#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
CCDC17	149483	hgsc.bcm.edu	37	1	46088962	46088962	+	Silent	SNP	C	C	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr1:46088962C>T	ENST00000528266.1	-	3	567	c.420G>A	c.(418-420)gcG>gcA	p.A140A	CCDC17_ENST00000464739.1_5'Flank|CCDC17_ENST00000421127.2_Silent_p.A131A|CCDC17_ENST00000343901.2_Silent_p.A108A|CCDC17_ENST00000445048.2_Intron			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	140										kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					TCCTGAACAGCGCCCGCAGCC	0.721																																					p.A140A		Atlas-SNP	.											.	CCDC17	54	.	0			c.G420A						.						6.0	9.0	8.0					1																	46088962		689	1581	2270	SO:0001819	synonymous_variant	149483	exon3			GAACAGCGCCCGC		CCDS44131.1, CCDS44131.2, CCDS53314.1	1p34.1	2014-02-12			ENSG00000159588	ENSG00000159588			26574	protein-coding gene	gene with protein product							Standard	NM_001190182		Approved	FLJ33084	uc010olt.2	Q96LX7	OTTHUMG00000007822	ENST00000528266.1:c.420G>A	chr1.hg19:g.46088962C>T		44.0	0.0		51.0	28.0	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Silent	SNP	ENST00000528266.1	hg19	CCDS44131.2																																																																																			.	.		0.721	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500	
DDX20	11218	hgsc.bcm.edu	37	1	112309297	112309297	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr1:112309297C>A	ENST00000369702.4	+	11	2871	c.2251C>A	c.(2251-2253)Cag>Aag	p.Q751K	DDX20_ENST00000475700.1_Missense_Mutation_p.Q359K	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	751					ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GACTGAAGCCCAGGAAGATGA	0.483																																					p.Q751K		Atlas-SNP	.											.	DDX20	50	.	0			c.C2251A						.						91.0	90.0	90.0					1																	112309297		2203	4300	6503	SO:0001583	missense	11218	exon11			GAAGCCCAGGAAG	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.2251C>A	chr1.hg19:g.112309297C>A	ENSP00000358716:p.Gln751Lys	165.0	0.0		212.0	59.0	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	hg19	CCDS842.1	.	.	.	.	.	.	.	.	.	.	C	7.570	0.666613	0.14710	.	.	ENSG00000064703	ENST00000369702;ENST00000475700	T;T	0.32023	1.47;1.99	5.82	3.96	0.45880	.	0.823783	0.11427	N	0.565143	T	0.13415	0.0325	L	0.60455	1.87	0.45307	D	0.9983	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.04946	-1.0916	9	.	.	.	-1.705	7.4811	0.27406	0.3537:0.5695:0.0:0.0769	.	359;751	E9PJ60;Q9UHI6	.;DDX20_HUMAN	K	751;359	ENSP00000358716:Q751K;ENSP00000435660:Q359K	.	Q	+	1	0	DDX20	112110820	0.011000	0.17503	0.950000	0.38849	0.160000	0.22226	0.599000	0.24089	0.815000	0.34398	-0.152000	0.13540	CAG	.	.		0.483	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
GATAD2B	57459	hgsc.bcm.edu	37	1	153788806	153788806	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr1:153788806C>A	ENST00000368655.4	-	7	1402	c.1159G>T	c.(1159-1161)Gag>Tag	p.E387*		NM_020699.2	NP_065750.1	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	387	CR2; histone tail-binding.				ATP-dependent chromatin remodeling (GO:0043044)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	38	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TAGATGAACTCGCTATTGGCT	0.463																																					p.E387X		Atlas-SNP	.											.	GATAD2B	62	.	0			c.G1159T						.						92.0	78.0	83.0					1																	153788806		2203	4300	6503	SO:0001587	stop_gained	57459	exon7			TGAACTCGCTATT	AF411836	CCDS1054.1	1q21.3	2013-01-25			ENSG00000143614	ENSG00000143614		"""GATA zinc finger domain containing"""	30778	protein-coding gene	gene with protein product	"""transcription repressor p66 beta component of the MeCP1 complex"""	614998				10574461, 11756549	Standard	NM_020699		Approved	P66beta	uc001fdb.4	Q8WXI9	OTTHUMG00000037162	ENST00000368655.4:c.1159G>T	chr1.hg19:g.153788806C>A	ENSP00000357644:p.Glu387*	127.0	0.0		165.0	83.0	NM_020699	D3DUZ2|Q5VUR2|Q7LG68|Q9ULS0	Nonsense_Mutation	SNP	ENST00000368655.4	hg19	CCDS1054.1	.	.	.	.	.	.	.	.	.	.	C	38	6.995398	0.97990	.	.	ENSG00000143614	ENST00000368655	.	.	.	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-0.0201	17.0353	0.86473	0.0:1.0:0.0:0.0	.	.	.	.	X	387	.	ENSP00000357644:E387X	E	-	1	0	GATAD2B	152055430	1.000000	0.71417	0.995000	0.50966	0.982000	0.71751	7.626000	0.83164	2.549000	0.85964	0.563000	0.77884	GAG	.	.		0.463	GATAD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090305.1	NM_020699	
TNN	63923	hgsc.bcm.edu	37	1	175067569	175067569	+	Missense_Mutation	SNP	C	C	T	rs199634558		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr1:175067569C>T	ENST00000239462.4	+	9	2070	c.1957C>T	c.(1957-1959)Cgc>Tgc	p.R653C		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	653	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GTACGTGGTGCGCTACACCTC	0.597																																					p.R653C		Atlas-SNP	.											.	TNN	297	.	0			c.C1957T						.	C	CYS/ARG	0,4406		0,0,2203	92.0	89.0	90.0		1957	0.7	1.0	1		90	1,8599	1.2+/-3.3	0,1,4299	no	missense	TNN	NM_022093.1	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	653/1300	175067569	1,13005	2203	4300	6503	SO:0001583	missense	63923	exon9			GTGGTGCGCTACA	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.1957C>T	chr1.hg19:g.175067569C>T	ENSP00000239462:p.Arg653Cys	383.0	0.0		598.0	292.0	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	hg19	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	C	10.93	1.489934	0.26686	0.0	1.16E-4	ENSG00000120332	ENST00000239462	T	0.58652	0.32	5.14	0.658	0.17855	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.336638	0.35555	N	0.003128	T	0.73001	0.3531	M	0.89478	3.035	0.31421	N	0.674312	D;D	0.71674	0.997;0.998	P;D	0.63381	0.86;0.914	T	0.74300	-0.3710	10	0.49607	T	0.09	.	9.5181	0.39117	0.6598:0.265:0.0:0.0752	.	653;653	B3KXB6;Q9UQP3	.;TENN_HUMAN	C	653	ENSP00000239462:R653C	ENSP00000239462:R653C	R	+	1	0	TNN	173334192	1.000000	0.71417	0.995000	0.50966	0.045000	0.14185	2.396000	0.44468	-0.085000	0.12573	-0.378000	0.06908	CGC	.	.		0.597	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
