59L	Q	+	2	0	AR	66681889	0.995000	0.38212	0.864000	0.33941	0.503000	0.33858	0.245000	0.18142	0.000000	0.14550	0.000000	0.15137	CAG	.	.	.	none		0.677	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044	
MAGT1	84061	hgsc.bcm.edu	37	X	77131066	77131066	+	Missense_Mutation	SNP	A	A	G			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chrX:77131066A>G	ENST00000373336.3	-	2	160	c.131T>C	c.(130-132)cTg>cCg	p.L44P	MAGT1_ENST00000358075.6_Missense_Mutation_p.L76P			Q9H0U3	MAGT1_HUMAN	magnesium transporter 1	44					cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(1)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	17						CCATTCCATCAGCTGACTAAC	0.388																																					p.L76P		Atlas-SNP	.											.	MAGT1	51	.	0			c.T227C						PASS	.						174.0	163.0	167.0					X																	77131066		2203	4296	6499	SO:0001583	missense	84061	exon2			TCCATCAGCTGAC		CCDS14436.2	Xq21.1	2014-09-17			ENSG00000102158	ENSG00000102158			28880	protein-coding gene	gene with protein product	"""oligosaccharyltransferase 3 homolog B (S. cerevisiae)"""	300715				15804357	Standard	NM_032121		Approved	DKFZp564K142, IAP, OST3B, MRX95	uc004fof.3	Q9H0U3	OTTHUMG00000021882	ENST00000373336.3:c.131T>C	chrX.hg19:g.77131066A>G	ENSP00000362433:p.Leu44Pro	141.0	0.0	.		167.0	71.0	.	NM_032121	B2RAR4|D3DTE3|Q53G00|Q6P577|Q8NBN6	Missense_Mutation	SNP	ENST00000373336.3	hg19		.	.	.	.	.	.	.	.	.	.	A	23.4	4.407210	0.83230	.	.	ENSG00000102158	ENST00000358075;ENST00000373336	T;T	0.26067	1.76;1.76	5.69	5.69	0.88448	.	0.063289	0.64402	U	0.000008	T	0.54886	0.1886	M	0.82823	2.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75484	0.977;0.986	T	0.61946	-0.6958	10	0.87932	D	0	-6.7821	14.9683	0.71213	1.0:0.0:0.0:0.0	.	44;76	Q9H0U3;B4DH58	MAGT1_HUMAN;.	P	76;44	ENSP00000354649:L76P;ENSP00000362433:L44P	ENSP00000354649:L76P	L	-	2	0	MAGT1	77017722	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.859000	0.92264	1.917000	0.55516	0.486000	0.48141	CTG	.	.	.	none		0.388	MAGT1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000057302.2	NM_032121	
RBM33	155435	hgsc.bcm.edu	37	7	155530893	155530893	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:155530893delA	ENST00000401878.3	+	11	1731	c.1533delA	c.(1531-1533)ccafs	p.P511fs		NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	511	Pro-rich.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		AGCCAGGACCAGCATTTAATC	0.572																																					p.P511fs		Atlas-Indel,Pindel	.											.	RBM33	157	.	0			c.1532delC						PASS	.						116.0	123.0	121.0					7																	155530893		2083	4230	6313	SO:0001589	frameshift_variant	155435	exon11			.	AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"""RNA binding motif (RRM) containing"""	27223	protein-coding gene	gene with protein product			"""proline rich 8"""	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.1533delA	chr7.hg19:g.155530893delA	ENSP00000384160:p.Pro511fs	143.0	0.0	0		165.0	77.0	0.466667	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Frame_Shift_Del	DEL	ENST00000401878.3	hg19	CCDS5941.2																																																																																			.	.	.	none		0.572	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408	
GABRG3	2567	hgsc.bcm.edu	37	15	27777821	27777821	+	Frame_Shift_Del	DEL	T	T	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr15:27777821delT	ENST00000333743.6	+	10	1452	c.1198delT	c.(1198-1200)tttfs	p.F400fs	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	400					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CTGGCAGGAATTTGAAGATAC	0.453																																					p.E399fs	NSCLC(114;800 1656 7410 37729 45293)	Atlas-Indel,Pindel	.											.	GABRG3	115	.	0			c.1197delA						PASS	.						91.0	94.0	93.0					15																	27777821		1976	4150	6126	SO:0001589	frameshift_variant	2567	exon10			.		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4088	protein-coding gene	gene with protein product	"""GABA(G) receptor, gamma 3"""	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.1198delT	chr15.hg19:g.27777821delT	ENSP00000331912:p.Phe400fs	129.0	0.0	0		160.0	33.0	0.20625	NM_033223	G3V594|Q9HD46|Q9NYT2	Frame_Shift_Del	DEL	ENST00000333743.6	hg19	CCDS45195.1																																																																																			.	.	.	none		0.453	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
DCST2	127579	hgsc.bcm.edu	37	1	155005652	155005652	+	Frame_Shift_Del	DEL	G	G	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:155005652delG	ENST00000368424.3	-	2	415	c.357delC	c.(355-357)gccfs	p.A119fs	DCST1_ENST00000392480.1_5'Flank|DCST1_ENST00000368419.2_5'Flank|DCST1_ENST00000423025.2_5'Flank|DCST2_ENST00000295536.5_Frame_Shift_Del_p.A119fs|DCST1_ENST00000295542.1_5'Flank	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	119						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|prostate(1)|skin(1)	38	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CAGCCTCGCTGGCCCGGGTGA	0.617																																					p.S120fs		Atlas-Indel,Pindel	.											.	DCST2	80	.	0			c.358delA						PASS	.						52.0	50.0	51.0					1																	155005652		2203	4300	6503	SO:0001589	frameshift_variant	127579	exon2			.	AK057496	CCDS1082.2	1q22	2008-02-05		2005-08-09	ENSG00000163354	ENSG00000163354			26562	protein-coding gene	gene with protein product							Standard	NM_144622		Approved	FLJ32934	uc001fgm.3	Q5T1A1	OTTHUMG00000037371	ENST00000368424.3:c.357delC	chr1.hg19:g.155005652delG	ENSP00000357409:p.Ala119fs	204.0	0.0	0		235.0	112.0	0.476596	NM_144622	Q2M2R2|Q8N810|Q96M03	Frame_Shift_Del	DEL	ENST00000368424.3	hg19	CCDS1082.2																																																																																			.	.	.	none		0.617	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622	
TRPM6	140803	hgsc.bcm.edu	37	9	77407567	77407567	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr9:77407567delA	ENST00000360774.1	-	19	2748	c.2511delT	c.(2509-2511)gctfs	p.A837fs	TRPM6_ENST00000376864.4_Frame_Shift_Del_p.A837fs|TRPM6_ENST00000451710.3_Frame_Shift_Del_p.A837fs|TRPM6_ENST00000361255.3_Frame_Shift_Del_p.A832fs|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_Frame_Shift_Del_p.A832fs|TRPM6_ENST00000376871.3_Intron	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	837					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						TGACAATTGGAGCACTGTAGA	0.408																																					p.P838fs		Atlas-INDEL	.											.	TRPM6	377	.	0			c.2512delC						PASS	.						149.0	130.0	136.0					9																	77407567		2203	4300	6503	SO:0001589	frameshift_variant	140803	exon19			.	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.2511delT	chr9.hg19:g.77407567delA	ENSP00000354006:p.Ala837fs	135.0	0.0	0		120.0	55.0	0.458333	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Frame_Shift_Del	DEL	ENST00000360774.1	hg19	CCDS6647.1																																																																																			.	.	.	none		0.408	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
FAM200A	221786	hgsc.bcm.edu	37	7	99145242	99145243	+	Frame_Shift_Ins	INS	-	-	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:99145242_99145243insT	ENST00000449309.1	-	2	1167_1168	c.788_789insA	c.(787-789)aatfs	p.N263fs		NM_145111.3	NP_659802.1	Q8TCP9	F200A_HUMAN	family with sequence similarity 200, member A	263						integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			endometrium(1)|kidney(5)|large_intestine(2)|ovary(2)|skin(1)	11						ttttcactgcatttttcaatac	0.366																																					p.N263fs		Atlas-Indel,Pindel	.											.	FAM200A	27	.	0			c.789_790insA						PASS	.																																			SO:0001589	frameshift_variant	221786	exon2			.		CCDS5668.1	7q22.1	2010-02-22	2010-02-22	2010-02-22	ENSG00000221909	ENSG00000221909			25401	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 38"""	C7orf38		10607616	Standard	NM_145111		Approved	FLJ36794, DKFZp727G131	uc003ura.3	Q8TCP9	OTTHUMG00000156723	ENST00000449309.1:c.789dupA	chr7.hg19:g.99145247_99145247dupT	ENSP00000411372:p.Asn263fs	93.0	0.0	0		125.0	54.0	0.432	NM_145111	A4D293|A8K3V9|B2RD92|C9J6A8|D6W5T2|Q8N9P3	Frame_Shift_Ins	INS	ENST00000449309.1	hg19	CCDS5668.1																																																																																			.	.	.	none		0.366	FAM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345467.1	NM_145111	
ZNF407	55628	hgsc.bcm.edu	37	18	72352965	72352973	+	Splice_Site	DEL	ATCAAAACC	ATCAAAACC	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	ATCAAAACC	ATCAAAACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr18:72352965_72352973delATCAAAACC	ENST00000299687.5	+	2	4689_4697	c.4689_4697delATCAAAACC	c.(4687-4698)ggatcaaaacca>gga	p.SKP1564del	ZNF407_ENST00000577538.1_Splice_Site_p.SKP1564del|ZNF407_ENST00000309902.6_Splice_Site_p.SKP1564del|ZNF407_ENST00000582337.1_Splice_Site_p.SKP1564del	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1564					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TTTACTCAGGATCAAAACCATTCAAGTGC	0.349																																					p.1563_1566del		Atlas-Indel,Pindel	.											.	ZNF407	231	.	0			c.4688_4696del						PASS	.																																			SO:0001630	splice_region_variant	55628	exon2			.	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.4688-1ATCAAAACC>-	chr18.hg19:g.72352965_72352973delATCAAAACC		222.0	0.0	0		214.0	70.0	0.327103	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	In_Frame_Del	DEL	ENST00000299687.5	hg19	CCDS45885.1																																																																																			.	.	.	none		0.349	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	In_Frame_Del