SDCCAG8	10806	hgsc.bcm.edu	37	1	243589739	243589739	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr1:243589739G>T	ENST00000366541.3	+	16	1982	c.1864G>T	c.(1864-1866)Gct>Tct	p.A622S	SDCCAG8_ENST00000343783.6_Missense_Mutation_p.A477S|SDCCAG8_ENST00000355875.4_Missense_Mutation_p.A579S	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	622	Gln-rich.|Mediates interaction with OFD1.|Sufficient for homodimerization. {ECO:0000250}.				establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		ATCTGAAATAGCTCAACTCAG	0.318																																					p.A622S		Atlas-SNP	.											.	SDCCAG8	73	.	0			c.G1864T						.						66.0	64.0	65.0					1																	243589739		2203	4300	6503	SO:0001583	missense	10806	exon16			GAAATAGCTCAAC	AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.1864G>T	chr1.hg19:g.243589739G>T	ENSP00000355499:p.Ala622Ser	377.0	0.0		379.0	132.0	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Missense_Mutation	SNP	ENST00000366541.3	hg19	CCDS31075.1	.	.	.	.	.	.	.	.	.	.	G	10.93	1.488945	0.26686	.	.	ENSG00000054282	ENST00000355875;ENST00000366541;ENST00000343783;ENST00000435549	T;T;T;T	0.43294	0.95;1.02;0.97;0.99	6.17	0.559	0.17272	.	1.082370	0.06931	N	0.811054	T	0.21801	0.0525	N	0.14661	0.345	0.09310	N	1	B;B	0.17667	0.008;0.023	B;B	0.12156	0.007;0.007	T	0.25467	-1.0131	10	0.10902	T	0.67	-0.1395	5.3204	0.15878	0.0719:0.1051:0.3617:0.4613	.	579;622	E9PFS7;Q86SQ7	.;SDCG8_HUMAN	S	579;622;477;323	ENSP00000348137:A579S;ENSP00000355499:A622S;ENSP00000341260:A477S;ENSP00000410200:A323S	ENSP00000341260:A477S	A	+	1	0	SDCCAG8	241656362	0.941000	0.31946	0.981000	0.43875	0.918000	0.54935	0.960000	0.29253	0.418000	0.25898	-0.169000	0.13324	GCT	.	.		0.318	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642	
ZBTB18	10472	hgsc.bcm.edu	37	1	244218178	244218178	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr1:244218178G>T	ENST00000358704.4	+	2	1251	c.1102G>T	c.(1102-1104)Gtc>Ttc	p.V368F		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	359	Interaction with DNMT3A.				cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GCTCCCCTACGTCTCCAACAT	0.617																																					p.V368F		Atlas-SNP	.											.	.	.	.	0			c.G1102T						.						69.0	60.0	63.0					1																	244218178		2203	4300	6503	SO:0001583	missense	10472	exon2			CCCTACGTCTCCA	U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13030	protein-coding gene	gene with protein product		608433	"""zinc finger protein 238"""	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.1102G>T	chr1.hg19:g.244218178G>T	ENSP00000351539:p.Val368Phe	85.0	0.0		94.0	44.0	NM_205768	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Missense_Mutation	SNP	ENST00000358704.4	hg19	CCDS1622.1	.	.	.	.	.	.	.	.	.	.	G	19.63	3.862771	0.71949	.	.	ENSG00000179456	ENST00000366538;ENST00000358704	T	0.13089	2.62	5.83	5.83	0.93111	.	0.059626	0.64402	D	0.000003	T	0.28632	0.0709	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.85130	0.993;0.997	T	0.01371	-1.1372	10	0.56958	D	0.05	.	20.1184	0.97949	0.0:0.0:1.0:0.0	.	359;368	Q99592;Q99592-2	ZN238_HUMAN;.	F	368	ENSP00000351539:V368F	ENSP00000351539:V368F	V	+	1	0	ZNF238	242284801	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.824000	0.99380	2.775000	0.95449	0.650000	0.86243	GTC	.	.		0.617	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768	
ZNF672	79894	hgsc.bcm.edu	37	1	249142142	249142142	+	Silent	SNP	G	G	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr1:249142142G>C	ENST00000306562.3	+	4	1415	c.669G>C	c.(667-669)ggG>ggC	p.G223G		NM_024836.1	NP_079112.1	Q499Z4	ZN672_HUMAN	zinc finger protein 672	223					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G223G(1)		endometrium(2)|kidney(2)|large_intestine(1)	5	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			CGCACTCGGGGGAGAAACCCT	0.662																																					p.G223G		Atlas-SNP	.											ZNF672,caecum,carcinoma,0,1	ZNF672	32	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G669C						.						10.0	10.0	10.0					1																	249142142		2195	4289	6484	SO:0001819	synonymous_variant	79894	exon4			CTCGGGGGAGAAA	AK027476	CCDS1638.1	1q44	2013-01-08			ENSG00000171161	ENSG00000171161		"""Zinc fingers, C2H2-type"""	26179	protein-coding gene	gene with protein product	"""hypothetical protein FLJ22301"""					12477932	Standard	NM_024836		Approved	FLJ22301	uc001iex.3	Q499Z4	OTTHUMG00000040377	ENST00000306562.3:c.669G>C	chr1.hg19:g.249142142G>C		75.0	0.0		62.0	16.0	NM_024836	Q96H65|Q96IM3|Q9H6G5	Silent	SNP	ENST00000306562.3	hg19	CCDS1638.1																																																																																			.	.		0.662	ZNF672-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097125.2	NM_024836	
TMEM247	388946	hgsc.bcm.edu	37	2	46707887	46707887	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:46707887A>C	ENST00000434431.1	+	2	461	c.461A>C	c.(460-462)gAg>gCg	p.E154A		NM_001145051.2	NP_001138523.1	A6NEH6	TM247_HUMAN	transmembrane protein 247	154						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											CTGCAGCAAGAGGCGGCGCCC	0.687																																					p.E154A		Atlas-SNP	.											.	.	.	.	0			c.A461C						.						16.0	20.0	19.0					2																	46707887		690	1590	2280	SO:0001583	missense	388946	exon2			AGCAAGAGGCGGC		CCDS56117.1	2p21	2012-04-11			ENSG00000187600	ENSG00000187600			42967	protein-coding gene	gene with protein product							Standard	NM_001145051		Approved		uc010yod.3	A6NEH6	OTTHUMG00000153137	ENST00000434431.1:c.461A>C	chr2.hg19:g.46707887A>C	ENSP00000388684:p.Glu154Ala	117.0	0.0		101.0	19.0	NM_001145051		Missense_Mutation	SNP	ENST00000434431.1	hg19	CCDS56117.1	.	.	.	.	.	.	.	.	.	.	A	4.562	0.104456	0.08731	.	.	ENSG00000187600	ENST00000434431	.	.	.	4.12	1.52	0.23074	.	.	.	.	.	T	0.25531	0.0621	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.04013	0.001	T	0.18967	-1.0320	7	0.37606	T	0.19	.	8.7168	0.34416	0.6235:0.3765:0.0:0.0	.	154	A6NEH6	YB028_HUMAN	A	154	.	ENSP00000388684:E154A	E	+	2	0	AC018682.6	46561391	0.914000	0.31030	0.027000	0.17364	0.000000	0.00434	2.075000	0.41538	0.127000	0.18452	-0.461000	0.05368	GAG	.	.		0.687	TMEM247-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329726.1	NM_001145051	