RNF103	7844	hgsc.bcm.edu	37	2	86839326	86839326	+	Frame_Shift_Del	DEL	T	T	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:86839326delT	ENST00000237455.4	-	3	1406	c.438delA	c.(436-438)agafs	p.R146fs	AC015971.2_ENST00000597638.1_RNA|AC015971.2_ENST00000424788.1_RNA|AC015971.2_ENST00000426549.1_RNA|RNF103_ENST00000477307.1_5'UTR|CHMP3_ENST00000439940.2_Intron|RNF103-CHMP3_ENST00000604011.1_Intron|AC015971.2_ENST00000439077.1_RNA	NM_001198951.1|NM_005667.3	NP_001185880.1|NP_005658.1	O00237	RN103_HUMAN	ring finger protein 103	146					central nervous system development (GO:0007417)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(7)|skin(2)	25						GTATTCCAAATCTTGACACCT	0.378																																					p.F147fs		Atlas-Indel,Pindel	.											.	RNF103	58	.	0			c.439delT						PASS	.						133.0	126.0	128.0					2																	86839326		2203	4300	6503	SO:0001589	frameshift_variant	7844	exon3			.	D76444	CCDS33237.1	2p11.2	2013-01-09	2003-05-14	2003-05-16	ENSG00000239305	ENSG00000239305		"""RING-type (C3HC4) zinc fingers"""	12859	protein-coding gene	gene with protein product		602507	"""zinc finger protein 103 homolog (mouse)"""	ZFP103		9070305	Standard	NM_005667		Approved	hkf-1, KF1	uc021vkg.1	O00237	OTTHUMG00000153197	ENST00000237455.4:c.438delA	chr2.hg19:g.86839326delT	ENSP00000237455:p.Arg146fs	130.0	0.0	0		137.0	59.0	0.430657	NM_005667	A6NFV6|B2RAG4|Q53SU6|Q8IVB9	Frame_Shift_Del	DEL	ENST00000237455.4	hg19	CCDS33237.1																																																																																			.	.	.	none		0.378	RNF103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330041.2	NM_005667	
TRPM6	140803	hgsc.bcm.edu	37	9	77407562	77407564	+	In_Frame_Del	DEL	ATT	ATT	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	ATT	ATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr9:77407562_77407564delATT	ENST00000360774.1	-	19	2751_2753	c.2514_2516delAAT	c.(2512-2517)ccaatt>cct	p.I839del	TRPM6_ENST00000376864.4_In_Frame_Del_p.I839del|TRPM6_ENST00000451710.3_In_Frame_Del_p.I839del|TRPM6_ENST00000361255.3_In_Frame_Del_p.I834del|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_In_Frame_Del_p.I834del|TRPM6_ENST00000376871.3_Intron	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	839					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						AAACTTGACAATTGGAGCACTGT	0.394																																					p.839_839del		Atlas-INDEL	.											.	TRPM6	377	.	0			c.2515_2517del						PASS	.																																			SO:0001651	inframe_deletion	140803	exon19			.	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.2514_2516delAAT	chr9.hg19:g.77407562_77407564delATT	ENSP00000354006:p.Ile839del	137.0	0.0	0		113.0	51.0	0.451327	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	In_Frame_Del	DEL	ENST00000360774.1	hg19	CCDS6647.1																																																																																			.	.	.	none		0.394	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
TNIP1	10318	hgsc.bcm.edu	37	5	150443282	150443283	+	In_Frame_Ins	INS	-	-	ATA			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:150443282_150443283insATA	ENST00000389378.2	-	3	750_751	c.162_163insTAT	c.(160-165)atggaa>atgTATgaa	p.54_55ME>MYE	TNIP1_ENST00000523338.1_In_Frame_Ins_p.54_55ME>MYE|TNIP1_ENST00000315050.7_In_Frame_Ins_p.54_55ME>MYE|TNIP1_ENST00000522226.1_In_Frame_Ins_p.54_55ME>MYE|TNIP1_ENST00000521591.1_In_Frame_Ins_p.54_55ME>MYE|TNIP1_ENST00000523200.1_In_Frame_Ins_p.54_55ME>MYE|TNIP1_ENST00000524280.1_In_Frame_Ins_p.54_55ME>MYE|TNIP1_ENST00000518977.1_In_Frame_Ins_p.54_55ME>MYE|TNIP1_ENST00000520931.1_In_Frame_Ins_p.1_2ME>MYE	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1	54					defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGGTCGCTTCCATCTGGGACT	0.589																																					p.E55delinsYE		Atlas-INDEL	.											.	TNIP1	51	.	0			c.163_164insTAT						PASS	.																																			SO:0001652	inframe_insertion	10318	exon3			.	AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"""virion-associated nuclear-shuttling protein"", ""Nef-associated factor 1 SNP"""	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025		ENST00000389378.2:c.162_163insTAT	chr5.hg19:g.150443282_150443283insATA	ENSP00000374029:p.Met54_Glu55insTyr	79.0	0.0	0		68.0	18.0	0.264706	NM_001252385	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	In_Frame_Ins	INS	ENST00000389378.2	hg19	CCDS34280.1																																																																																			.	.	.	none		0.589	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12918882	12918890	+	In_Frame_Del	DEL	ACCGAGACT	ACCGAGACT	-	rs149417814|rs17404792|rs138447851	byFrequency	TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	ACCGAGACT	ACCGAGACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:12918882_12918890delACCGAGACT	ENST00000240189.2	+	2	105_113	c.18_26delACCGAGACT	c.(16-27)ccaccgagacta>cca	p.PRL7del		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	7					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TCCAGGCCCCACCGAGACTACTGGAGCTG	0.55																																					p.6_9del		Atlas-Indel,Pindel	.											.	PRAMEF2	85	.	0			c.17_25del						PASS	.																																			SO:0001651	inframe_deletion	65122	exon2			.		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.18_26delACCGAGACT	chr1.hg19:g.12918882_12918890delACCGAGACT	ENSP00000240189:p.Pro7_Leu9del	179.0	0.0	0		208.0	73.0	0.350962	NM_023014		In_Frame_Del	DEL	ENST00000240189.2	hg19	CCDS149.1																																																																																			.	.	.	none		0.550	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
NSMAF	8439	hgsc.bcm.edu	37	8	59510054	59510055	+	Frame_Shift_Ins	INS	-	-	C			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr8:59510054_59510055insC	ENST00000038176.3	-	21	1895_1896	c.1683_1684insG	c.(1681-1686)gggcagfs	p.Q562fs	NSMAF_ENST00000427130.2_Frame_Shift_Ins_p.Q593fs	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	562	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				TTTGGTGTCTGCCCAAATTCCA	0.441																																					p.Q593fs		Atlas-Indel,Pindel	.											.	NSMAF	156	.	0			c.1777_1778insG						PASS	.																																			SO:0001589	frameshift_variant	8439	exon21			.	X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"""WD repeat domain containing"""	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.1684dupG	chr8.hg19:g.59510057_59510057dupC	ENSP00000038176:p.Gln562fs	96.0	0.0	0		114.0	47.0	0.412281	NM_001144772	B4DFB0|E9PCH0|Q8IW26	Frame_Shift_Ins	INS	ENST00000038176.3	hg19	CCDS6173.1																																																																																			.	.	.	none		0.441	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580	
NCOA1	8648	hgsc.bcm.edu	37	2	24930212	24930212	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:24930212delA	ENST00000406961.1	+	13	2525	c.1873delA	c.(1873-1875)aaafs	p.K625fs	NCOA1_ENST00000395856.3_Frame_Shift_Del_p.K625fs|NCOA1_ENST00000288599.5_Frame_Shift_Del_p.K625fs|NCOA1_ENST00000538539.1_Frame_Shift_Del_p.K625fs|NCOA1_ENST00000405141.1_Frame_Shift_Del_p.K625fs|NCOA1_ENST00000348332.3_Frame_Shift_Del_p.K625fs|NCOA1_ENST00000407230.1_Frame_Shift_Del_p.K474fs			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	625	Ser-rich.				androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGAGACAGTAAATACTCTCA	0.418			T	PAX3	alveolar rhadomyosarcoma																																p.S624fs		Atlas-Indel,Pindel	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.1872delT						PASS	.						52.0	50.0	51.0					2																	24930212		2203	4300	6503	SO:0001589	frameshift_variant	8648	exon11			.	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.1873delA	chr2.hg19:g.24930212delA	ENSP00000385216:p.Lys625fs	204.0	0.0	0		206.0	78.0	0.378641	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Frame_Shift_Del	DEL	ENST00000406961.1	hg19	CCDS1712.1																																																																																			.	.	.	none		0.418	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223	
C12orf40	283461	hgsc.bcm.edu	37	12	40034792	40034792	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:40034792delA	ENST00000324616.5	+	2	213	c.59delA	c.(58-60)caafs	p.Q20fs	C12orf40_ENST00000405531.3_Frame_Shift_Del_p.Q20fs|C12orf40_ENST00000398716.1_5'UTR	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	20										breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						AGAAGAAAGCAAAAGGTAAAG	0.353																																					p.Q20fs		Atlas-Indel,Pindel	.											.	C12orf40	118	.	0			c.58delC						PASS	.						76.0	75.0	76.0					12																	40034792		1815	4075	5890	SO:0001589	frameshift_variant	283461	exon2			.	AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.59delA	chr12.hg19:g.40034792delA	ENSP00000317671:p.Gln20fs	95.0	0.0	0		197.0	42.0	0.213198	NM_001031748	B7WNU1|Q8IXY6|Q8N818|V9HW02	Frame_Shift_Del	DEL	ENST00000324616.5	hg19	CCDS41770.1																																																																																			.	.	.	none		0.353	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599	
SLC12A6	9990	hgsc.bcm.edu	37	15	34551060	34551067	+	Frame_Shift_Del	DEL	TGTTCCTT	TGTTCCTT	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	TGTTCCTT	TGTTCCTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr15:34551060_34551067delTGTTCCTT	ENST00000354181.3	-	5	982_989	c.490_497delAAGGAACA	c.(490-498)aaggaacatfs	p.KEH164fs	SLC12A6_ENST00000558589.1_Frame_Shift_Del_p.KEH155fs|RP11-1084A12.2_ENST00000559867.1_RNA|SLC12A6_ENST00000451844.2_Frame_Shift_Del_p.KEH25fs|SLC12A6_ENST00000560164.1_Frame_Shift_Del_p.KEH25fs|SLC12A6_ENST00000560611.1_Frame_Shift_Del_p.KEH164fs|SLC12A6_ENST00000558667.1_Frame_Shift_Del_p.KEH164fs|SLC12A6_ENST00000397707.2_Frame_Shift_Del_p.KEH149fs|SLC12A6_ENST00000290209.5_Frame_Shift_Del_p.KEH113fs|SLC12A6_ENST00000458406.2_Frame_Shift_Del_p.KEH105fs|SLC12A6_ENST00000397702.2_Frame_Shift_Del_p.KEH105fs			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	164					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	TGCCTCTTCATGTTCCTTTGCTCCTTGA	0.447																																					p.164_166del		Atlas-Indel,Pindel	.											.	SLC12A6	205	.	0			c.491_498del						PASS	.																																			SO:0001589	frameshift_variant	9990	exon4			.	AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"""Solute carriers"""	10914	protein-coding gene	gene with protein product		604878	"""agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"""	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.490_497delAAGGAACA	chr15.hg19:g.34551060_34551067delTGTTCCTT	ENSP00000346112:p.Lys164fs	108.0	0.0	0		113.0	17.0	0.150442	NM_133647	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Frame_Shift_Del	DEL	ENST00000354181.3	hg19	CCDS58352.1																																																																																			.	.	.	none		0.447	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102431117	102431140	+	In_Frame_Del	DEL	TGCAGAAGCACCTGCGCAAGCTGG	TGCAGAAGCACCTGCGCAAGCTGG	-	rs369058949		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	TGCAGAAGCACCTGCGCAAGCTGG	TGCAGAAGCACCTGCGCAAGCTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr14:102431117_102431140delTGCAGAAGCACCTGCGCAAGCTGG	ENST00000360184.4	+	1	253_276	c.89_112delTGCAGAAGCACCTGCGCAAGCTGG	c.