UGP2	7360	hgsc.bcm.edu	37	2	64114716	64114716	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:64114716A>C	ENST00000337130.5	+	8	1728	c.1252A>C	c.(1252-1254)Atg>Ctg	p.M418L	UGP2_ENST00000394417.2_Missense_Mutation_p.M407L|UGP2_ENST00000445915.2_Missense_Mutation_p.M427L|UGP2_ENST00000467648.2_Missense_Mutation_p.M407L	NM_006759.3	NP_006750.3	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2	418					carbohydrate metabolic process (GO:0005975)|cellular glucuronidation (GO:0052695)|glucose 1-phosphate metabolic process (GO:0019255)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	glucose binding (GO:0005536)|metal ion binding (GO:0046872)|pyrimidine ribonucleotide binding (GO:0032557)|UTP:glucose-1-phosphate uridylyltransferase activity (GO:0003983)			endometrium(2)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)	18						ATCTCTGACAATGAGTGAAAA	0.393																																					p.M418L		Atlas-SNP	.											.	UGP2	38	.	0			c.A1252C						.						150.0	153.0	152.0					2																	64114716		2203	4300	6503	SO:0001583	missense	7360	exon8			CTGACAATGAGTG		CCDS1875.1, CCDS42690.1	2p14-p13	2012-10-02			ENSG00000169764	ENSG00000169764	2.7.7.9		12527	protein-coding gene	gene with protein product		191760	"""UDP-glucose pyrophosphorylase 1"""	UGP1			Standard	NM_006759		Approved	UGPP1	uc002scm.3	Q16851	OTTHUMG00000129513	ENST00000337130.5:c.1252A>C	chr2.hg19:g.64114716A>C	ENSP00000338703:p.Met418Leu	181.0	0.0		197.0	67.0	NM_006759	Q07131|Q0P6K2|Q86Y81|Q9BU15	Missense_Mutation	SNP	ENST00000337130.5	hg19	CCDS1875.1	.	.	.	.	.	.	.	.	.	.	A	13.53	2.265630	0.40095	.	.	ENSG00000169764	ENST00000394417;ENST00000467648;ENST00000337130;ENST00000445915	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	5.81	5.81	0.92471	.	0.034479	0.85682	D	0.000000	T	0.09774	0.0240	N	0.11427	0.14	0.80722	D	1	B;B	0.20887	0.049;0.049	B;B	0.31016	0.123;0.123	T	0.33394	-0.9870	10	0.16420	T	0.52	2.8559	16.1536	0.81640	1.0:0.0:0.0:0.0	.	427;418	E7EUC7;Q16851	.;UGPA_HUMAN	L	407;407;418;427	ENSP00000377939:M407L;ENSP00000420793:M407L;ENSP00000338703:M418L;ENSP00000411803:M427L	ENSP00000338703:M418L	M	+	1	0	UGP2	63968220	1.000000	0.71417	0.957000	0.39632	0.971000	0.66376	7.302000	0.78861	2.203000	0.70933	0.528000	0.53228	ATG	.	.		0.393	UGP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251688.1	NM_006759	
VPS54	51542	hgsc.bcm.edu	37	2	64176272	64176272	+	Silent	SNP	A	A	G			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:64176272A>G	ENST00000272322.4	-	8	1190	c.1036T>C	c.(1036-1038)Tta>Cta	p.L346L	VPS54_ENST00000354504.3_Silent_p.L229L|VPS54_ENST00000409558.4_Silent_p.L334L			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	346					growth (GO:0040007)|homeostasis of number of cells within a tissue (GO:0048873)|musculoskeletal movement (GO:0050881)|neurofilament cytoskeleton organization (GO:0060052)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)				endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						AGTTTTTCTAATTCACAAAGC	0.318																																					p.L346L		Atlas-SNP	.											.	VPS54	57	.	0			c.T1036C						.						56.0	54.0	54.0					2																	64176272		2201	4299	6500	SO:0001819	synonymous_variant	51542	exon8			TTTCTAATTCACA	AF102177	CCDS33208.1, CCDS46302.1	2p15-p14	2014-06-13	2006-12-19		ENSG00000143952	ENSG00000143952			18652	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 164"""	614633	"""vacuolar protein sorting 54 (yeast)"""			12039048	Standard	NM_016516		Approved	HCC8, PPP1R164	uc002scq.3	Q9P1Q0	OTTHUMG00000152627	ENST00000272322.4:c.1036T>C	chr2.hg19:g.64176272A>G		57.0	0.0		57.0	14.0	NM_016516	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Silent	SNP	ENST00000272322.4	hg19	CCDS33208.1																																																																																			.	.		0.318	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516	
CD302	9936	hgsc.bcm.edu	37	2	160654643	160654643	+	Splice_Site	SNP	C	C	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:160654643C>A	ENST00000259053.4	-	1	110	c.67G>T	c.(67-69)Gac>Tac	p.D23Y	LY75_ENST00000554112.1_Intron|LY75_ENST00000553424.1_Intron|LY75-CD302_ENST00000504764.1_Intron|LY75-CD302_ENST00000505052.1_Intron|CD302_ENST00000480212.1_5'UTR|CD302_ENST00000429078.2_Splice_Site_p.D23Y	NM_001198764.1|NM_014880.4	NP_001185693.1|NP_055695.2	Q8IX05	CD302_HUMAN	CD302 molecule	23					phagocytosis (GO:0006909)	cell cortex (GO:0005938)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						AAGGGCTTACCCgcgacggca	0.771																																					p.G23X		Atlas-SNP	.											.	CD302	22	.	0			c.G67T						.						6.0	7.0	7.0					2																	160654643		1735	3220	4955	SO:0001630	splice_region_variant	9936	exon1			GCTTACCCGCGAC	AY314007	CCDS33308.1, CCDS56139.1, CCDS74595.1	2q24.2	2011-08-30	2006-03-28		ENSG00000241399	ENSG00000241399		"""CD molecules"", ""C-type lectin domain containing"""	30843	protein-coding gene	gene with protein product	"""C-type lectin domain family 13, member A"""	612246	"""CD302 antigen"""			7584026, 7584028	Standard	NM_014880		Approved	DCL-1, KIAA0022, BIMLEC, CLEC13A		Q8IX05	OTTHUMG00000154080	ENST00000259053.4:c.67+1G>T	chr2.hg19:g.160654643C>A		43.0	0.0		66.0	20.0	NM_001198764	A8K5G4|B4E2T9|Q15009	Nonsense_Mutation	SNP	ENST00000259053.4	hg19	CCDS33308.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.392147	0.42410	.	.	ENSG00000241399	ENST00000259053;ENST00000429078	T;T	0.07908	3.15;3.15	3.34	1.46	0.22682	C-type lectin fold (1);C-type lectin-like (1);	0.225788	0.29172	U	0.012922	T	0.18923	0.0454	.	.	.	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.71184	0.922;0.972	T	0.01448	-1.1352	8	.	.	.	-24.5116	4.657	0.12622	0.0:0.6475:0.2253:0.1273	.	23;23	B4E2T9;Q8IX05	.;CD302_HUMAN	Y	23	ENSP00000259053:D23Y;ENSP00000394301:D23Y	.	D	-	1	0	CD302	160362889	0.981000	0.34729	0.965000	0.40720	0.144000	0.21451	1.642000	0.37207	0.389000	0.25086	0.462000	0.41574	GAC	.	.		0.771	CD302-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333760.1	NM_014880	Missense_Mutation