(88-114)ctgcagaagcacctgcgcaagctggtg>ctg	p.QKHLRKLV31del		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	31					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GTGTCGGTGCTGCAGAAGCACCTGCGCAAGCTGGTGCCGCTGCT	0.714																																					p.30_37del		Atlas-Indel,Pindel	.											.	DYNC1H1	395	.	0			c.88_111del						PASS	.																																			SO:0001651	inframe_deletion	1778	exon1			.	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.89_112delTGCAGAAGCACCTGCGCAAGCTGG	chr14.hg19:g.102431117_102431140delTGCAGAAGCACCTGCGCAAGCTGG	ENSP00000348965:p.Gln31_Val38del	93.0	0.0	0		106.0	36.0	0.339623	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	In_Frame_Del	DEL	ENST00000360184.4	hg19	CCDS9966.1																																																																																			.	.	.	none		0.714	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
SYNCRIP	10492	hgsc.bcm.edu	37	6	86324737	86324740	+	Frame_Shift_Del	DEL	CTCG	CTCG	-	rs371636541		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	CTCG	CTCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr6:86324737_86324740delCTCG	ENST00000369622.3	-	11	2106_2109	c.1606_1609delCGAG	c.(1606-1611)cgaggtfs	p.RG536fs	RP11-321N4.5_ENST00000503906.1_Frame_Shift_Del_p.FE71fs|SYNCRIP_ENST00000355238.6_Frame_Shift_Del_p.RG536fs	NM_001159675.1|NM_006372.4	NP_001153147.1|NP_006363.4	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA interacting protein	536	8 X 3 AA repeats of R-G-G.|Interaction with APOBEC1.|Interaction with SMN.				cellular response to interferon-gamma (GO:0071346)|CRD-mediated mRNA stabilization (GO:0070934)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|endoplasmic reticulum (GO:0005783)|GAIT complex (GO:0097452)|histone pre-mRNA 3'end processing complex (GO:0071204)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		CCTCTCGCACCTCGAACGCCTCTT	0.623																																					p.536_537del		Atlas-Indel,Pindel	.											.	SYNCRIP	80	.	0			c.1607_1610del						PASS	.																																			SO:0001589	frameshift_variant	10492	exon11			.	AF037448	CCDS5005.1, CCDS55041.1, CCDS75491.1	6q14-q15	2013-05-23			ENSG00000135316	ENSG00000135316		"""RNA binding motif (RRM) containing"""	16918	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein Q"""					9847309, 11352648	Standard	NM_006372		Approved	NSAP1, GRY-RBP, dJ3J17.2, HNRPQ1, hnRNP-Q, HNRNPQ	uc003pla.2	O60506	OTTHUMG00000015141	ENST00000369622.3:c.1606_1609delCGAG	chr6.hg19:g.86324737_86324740delCTCG	ENSP00000358635:p.Arg536fs	83.0	0.0	0		98.0	37.0	0.377551	NM_001159677	E1P501|E1P502|Q53H05|Q5TCG2|Q5TCG3|Q8IW78|Q8N599|Q96LC1|Q96LC2|Q9Y583	Frame_Shift_Del	DEL	ENST00000369622.3	hg19	CCDS5005.1																																																																																			.	.	.	none		0.623	SYNCRIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041396.1	NM_006372	
WDR19	57728	hgsc.bcm.edu	37	4	39206803	39206804	+	Frame_Shift_Ins	INS	-	-	T			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr4:39206803_39206804insT	ENST00000399820.3	+	8	787_788	c.633_634insT	c.(634-636)tttfs	p.F212fs	WDR19_ENST00000506503.1_Frame_Shift_Ins_p.F212fs|WDR19_ENST00000288634.7_Frame_Shift_Ins_p.F52fs	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	212					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						AGAAAACTTTGTTTTTTTTAAA	0.361																																					p.L211fs		Atlas-Indel,Pindel	.											.,2	WDR19	96	.	0			c.633_634insT						PASS	.																																			SO:0001589	frameshift_variant	57728	exon8			.	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	18340	protein-coding gene	gene with protein product	"""intraflagellar transport 144 homolog (Chlamydomonas)"""	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.641dupT	chr4.hg19:g.39206811_39206811dupT	ENSP00000382717:p.Phe212fs	62.0	0.0	0		72.0	30.0	0.416667	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Frame_Shift_Ins	INS	ENST00000399820.3	hg19	CCDS47042.1																																																																																			.	.	.	none		0.361	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1		
TCP10L2	401285	hgsc.bcm.edu	37	6	167591988	167591988	+	Frame_Shift_Del	DEL	G	G	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr6:167591988delG	ENST00000366832.2	+	5	746	c.615delG	c.(613-615)ccgfs	p.P205fs		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	205										endometrium(1)|kidney(2)|lung(3)	6						CTGGAAGGCCGACTCCCGGTG	0.522																																					p.P205fs		Atlas-Indel,Pindel	.											TCP10L2_ENST00000366832,NS,carcinoma,0,2	TCP10L2	41	.	0			c.614delC						PASS	.						229.0	205.0	212.0					6																	167591988		692	1590	2282	SO:0001589	frameshift_variant	401285	exon5			.		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.615delG	chr6.hg19:g.167591988delG	ENSP00000355797:p.Pro205fs	620.0	0.0	0		647.0	129.0	0.199382	NM_001145121		Frame_Shift_Del	DEL	ENST00000366832.2	hg19	CCDS47514.1																																																																																			.	.	.	none		0.522	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
FAM208A	23272	hgsc.bcm.edu	37	3	56694972	56694972	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr3:56694972delA	ENST00000493960.2	-	10	1244	c.1234delT	c.(1234-1236)tatfs	p.Y412fs	FAM208A_ENST00000355628.5_Frame_Shift_Del_p.Y412fs|FAM208A_ENST00000431842.2_Frame_Shift_Del_p.Y16fs	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	412							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						GTTTCCTTATAAAACAGTGCT	0.289																																					p.Y412fs		Atlas-Indel,Pindel	.											.	FAM208A	113	.	0			c.1235delA						PASS	.						112.0	112.0	112.0					3																	56694972		2202	4298	6500	SO:0001589	frameshift_variant	23272	exon10			.	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 63"""	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.1234delT	chr3.hg19:g.56694972delA	ENSP00000417509:p.Tyr412fs	148.0	0.0	0		152.0	58.0	0.381579	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Frame_Shift_Del	DEL	ENST00000493960.2	hg19	CCDS46853.1																																																																																			.	.	.	none		0.289	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224	
ARAP1	116985	hgsc.bcm.edu	37	11	72408128	72408132	+	Frame_Shift_Del	DEL	CTGCT	CTGCT	-	rs377204604		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	CTGCT	CTGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:72408128_72408132delCTGCT	ENST00000393609.3	-	22	3264_3268	c.3062_3066delAGCAG	c.(3061-3066)gagcagfs	p.EQ1021fs	ARAP1_ENST00000359373.5_Frame_Shift_Del_p.EQ1021fs|ARAP1_ENST00000455638.2_Frame_Shift_Del_p.EQ1021fs|ARAP1_ENST00000429686.1_Frame_Shift_Del_p.EQ715fs|ARAP1_ENST00000426523.1_Frame_Shift_Del_p.EQ776fs|ARAP1_ENST00000334211.8_Frame_Shift_Del_p.EQ776fs|ARAP1_ENST00000393605.3_Frame_Shift_Del_p.EQ781fs|ARAP1_ENST00000495878.1_5'UTR	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	1021	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						CATCCACGTGCTGCTCGCCCTCCTT	0.649																																					p.1021_1023del	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-Indel,Pindel	.											.	ARAP1	168	.	0			c.3063_3067del						PASS	.																																			SO:0001589	frameshift_variant	116985	exon22			.	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16925	protein-coding gene	gene with protein product		606646	"""centaurin, delta 2"""	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.3062_3066delAGCAG	chr11.hg19:g.72408128_72408132delCTGCT	ENSP00000377233:p.Glu1021fs	84.0	0.0	0		69.0	24.0	0.347826	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Frame_Shift_Del	DEL	ENST00000393609.3	hg19	CCDS41687.1																																																																																			.	.	.	none		0.649	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118	
BCAS1	8537	hgsc.bcm.edu	37	20	52569985	52569991	+	Frame_Shift_Del	DEL	AGCCCCC	AGCCCCC	-	rs200870946|rs375030303	byFrequency	TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	AGCCCCC	AGCCCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr20:52569985_52569991delAGCCCCC	ENST00000395961.3	-	11	1826_1832	c.1660_1666delGGGGGCT	c.(1660-1668)gggggcttcfs	p.GGF554fs	BCAS1_ENST00000434986.2_Frame_Shift_Del_p.GGF220fs|BCAS1_ENST00000371435.2_Frame_Shift_Del_p.GGF476fs|BCAS1_ENST00000371440.3_Frame_Shift_Del_p.GGF563fs	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	554						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			CCTTTAAAGAAGCCCCCAAGGGACTGC	0.527																																					p.554_556del		Atlas-Indel,Pindel	.											.	BCAS1	77	.	0			c.1661_1667del						PASS	.																																			SO:0001589	frameshift_variant	8537	exon11			.	AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787			974	protein-coding gene	gene with protein product		602968				9671742	Standard	NM_003657		Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772	ENST00000395961.3:c.1660_1666delGGGGGCT	chr20.hg19:g.52569985_52569991delAGCCCCC	ENSP00000379290:p.Gly554fs	61.0	0.0	0		68.0	19.0	0.279412	NM_003657	A0AVG5|Q68CZ3	Frame_Shift_Del	DEL	ENST00000395961.3	hg19	CCDS13444.1																																																																																			.	.	.	none		0.527	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657	
NUDT16L1	84309	hgsc.bcm.edu	37	16	4743827	4743827	+	Frame_Shift_Del	DEL	G	G	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr16:4743827delG	ENST00000304301.6	+	1	133	c.100delG	c.(100-102)gccfs	p.A35fs	NUDT16L1_ENST00000405142.1_Frame_Shift_Del_p.A35fs|NUDT16L1_ENST00000586252.1_Frame_Shift_Del_p.A35fs|NUDT16L1_ENST00000586536.1_Frame_Shift_Del_p.A35fs	NM_032349.3	NP_115725.1	Q9BRJ7	SDOS_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1	35						cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			endometrium(1)|large_intestine(1)|lung(1)|skin(1)	4						CATGCTGTACGCCGCCAACCC	0.736																																					p.Y33X		Atlas-INDEL	.											.	NUDT16L1	13	.	0			c.99delC						PASS	.						18.0	17.0	17.0					16																	4743827		2174	4289	6463	SO:0001589	frameshift_variant	84309	exon1			.	BC006223	CCDS10519.1, CCDS59257.1	16p13.3	2008-02-05			ENSG00000168101	ENSG00000168101		"""Nudix motif containing"""	28154	protein-coding gene	gene with protein product						11805099	Standard	NM_032349		Approved	SDOS	uc002cxe.3	Q9BRJ7	OTTHUMG00000129471	ENST00000304301.6:c.100delG	chr16.hg19:g.4743827delG	ENSP00000306670:p.Ala35fs	81.0	0.0	0		142.0	77.0	0.542253	NM_001193452	Q8NAI2	Frame_Shift_Del	DEL	ENST00000304301.6	hg19	CCDS10519.1																																																																																			.	.	.	none		0.736	NUDT16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251634.1	NM_032349	