ITGA6	3655	hgsc.bcm.edu	37	2	173355794	173355794	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:173355794C>G	ENST00000264106.6	+	22	3042	c.2839C>G	c.(2839-2841)Cag>Gag	p.Q947E	ITGA6_ENST00000264107.7_Missense_Mutation_p.Q908E|ITGA6_ENST00000409080.1_Missense_Mutation_p.Q908E|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000409532.1_Missense_Mutation_p.Q789E|ITGA6_ENST00000343713.4_Missense_Mutation_p.Q903E|ITGA6_ENST00000375221.2_Missense_Mutation_p.Q947E			P23229	ITA6_HUMAN	integrin, alpha 6	947					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			TACTGAAAAACAGATAGATGA	0.303																																					p.Q908E		Atlas-SNP	.											.	ITGA6	171	.	0			c.C2722G						.						113.0	139.0	130.0					2																	173355794		2202	4299	6501	SO:0001583	missense	3655	exon21			GAAAAACAGATAG		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"""CD molecules"", ""Integrins"""	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.2839C>G	chr2.hg19:g.173355794C>G	ENSP00000264106:p.Gln947Glu	349.0	0.0		383.0	127.0	NM_000210	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Missense_Mutation	SNP	ENST00000264106.6	hg19		.	.	.	.	.	.	.	.	.	.	C	5.608	0.296873	0.10622	.	.	ENSG00000091409	ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358;ENST00000416789	T;T;T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;1.96	5.4	5.4	0.78164	.	0.361759	0.32015	N	0.006702	T	0.36386	0.0965	L	0.41824	1.3	0.52099	D	0.999942	B;B;P;P	0.37352	0.02;0.003;0.591;0.591	B;B;B;B	0.39876	0.03;0.018;0.312;0.312	T	0.08249	-1.0731	10	0.09590	T	0.72	.	16.3226	0.82956	0.0:1.0:0.0:0.0	.	903;932;908;908	P23229-4;P23229-9;G5E9H1;P23229-2	.;.;.;.	E	789;908;947;947;903;908;947;903;75	ENSP00000386614:Q789E;ENSP00000264107:Q908E;ENSP00000264106:Q947E;ENSP00000364369:Q947E;ENSP00000341078:Q903E;ENSP00000386896:Q908E;ENSP00000406694:Q947E;ENSP00000394169:Q903E;ENSP00000388435:Q75E	ENSP00000264106:Q947E	Q	+	1	0	ITGA6	173064040	0.073000	0.21202	1.000000	0.80357	0.907000	0.53573	1.103000	0.31062	2.534000	0.85438	0.460000	0.39030	CAG	.	.		0.303	ITGA6-201	KNOWN	basic	protein_coding	protein_coding			
PGAP1	80055	hgsc.bcm.edu	37	2	197738476	197738476	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:197738476G>C	ENST00000354764.4	-	15	1547	c.1433C>G	c.(1432-1434)tCt>tGt	p.S478C	PGAP1_ENST00000409475.1_Missense_Mutation_p.S478C	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	478					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						TTTCCTTGAAGACAATCCTGT	0.303																																					p.S478C		Atlas-SNP	.											.	PGAP1	84	.	0			c.C1433G						.						87.0	90.0	89.0					2																	197738476		2202	4288	6490	SO:0001583	missense	80055	exon15			CTTGAAGACAATC		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"""GPI inositol-deacylase"""	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.1433C>G	chr2.hg19:g.197738476G>C	ENSP00000346809:p.Ser478Cys	182.0	0.0		165.0	53.0	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	hg19	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.053488	0.55218	.	.	ENSG00000197121	ENST00000422382;ENST00000354764;ENST00000409475	.	.	.	5.13	4.25	0.50352	.	0.171557	0.52532	D	0.000070	T	0.47358	0.1441	N	0.19112	0.55	0.80722	D	1	D;D	0.57257	0.973;0.979	P;P	0.53360	0.724;0.514	T	0.43877	-0.9364	9	0.38643	T	0.18	-12.5885	11.7902	0.52065	0.0821:0.0:0.9179:0.0	.	478;478	Q75T13-3;Q75T13	.;PGAP1_HUMAN	C	258;478;478	.	ENSP00000346809:S478C	S	-	2	0	PGAP1	197446721	1.000000	0.71417	0.997000	0.53966	0.822000	0.46500	4.128000	0.57951	1.522000	0.49001	0.655000	0.94253	TCT	.	.		0.303	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989	
CELSR3	1951	hgsc.bcm.edu	37	3	48680218	48680218	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr3:48680218A>G	ENST00000164024.4	-	30	8786	c.8506T>C	c.(8506-8508)Tcc>Ccc	p.S2836P	CELSR3_ENST00000544264.1_Missense_Mutation_p.S2841P|MIR4793_ENST00000577502.1_RNA	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	2836					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GTCCGGCCGGAGCGGGCACTG	0.647																																					p.S2836P		Atlas-SNP	.											.	CELSR3	237	.	0			c.T8506C						.						42.0	47.0	45.0					3																	48680218		2203	4299	6502	SO:0001583	missense	1951	exon30			GGCCGGAGCGGGC	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3230	protein-coding gene	gene with protein product	"""flamingo homolog 1 (Drosophila)"""	604264	"""cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"""	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.8506T>C	chr3.hg19:g.48680218A>G	ENSP00000164024:p.Ser2836Pro	83.0	0.0		62.0	38.0	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.906139	0.92107	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.72942	-0.7;-0.7	5.52	5.52	0.82312	.	.	.	.	.	D	0.83367	0.5239	M	0.77820	2.39	0.47819	D	0.999526	D;D;D	0.76494	0.998;0.996;0.999	P;P;D	0.66196	0.862;0.731;0.942	D	0.85871	0.1416	9	0.87932	D	0	.	15.6403	0.76993	1.0:0.0:0.0:0.0	.	2841;2836;2934	Q9NYQ7-2;Q9NYQ7;Q5Y190	.;CELR3_HUMAN;.	P	2836;2841	ENSP00000164024:S2836P;ENSP00000445694:S2841P	ENSP00000164024:S2836P	S	-	1	0	CELSR3	48655222	1.000000	0.71417	0.995000	0.50966	0.703000	0.40648	7.529000	0.81952	2.106000	0.64143	0.459000	0.35465	TCC	.	.		0.647	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407	
PROK2	60675	hgsc.bcm.edu	37	3	71830662	71830662	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr3:71830662G>T	ENST00000295619.3	-	2	186	c.178C>A	c.(178-180)Cct>Act	p.P60T	PROK2_ENST00000353065.3_Missense_Mutation_p.P60T	NM_001126128.1	NP_001119600.1	Q9HC23	PROK2_HUMAN	prokineticin 2	60					activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|cell proliferation (GO:0008283)|chemotaxis (GO:0006935)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of apoptotic process (GO:0043066)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of smooth muscle contraction (GO:0045987)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	G-protein coupled receptor binding (GO:0001664)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6		Prostate(10;0.00899)		BRCA - Breast invasive adenocarcinoma(55;1.89e-05)|Epithelial(33;0.000173)|LUSC - Lung squamous cell carcinoma(21;0.00168)|Lung(16;0.00306)		TTGCCCATAGGTGTGCAAATC	0.443																																					p.P60T		Atlas-SNP	.											.	PROK2	13	.	0			c.C178A						.						123.0	111.0	115.0					3																	71830662		2203	4300	6503	SO:0001583	missense	60675	exon2			CCATAGGTGTGCA	AF333025	CCDS2916.1, CCDS46868.1	3p21.1	2013-02-28			ENSG00000163421	ENSG00000163421		"""Endogenous ligands"""	18455	protein-coding gene	gene with protein product	"""protein Bv8 homolog"""	607002				11054548, 11259612	Standard	NM_021935		Approved	PK2, BV8, MIT1, KAL4	uc003dpa.4	Q9HC23	OTTHUMG00000158809	ENST00000295619.3:c.178C>A	chr3.hg19:g.71830662G>T	ENSP00000295619:p.Pro60Thr	224.0	0.0		152.0	76.0	NM_001126128	Q53Z79|Q6ISR0	Missense_Mutation	SNP	ENST00000295619.3	hg19	CCDS46868.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.717488	0.89205	.	.	ENSG00000163421	ENST00000353065;ENST00000295619	D;D	0.90563	-2.69;-2.69	5.72	5.72	0.89469	Prokineticin domain (2);	0.000000	0.85682	D	0.000000	D	0.95287	0.8471	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.95382	0.8474	10	0.87932	D	0	-2.2696	18.6538	0.91441	0.0:0.0:1.0:0.0	.	60;60	Q9HC23;Q6ISR0	PROK2_HUMAN;.	T	60	ENSP00000295618:P60T;ENSP00000295619:P60T	ENSP00000295619:P60T	P	-	1	0	PROK2	71913352	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	8.921000	0.92784	2.692000	0.91855	0.650000	0.86243	CCT	.	.		0.443	PROK2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352302.1	NM_001126128	
CNTN3	5067	hgsc.bcm.edu	37	3	74548904	74548904	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr3:74548904T>C	ENST00000263665.6	-	2	115	c.88A>G	c.(88-90)Aaa>Gaa	p.K30E		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	30	Ig-like C2-type 1.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		CTGGGTTCTTTGATAAATACA	0.378																																					p.K30E		Atlas-SNP	.											.	CNTN3	174	.	0			c.A88G						.						91.0	97.0	95.0					3																	74548904		2203	4300	6503	SO:0001583	missense	5067	exon2			GTTCTTTGATAAA	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.88A>G	chr3.hg19:g.74548904T>C	ENSP00000263665:p.Lys30Glu	66.0	0.0		41.0	24.0	NM_020872	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	hg19	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	T	6.701	0.498019	0.12762	.	.	ENSG00000113805	ENST00000263665	T	0.42131	0.98	5.54	4.34	0.51931	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.413872	0.24031	N	0.042191	T	0.18759	0.0450	N	0.05574	-0.02	0.34971	D	0.753177	B	0.02656	0.0	B	0.12156	0.007	T	0.22417	-1.0217	10	0.02654	T	1	.	9.3228	0.37975	0.0:0.0:0.1812:0.8188	.	30	Q9P232	CNTN3_HUMAN	E	30	ENSP00000263665:K30E	ENSP00000263665:K30E	K	-	1	0	CNTN3	74631594	1.000000	0.71417	0.956000	0.39512	0.950000	0.60333	1.601000	0.36773	0.882000	0.36016	0.533000	0.62120	AAA	.	.		0.378	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	
GOLIM4	27333	hgsc.bcm.edu	37	3	167750442	167750442	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr3:167750442T>C	ENST00000470487.1	-	9	1731	c.1042A>G	c.(1042-1044)Atg>Gtg	p.M348V	GOLIM4_ENST00000309027.4_Missense_Mutation_p.M320V	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	348	Glu-rich.				transport (GO:0006810)	cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						ACCTGCTCCATTTCTTCCTCC	0.557																																					p.M348V		Atlas-SNP	.											.	GOLIM4	71	.	0			c.A1042G						.						207.0	183.0	191.0					3																	167750442		2203	4300	6503	SO:0001583	missense	27333	exon9			GCTCCATTTCTTC	U55853	CCDS3204.1	3q26	2007-07-30	2007-07-30	2007-07-30	ENSG00000173905	ENSG00000173905			15448	protein-coding gene	gene with protein product		606805	"""golgi phosphoprotein 4"""	GOLPH4		9201717, 15004235	Standard	NM_014498		Approved	GPP130, GIMPC, P138	uc003ffe.2	O00461	OTTHUMG00000158554	ENST00000470487.1:c.1042A>G	chr3.hg19:g.167750442T>C	ENSP00000417354:p.Met348Val	123.0	0.0		265.0	49.0	NM_014498		Missense_Mutation	SNP	ENST00000470487.1	hg19	CCDS3204.1	.	.	.	.	.	.	.	.	.	.	T	17.70	3.454101	0.63290	.	.	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	5.36	5.36	0.76844	.	0.152354	0.64402	D	0.000001	T	0.65842	0.2730	M	0.72118	2.19	0.51482	D	0.999929	D;P	0.54772	0.968;0.907	P;P	0.51415	0.6;0.669	T	0.65311	-0.6199	9	0.28530	T	0.3	-14.8158	15.0611	0.71955	0.0:0.0:0.0:1.0	.	320;348	F8W785;O00461	.;GOLI4_HUMAN	V	348;320	.	ENSP00000309893:M320V	M	-	1	0	GOLIM4	169233136	1.000000	0.71417	0.919000	0.36401	0.593000	0.36681	5.365000	0.66116	2.044000	0.60594	0.454000	0.30748	ATG	.	.		0.557	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2		
PCYT1A	5130	hgsc.bcm.edu	37	3	195997368	195997368	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr3:195997368C>T	ENST00000292823.2	-	3	207	c.35G>A	c.(34-36)aGg>aAg	p.R12K	PCYT1A_ENST00000431016.1_Missense_Mutation_p.R12K|RP11-447L10.1_ENST00000431391.1_3'UTR|PCYT1A_ENST00000419333.1_Missense_Mutation_p.R12K|PCYT1A_ENST00000491544.1_5'UTR	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha	12					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|glycogen granule (GO:0042587)	choline-phosphate cytidylyltransferase activity (GO:0004105)|lipid binding (GO:0008289)			cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)|Lamivudine(DB00709)	TCTCCTCTTCCTTGCATTGAC	0.468																																					p.R12K		Atlas-SNP	.											.	PCYT1A	34	.	0			c.G35A						.						217.0	216.0	217.0					3																	195997368		2203	4300	6503	SO:0001583	missense	5130	exon3			CTCTTCCTTGCAT	L28957	CCDS3315.1	3q29	2010-07-19	2005-09-05		ENSG00000161217	ENSG00000161217	2.7.7.15		8754	protein-coding gene	gene with protein product	"""phosphate cytidylyltransferase 1, choline, alpha isoform"""	123695	"""phosphate cytidylyltransferase 1, choline, alpha isoform"""	PCYT1		7918629	Standard	NM_005017		Approved	CT, CTPCT	uc003fwg.3	P49585	OTTHUMG00000155670	ENST00000292823.2:c.35G>A	chr3.hg19:g.195997368C>T	ENSP00000292823:p.Arg12Lys	136.0	0.0		188.0	34.0	NM_005017	A9LYK9|D3DXB1|Q86Y88	Missense_Mutation	SNP	ENST00000292823.2	hg19	CCDS3315.1	.	.	.	.	.	.	.	.	.	.	C	19.39	3.818075	0.71028	.	.	ENSG00000161217	ENST00000441879;ENST00000419333;ENST00000292823;ENST00000416798;ENST00000431016;ENST00000411591;ENST00000412869;ENST00000443555	.	.	.	5.82	5.82	0.92795	.	0.123828	0.56097	D	0.000021	T	0.52075	0.1712	L	0.55481	1.735	0.80722	D	1	P	0.42692	0.787	B	0.38056	0.264	T	0.50145	-0.8862	9	0.25751	T	0.34	-28.5008	15.5992	0.76611	0.0:1.0:0.0:0.0	.	12	P49585	PCY1A_HUMAN	K	12	.	ENSP00000292823:R12K	R	-	2	0	PCYT1A	197481765	1.000000	0.71417	0.993000	0.49108	0.991000	0.79684	4.022000	0.57203	2.752000	0.94435	0.655000	0.94253	AGG	.	.		0.468	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341147.1	NM_005017	