CTDSPL	10217	hgsc.bcm.edu	37	3	38017370	38017370	+	Frame_Shift_Del	DEL	C	C	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr3:38017370delC	ENST00000273179.5	+	7	716	c.690delC	c.(688-690)ttcfs	p.F230fs	CTDSPL_ENST00000443503.2_Frame_Shift_Del_p.F219fs|CTDSPL_ENST00000310189.3_3'UTR	NM_001008392.1	NP_001008393.1	O15194	CTDSL_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	230	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|large_intestine(4)|skin(1)	8		Melanoma(1037;0.0122)		KIRC - Kidney renal clear cell carcinoma(284;0.0729)|Kidney(284;0.0902)		CATACATCTTCCATCCTGAGA	0.507																																					p.F230fs		Atlas-Indel,Pindel	.											.	CTDSPL	17	.	0			c.689delT						PASS	.						93.0	92.0	92.0					3																	38017370		2203	4300	6503	SO:0001589	frameshift_variant	10217	exon7			.	D88153	CCDS33734.1, CCDS33735.1	3p21.3	2010-06-21	2003-10-27	2003-10-29	ENSG00000144677	ENSG00000144677	3.1.3.16	"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	16890	protein-coding gene	gene with protein product	"""small CTD phosphatase 3"", ""HYA22 protein"", ""RB protein serine phosphatase from chromosome 3"""	608592	"""chromosome 3 open reading frame 8"""	C3orf8		9179494, 12543795	Standard	NM_005808		Approved	HYA22, SCP3, PSR1, RBSP3	uc003chg.3	O15194	OTTHUMG00000155942	ENST00000273179.5:c.690delC	chr3.hg19:g.38017370delC	ENSP00000273179:p.Phe230fs	74.0	0.0	0		96.0	30.0	0.3125	NM_001008392	Q3ZTU0|Q70KI4|Q7Z5Q2	Frame_Shift_Del	DEL	ENST00000273179.5	hg19	CCDS33734.1																																																																																			.	.	.	none		0.507	CTDSPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342392.1	NM_005808	
PTPN14	5784	hgsc.bcm.edu	37	1	214588010	214588010	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:214588010delA	ENST00000366956.5	-	4	598	c.404delT	c.(403-405)ttgfs	p.L135fs	PTPN14_ENST00000543945.1_Frame_Shift_Del_p.L135fs	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	135	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		CACCTGGTCCAATGTACATCG	0.423																																					p.L135fs	Colon(92;557 1424 24372 34121 40073)	Atlas-Indel,Pindel	.											.	PTPN14	168	.	0			c.405delG						PASS	.						287.0	259.0	269.0					1																	214588010		2203	4300	6503	SO:0001589	frameshift_variant	5784	exon4			.	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.404delT	chr1.hg19:g.214588010delA	ENSP00000355923:p.Leu135fs	80.0	0.0	0		76.0	34.0	0.447368	NM_005401	Q5VSI0	Frame_Shift_Del	DEL	ENST00000366956.5	hg19	CCDS1514.1																																																																																			.	.	.	none		0.423	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401	
VN1R2	317701	hgsc.bcm.edu	37	19	53762550	53762564	+	In_Frame_Del	DEL	TCTCCTGGGAACAGA	TCTCCTGGGAACAGA	-	rs61732642|rs146904187	byFrequency	TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	TCTCCTGGGAACAGA	TCTCCTGGGAACAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:53762550_53762564delTCTCCTGGGAACAGA	ENST00000341702.3	+	1	1006_1020	c.922_936delTCTCCTGGGAACAGA	c.(922-936)tctcctgggaacagadel	p.SPGNR308del	VN1R2_ENST00000598458.1_3'UTR	NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	308					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)	p.G310G(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		CCCCAACTCTTCTCCTGGGAACAGAGCCATCCAAA	0.479																																					p.307_312del		Atlas-Indel,Pindel	.											.	VN1R2	71	.	1	Substitution - coding silent(1)	skin(1)	c.921_935del						PASS	.																																			SO:0001651	inframe_deletion	317701	exon1			.	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.922_936delTCTCCTGGGAACAGA	chr19.hg19:g.53762550_53762564delTCTCCTGGGAACAGA	ENSP00000351244:p.Ser308_Arg312del	105.0	0.0	0		131.0	39.0	0.29771	NM_173856	A1L411|Q8TDU4	In_Frame_Del	DEL	ENST00000341702.3	hg19	CCDS12862.1																																																																																			.	.	.	none		0.479	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856	