NR3C2	4306	hgsc.bcm.edu	37	4	149115896	149115896	+	Splice_Site	SNP	C	C	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr4:149115896C>A	ENST00000503313.1	-	2	211		c.e2+1		NR3C2_ENST00000511528.1_Splice_Site|RP11-76G10.1_ENST00000514843.1_RNA|NR3C2_ENST00000355292.3_Splice_Site|NR3C2_ENST00000344721.4_Splice_Site|NR3C2_ENST00000512865.1_Splice_Site|NR3C2_ENST00000358102.3_Splice_Site			P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2						gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	ACAAAACTTACCTCCTAAATT	0.353																																					.	Melanoma(27;428 957 40335 51025 51111)	Atlas-SNP	.											.	NR3C2	94	.	0			c.2014+1G>T						.						58.0	60.0	59.0					4																	149115896		2203	4300	6503	SO:0001630	splice_region_variant	4306	exon5			AACTTACCTCCTA	M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623		"""Nuclear hormone receptors"""	7979	protein-coding gene	gene with protein product		600983		MLR		2558856	Standard	NM_000901		Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000503313.1:c.666+1G>T	chr4.hg19:g.149115896C>A		35.0	0.0		17.0	6.0	NM_000901	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Splice_Site	SNP	ENST00000503313.1	hg19		.	.	.	.	.	.	.	.	.	.	C	25.7	4.662245	0.88251	.	.	ENSG00000151623	ENST00000344721;ENST00000355292;ENST00000358102;ENST00000512865;ENST00000342437;ENST00000511528	.	.	.	5.7	5.7	0.88788	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1979	0.98245	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NR3C2	149335346	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.776000	0.85560	2.846000	0.97976	0.650000	0.86243	.	.	.		0.353	NR3C2-007	PUTATIVE	basic|exp_conf	processed_transcript	protein_coding	OTTHUMT00000364990.1		Intron
PDZD2	23037	hgsc.bcm.edu	37	5	32087361	32087361	+	Silent	SNP	A	A	G			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr5:32087361A>G	ENST00000438447.1	+	20	4195	c.3807A>G	c.(3805-3807)gcA>gcG	p.A1269A	PDZD2_ENST00000282493.3_Silent_p.A1269A			O15018	PDZD2_HUMAN	PDZ domain containing 2	1269					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GCCAGCCTGCATCGCCCAGGG	0.647																																					p.A1269A		Atlas-SNP	.											.	PDZD2	306	.	0			c.A3807G						.						65.0	75.0	71.0					5																	32087361		2203	4300	6503	SO:0001819	synonymous_variant	23037	exon19			GCCTGCATCGCCC	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.3807A>G	chr5.hg19:g.32087361A>G		182.0	0.0		342.0	50.0	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	hg19	CCDS34137.1																																																																																			.	.		0.647	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
RREB1	6239	hgsc.bcm.edu	37	6	7230408	7230408	+	Silent	SNP	G	G	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr6:7230408G>T	ENST00000349384.6	+	10	2390	c.2076G>T	c.(2074-2076)acG>acT	p.T692T	RREB1_ENST00000379933.3_Silent_p.T692T|RREB1_ENST00000379938.2_Silent_p.T692T|RREB1_ENST00000334984.6_Silent_p.T692T	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	692					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				ACCTGCGCACGCACAGTGGGG	0.632																																					p.T692T		Atlas-SNP	.											.	RREB1	242	.	0			c.G2076T						.						65.0	59.0	61.0					6																	7230408		2203	4300	6503	SO:0001819	synonymous_variant	6239	exon10			GCGCACGCACAGT	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.2076G>T	chr6.hg19:g.7230408G>T		98.0	0.0		51.0	25.0	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	hg19	CCDS34336.1																																																																																			.	.		0.632	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
EDN1	1906	hgsc.bcm.edu	37	6	12294631	12294631	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr6:12294631A>C	ENST00000379375.5	+	4	794	c.527A>C	c.(526-528)cAa>cCa	p.Q176P		NM_001168319.1|NM_001955.4	NP_001161791.1|NP_001946.3	P05305	EDN1_HUMAN	endothelin 1	176					artery smooth muscle contraction (GO:0014824)|body fluid secretion (GO:0007589)|calcium-mediated signaling (GO:0019722)|cartilage development (GO:0051216)|cell growth (GO:0016049)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|dorsal/ventral pattern formation (GO:0009953)|epithelial fluid transport (GO:0042045)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose transport (GO:0015758)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|inositol phosphate-mediated signaling (GO:0048016)|leukocyte activation (GO:0045321)|maternal process involved in parturition (GO:0060137)|membrane depolarization (GO:0051899)|middle ear morphogenesis (GO:0042474)|multicellular organismal aging (GO:0010259)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of hormone secretion (GO:0046888)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell development (GO:0014032)|nitric oxide transport (GO:0030185)|patterning of blood vessels (GO:0001569)|peptide hormone secretion (GO:0030072)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase D-activating G-protein coupled receptor signaling pathway (GO:0031583)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of odontogenesis (GO:0042482)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of urine volume (GO:0035810)|prostaglandin biosynthetic process (GO:0001516)|protein kinase C deactivation (GO:0042313)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|respiratory gaseous exchange (GO:0007585)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to testosterone (GO:0033574)|rhythmic excitation (GO:0043179)|sensory perception of pain (GO:0019233)|superoxide anion generation (GO:0042554)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|endothelin A receptor binding (GO:0031707)|endothelin B receptor binding (GO:0031708)|hormone activity (GO:0005179)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	13	all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12)	all_hematologic(90;0.117)				CACCTAAGACAAACCAGGTAA	0.428																																					p.Q176P		Atlas-SNP	.											.	EDN1	23	.	0			c.A527C						.						72.0	74.0	73.0					6																	12294631		2203	4300	6503	SO:0001583	missense	1906	exon4			TAAGACAAACCAG	S56805	CCDS4522.1	6p24.1	2014-03-19			ENSG00000078401	ENSG00000078401		"""Endogenous ligands"""	3176	protein-coding gene	gene with protein product		131240					Standard	NM_001168319		Approved	ET1	uc003nae.4	P05305	OTTHUMG00000014266	ENST00000379375.5:c.527A>C	chr6.hg19:g.12294631A>C	ENSP00000368683:p.Gln176Pro	481.0	1.0		335.0	151.0	NM_001955	Q96DA1	Missense_Mutation	SNP	ENST00000379375.5	hg19	CCDS4522.1	.	.	.	.	.	.	.	.	.	.	A	9.235	1.036829	0.19669	.	.	ENSG00000078401	ENST00000379375	D	0.84146	-1.81	1.03	1.03	0.20045	.	0.534882	0.11761	U	0.532088	T	0.50205	0.1602	N	0.19112	0.55	0.19775	N	0.999955	B;B	0.33266	0.404;0.404	B;B	0.20384	0.029;0.029	T	0.40813	-0.9543	10	0.59425	D	0.04	.	4.4221	0.11486	1.0:0.0:0.0:0.0	.	176;176	Q6FH53;P05305	.;EDN1_HUMAN	P	176	ENSP00000368683:Q176P	ENSP00000368683:Q176P	Q	+	2	0	EDN1	12402617	0.314000	0.24563	0.420000	0.26596	0.304000	0.27724	0.681000	0.25320	0.263000	0.21812	0.260000	0.18958	CAA	.	.		0.428	EDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039872.1	NM_001955	
DNAH8	1769	hgsc.bcm.edu	37	6	38885133	38885133	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr6:38885133T>C	ENST00000359357.3	+	67	9862	c.9608T>C	c.(9607-9609)aTg>aCg	p.M3203T	DNAH8_ENST00000441566.1_Missense_Mutation_p.M3167T|DNAH8_ENST00000449981.2_Missense_Mutation_p.M3420T			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3203	Stalk. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						CCTGTTACTATGGATCCAGAA	0.388																																					p.M3420T		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T10259C						.						135.0	127.0	130.0					6																	38885133		2203	4300	6503	SO:0001583	missense	1769	exon69			TTACTATGGATCC	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.9608T>C	chr6.hg19:g.38885133T>C	ENSP00000352312:p.Met3203Thr	91.0	0.0		97.0	39.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	T	10.20	1.284702	0.23392	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.73681	-0.77;-0.77;-0.77	5.75	5.75	0.90469	Dynein heavy chain, coiled coil stalk (1);	0.082491	0.85682	D	0.000000	T	0.46580	0.1400	N	0.20685	0.6	0.46222	D	0.998937	B	0.06786	0.001	B	0.14023	0.01	T	0.45600	-0.9250	10	0.22706	T	0.39	.	16.0591	0.80826	0.0:0.0:0.0:1.0	.	3203	Q96JB1	DYH8_HUMAN	T	3408;3408;3203;3167	ENSP00000333363:M3408T;ENSP00000352312:M3203T;ENSP00000402294:M3167T	ENSP00000333363:M3408T	M	+	2	0	DNAH8	38993111	0.990000	0.36364	1.000000	0.80357	0.994000	0.84299	2.214000	0.42853	2.190000	0.69967	0.482000	0.46254	ATG	.	.		0.388	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
SLC29A1	2030	hgsc.bcm.edu	37	6	44197363	44197363	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr6:44197363C>A	ENST00000393841.1	+	5	640	c.149C>A	c.(148-150)tCc>tAc	p.S50Y	SLC29A1_ENST00000371740.5_Missense_Mutation_p.S50Y|SLC29A1_ENST00000472176.1_3'UTR|SLC29A1_ENST00000313248.7_Missense_Mutation_p.S129Y|SLC29A1_ENST00000371755.3_Missense_Mutation_p.S50Y|SLC29A1_ENST00000371713.1_Missense_Mutation_p.S50Y|SLC29A1_ENST00000393844.1_Missense_Mutation_p.S50Y|SLC29A1_ENST00000371724.1_Missense_Mutation_p.S50Y|SLC29A1_ENST00000427851.2_Missense_Mutation_p.S50Y|SLC29A1_ENST00000371708.1_Missense_Mutation_p.S50Y|SLC29A1_ENST00000371731.1_Missense_Mutation_p.S50Y	NM_001078177.1	NP_001071645.1	Q99808	S29A1_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 1	50					cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|lactation (GO:0007595)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sleep (GO:0030431)|transmembrane transport (GO:0055085)|uridine transport (GO:0015862)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	17	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Cytarabine(DB00987)|Didanosine(DB00900)|Fludarabine(DB01073)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Pemetrexed(DB00642)|Ribavirin(DB00811)|Zalcitabine(DB00943)	CAGAATGTGTCCTTGGTCACT	0.557																																					p.S50Y		Atlas-SNP	.											.	SLC29A1	45	.	0			c.C149A						.						113.0	107.0	109.0					6																	44197363		2203	4300	6503	SO:0001583	missense	2030	exon4			ATGTGTCCTTGGT	U81375	CCDS4908.1	6p21.1	2013-07-17	2013-07-17		ENSG00000112759	ENSG00000112759		"""Solute carriers"""	11003	protein-coding gene	gene with protein product		602193	"""solute carrier family 29 (nucleoside transporters), member 1"""	ENT1		8986748, 9344680	Standard	NM_004955		Approved		uc003owy.2	Q99808	OTTHUMG00000014759	ENST00000393841.1:c.149C>A	chr6.hg19:g.44197363C>A	ENSP00000377424:p.Ser50Tyr	64.0	0.0		76.0	29.0	NM_004955	B3KQV7|B3KQY5|Q5T9W9|Q9UJY2	Missense_Mutation	SNP	ENST00000393841.1	hg19	CCDS4908.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.846488	0.91277	.	.	ENSG00000112759	ENST00000544345;ENST00000393844;ENST00000313248;ENST00000427851;ENST00000371755;ENST00000371740;ENST00000371731;ENST00000393841;ENST00000371724;ENST00000371713;ENST00000371708	T;T;T;T;T;T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01;2.01;2.01;2.01;2.01;2.01	5.48	5.48	0.80851	.	1.265590	0.04916	N	0.454125	T	0.21387	0.0515	L	0.50333	1.59	0.20403	N	0.999902	P;P;D;P	0.53885	0.539;0.7;0.963;0.929	B;B;P;B	0.50970	0.281;0.281;0.655;0.427	T	0.22521	-1.0214	10	0.72032	D	0.01	-26.0206	12.8287	0.57735	0.0:0.8231:0.1769:0.0	.	50;69;129;50	B7Z1J8;B7Z914;B3KQV7;Q99808	.;.;.;S29A1_HUMAN	Y	69;50;129;50;50;50;50;50;50;50;50	ENSP00000377427:S50Y;ENSP00000319152:S129Y;ENSP00000392668:S50Y;ENSP00000360820:S50Y;ENSP00000360805:S50Y;ENSP00000360796:S50Y;ENSP00000377424:S50Y;ENSP00000360789:S50Y;ENSP00000360778:S50Y;ENSP00000360773:S50Y	ENSP00000319152:S129Y	S	+	2	0	SLC29A1	44305341	0.009000	0.17119	0.534000	0.28014	0.944000	0.59088	0.855000	0.27805	2.581000	0.87130	0.563000	0.77884	TCC	.	.		0.557	SLC29A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040721.1		