ZC3H6	376940	hgsc.bcm.edu	37	2	113089842	113089843	+	Frame_Shift_Del	DEL	AC	AC	-	rs371812950		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:113089842_113089843delAC	ENST00000409871.1	+	12	3748_3749	c.3347_3348delAC	c.(3346-3348)gacfs	p.D1116fs	ZC3H6_ENST00000343936.4_Frame_Shift_Del_p.D1116fs|AC115115.2_ENST00000607612.1_RNA	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	1116							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						CCACAGGCGGACGTTCCCAGGA	0.535																																					p.1116_1116del		Pindel	.											.	ZC3H6	93	.	0			c.3346_3347del						PASS	.																																			SO:0001589	frameshift_variant	376940	exon12			.	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"""Zinc fingers, CCCH-type domain containing"""	24762	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 6"""	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.3347_3348delAC	chr2.hg19:g.113089842_113089843delAC	ENSP00000386764:p.Asp1116fs	273.0	0.0	.		357.0	81.0	0.227	NM_198581	A9JR71|Q6ZW96	Frame_Shift_Del	DEL	ENST00000409871.1	hg19	CCDS46393.1																																																																																			.	.	.	none		0.535	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581	
TRPM6	140803	hgsc.bcm.edu	37	9	77407562	77407567	+	In_Frame_Del	DEL	ATTGGA	ATTGGA	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	ATTGGA	ATTGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr9:77407562_77407567delATTGGA	ENST00000360774.1	-	19	2748_2753	c.2511_2516delTCCAAT	c.(2509-2517)gctccaatt>gct	p.PI838del	TRPM6_ENST00000376864.4_In_Frame_Del_p.PI838del|TRPM6_ENST00000451710.3_In_Frame_Del_p.PI838del|TRPM6_ENST00000361255.3_In_Frame_Del_p.PI833del|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_In_Frame_Del_p.PI833del|TRPM6_ENST00000376871.3_Intron	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	838					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						AAACTTGACAATTGGAGCACTGTAGA	0.403																																					p.838_839del		Pindel	.											.	TRPM6	377	.	0			c.2512_2517del						PASS	.																																			SO:0001651	inframe_deletion	140803	exon19			.	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.2511_2516delTCCAAT	chr9.hg19:g.77407562_77407567delATTGGA	ENSP00000354006:p.Pro838_Ile839del	137.0	0.0	.		120.0	42.0	0.350	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	In_Frame_Del	DEL	ENST00000360774.1	hg19	CCDS6647.1																																																																																			.	.	.	none		0.403	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
TNIP1	10318	hgsc.bcm.edu	37	5	150443283	150443286	+	Frame_Shift_Del	DEL	CATC	CATC	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	CATC	CATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:150443283_150443286delCATC	ENST00000389378.2	-	3	747_750	c.159_162delGATG	c.(157-162)cagatgfs	p.QM53fs	TNIP1_ENST00000523338.1_Frame_Shift_Del_p.QM53fs|TNIP1_ENST00000315050.7_Frame_Shift_Del_p.QM53fs|TNIP1_ENST00000522226.1_Frame_Shift_Del_p.QM53fs|TNIP1_ENST00000521591.1_Frame_Shift_Del_p.QM53fs|TNIP1_ENST00000523200.1_Frame_Shift_Del_p.QM53fs|TNIP1_ENST00000524280.1_Frame_Shift_Del_p.QM53fs|TNIP1_ENST00000518977.1_Frame_Shift_Del_p.QM53fs|TNIP1_ENST00000520931.1_Start_Codon_Del	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1	53					defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGGTCGCTTCCATCTGGGACTCTT	0.588																																					p.54_55del		Pindel	.											.	TNIP1	51	.	0			c.160_163del						PASS	.																																			SO:0001589	frameshift_variant	10318	exon3			.	AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"""virion-associated nuclear-shuttling protein"", ""Nef-associated factor 1 SNP"""	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025		ENST00000389378.2:c.159_162delGATG	chr5.hg19:g.150443283_150443286delCATC	ENSP00000374029:p.Gln53fs	77.0	0.0	.		66.0	14.0	0.212	NM_001252385	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Frame_Shift_Del	DEL	ENST00000389378.2	hg19	CCDS34280.1																																																																																			.	.	.	none		0.588	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058	
NUDT16L1	84309	hgsc.bcm.edu	37	16	4743827	4743828	+	Frame_Shift_Del	DEL	GC	GC	-			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr16:4743827_4743828delGC	ENST00000304301.6	+	1	133_134	c.100_101delGC	c.(100-102)gccfs	p.A35fs	NUDT16L1_ENST00000405142.1_Frame_Shift_Del_p.A35fs|NUDT16L1_ENST00000586252.1_Frame_Shift_Del_p.A35fs|NUDT16L1_ENST00000586536.1_Frame_Shift_Del_p.A35fs	NM_032349.3	NP_115725.1	Q9BRJ7	SDOS_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1	35						cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			endometrium(1)|large_intestine(1)|lung(1)|skin(1)	4						CATGCTGTACGCCGCCAACCCT	0.738																																					p.33_34del		Pindel	.											.	NUDT16L1	13	.	0			c.99_100del						PASS	.																																			SO:0001589	frameshift_variant	84309	exon1			.	BC006223	CCDS10519.1, CCDS59257.1	16p13.3	2008-02-05			ENSG00000168101	ENSG00000168101		"""Nudix motif containing"""	28154	protein-coding gene	gene with protein product						11805099	Standard	NM_032349		Approved	SDOS	uc002cxe.3	Q9BRJ7	OTTHUMG00000129471	ENST00000304301.6:c.100_101delGC	chr16.hg19:g.4743827_4743828delGC	ENSP00000306670:p.Ala35fs	82.0	0.0	.		141.0	55.0	0.390	NM_001193452	Q8NAI2	Frame_Shift_Del	DEL	ENST00000304301.6	hg19	CCDS10519.1																																																																																			.	.	.	none		0.738	NUDT16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251634.1	NM_032349	