KIAA1244	57221	hgsc.bcm.edu	37	6	138611075	138611075	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr6:138611075A>G	ENST00000251691.4	+	18	3183	c.3017A>G	c.(3016-3018)cAc>cGc	p.H1006R		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		ATGGGAAGCCACAACCCGGAC	0.622																																					p.H1006R		Atlas-SNP	.											.	KIAA1244	236	.	0			c.A3017G						.						88.0	78.0	82.0					6																	138611075		2203	4300	6503	SO:0001583	missense	57221	exon18			GAAGCCACAACCC	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.3017A>G	chr6.hg19:g.138611075A>G	ENSP00000251691:p.His1006Arg	192.0	0.0		206.0	59.0	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	hg19	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	A	27.4	4.829504	0.90955	.	.	ENSG00000112379	ENST00000251691	T	0.28454	1.61	5.44	5.44	0.79542	.	0.186808	0.56097	D	0.000022	T	0.47322	0.1439	M	0.72894	2.215	0.58432	D	0.999999	D	0.63880	0.993	D	0.72338	0.977	T	0.52411	-0.8579	10	0.87932	D	0	-31.8043	15.7983	0.78428	1.0:0.0:0.0:0.0	.	1006	Q5TH69	BIG3_HUMAN	R	1006	ENSP00000251691:H1006R	ENSP00000251691:H1006R	H	+	2	0	KIAA1244	138652768	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.229000	0.95273	2.177000	0.69029	0.533000	0.62120	CAC	.	.		0.622	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
PHACTR2	9749	hgsc.bcm.edu	37	6	144086750	144086750	+	Silent	SNP	C	C	T	rs200488499		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr6:144086750C>T	ENST00000427704.2	+	6	1144	c.1014C>T	c.(1012-1014)ccC>ccT	p.P338P	PHACTR2_ENST00000305766.6_Silent_p.P258P|PHACTR2_ENST00000440869.2_Silent_p.P349P|PHACTR2_ENST00000367584.4_Silent_p.P326P|PHACTR2_ENST00000367582.3_Silent_p.P269P	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2	338							protein phosphatase inhibitor activity (GO:0004864)			NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)		CTCTGGCCCCCCCTCTCCCTC	0.587																																					p.P349P	Pancreas(12;292 433 7358 48260 52635)|Ovarian(20;501 618 3485 36581 49208)	Atlas-SNP	.											.	PHACTR2	99	.	0			c.C1047T						.						58.0	65.0	63.0					6																	144086750		2027	4161	6188	SO:0001819	synonymous_variant	9749	exon6			GGCCCCCCCTCTC	AB014580	CCDS43512.1, CCDS47492.1, CCDS47493.1, CCDS47494.1	6q24.1	2013-01-24	2004-05-20	2004-05-20	ENSG00000112419	ENSG00000112419		"""Phosphatase and actin regulators"""	20956	protein-coding gene	gene with protein product		608724	"""chromosome 6 open reading frame 56"""	C6orf56		9734811, 15107502	Standard	NM_001100164		Approved	KIAA0680	uc010khi.3	O75167	OTTHUMG00000015732	ENST00000427704.2:c.1014C>T	chr6.hg19:g.144086750C>T		126.0	0.0		107.0	48.0	NM_001100164	A6NKP5|A7MCZ5|A8MZC0|B2RWP7|B4DN76|B4DPB5|B4DTH7|Q5TFA0|Q68DM2	Silent	SNP	ENST00000427704.2	hg19	CCDS47492.1																																																																																			.	C|1.000;G|0.000		0.587	PHACTR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042528.2	NM_014721	
AUTS2	26053	hgsc.bcm.edu	37	7	70255636	70255636	+	Missense_Mutation	SNP	G	G	A	rs371317370		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr7:70255636G>A	ENST00000342771.4	+	19	3755	c.3434G>A	c.(3433-3435)cGg>cAg	p.R1145Q	AUTS2_ENST00000406775.2_Missense_Mutation_p.R1121Q	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	1145	His-rich.									breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		GAGCACGAGCGGGGAGGCCAC	0.692																																					p.R1145Q		Atlas-SNP	.											.	AUTS2	173	.	0			c.G3434A						.	G	GLN/ARG,GLN/ARG	2,4400		0,2,2199	21.0	23.0	22.0		3362,3434	4.8	0.9	7		22	2,8580		0,2,4289	no	missense,missense	AUTS2	NM_001127231.1,NM_015570.2	43,43	0,4,6488	AA,AG,GG		0.0233,0.0454,0.0308	probably-damaging,probably-damaging	1121/1236,1145/1260	70255636	4,12980	2201	4291	6492	SO:0001583	missense	26053	exon19			ACGAGCGGGGAGG	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.3434G>A	chr7.hg19:g.70255636G>A	ENSP00000344087:p.Arg1145Gln	124.0	0.0		143.0	54.0	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	hg19	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.903198	0.92035	4.54E-4	2.33E-4	ENSG00000158321	ENST00000406775;ENST00000342771	T;T	0.38722	1.17;1.12	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.60340	0.2261	L	0.56199	1.76	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.77557	0.99;0.99;0.99	T	0.59526	-0.7438	9	.	.	.	-14.7232	17.8486	0.88738	0.0:0.0:1.0:0.0	.	597;1121;1145	B4DLG0;Q8WXX7-2;Q8WXX7	.;.;AUTS2_HUMAN	Q	1121;1145	ENSP00000385263:R1121Q;ENSP00000344087:R1145Q	.	R	+	2	0	AUTS2	69893572	1.000000	0.71417	0.926000	0.36857	0.994000	0.84299	9.047000	0.93823	2.217000	0.71921	0.655000	0.94253	CGG	.	.		0.692	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2		
PON3	5446	hgsc.bcm.edu	37	7	95019498	95019498	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr7:95019498T>C	ENST00000265627.5	-	3	179	c.169A>G	c.(169-171)Ata>Gta	p.I57V	PON1_ENST00000542556.1_Intron|PON3_ENST00000475439.1_5'UTR|PON3_ENST00000451904.1_Missense_Mutation_p.I57V|PON3_ENST00000427422.1_Missense_Mutation_p.I57V	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	57					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	CTAGGAAGTATATCAATATCT	0.383																																					p.I57V		Atlas-SNP	.											.	PON3	59	.	0			c.A169G						.						205.0	216.0	212.0					7																	95019498		2203	4300	6503	SO:0001583	missense	5446	exon3			GAAGTATATCAAT	L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"""Paraoxonases"""	9206	protein-coding gene	gene with protein product	"""arylesterase 3"""	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.169A>G	chr7.hg19:g.95019498T>C	ENSP00000265627:p.Ile57Val	109.0	0.0		112.0	40.0	NM_000940	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Missense_Mutation	SNP	ENST00000265627.5	hg19	CCDS5639.1	.	.	.	.	.	.	.	.	.	.	T	9.170	1.020830	0.19433	.	.	ENSG00000105852	ENST00000265627;ENST00000427422	T;T	0.31247	1.5;1.5	4.93	3.78	0.43462	Six-bladed beta-propeller, TolB-like (1);	0.046816	0.85682	N	0.000000	T	0.24431	0.0592	L	0.49640	1.575	0.45662	D	0.998584	B;B	0.24426	0.103;0.004	B;B	0.20767	0.031;0.007	T	0.05194	-1.0900	10	0.27082	T	0.32	-14.874	7.4731	0.27361	0.0:0.0967:0.0:0.9033	.	57;57	B4E2I0;Q15166	.;PON3_HUMAN	V	57	ENSP00000265627:I57V;ENSP00000413276:I57V	ENSP00000265627:I57V	I	-	1	0	PON3	94857434	1.000000	0.71417	0.998000	0.56505	0.327000	0.28475	2.194000	0.42668	1.032000	0.39892	0.460000	0.39030	ATA	.	.		0.383	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940	
DLX6	1750	hgsc.bcm.edu	37	7	96635420	96635420	+	Missense_Mutation	SNP	A	A	C	rs570498188|rs559903070	byFrequency	TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr7:96635420A>C	ENST00000518156.2	+	1	561	c.131A>C	c.(130-132)cAg>cCg	p.Q44P	DLX6-AS1_ENST00000458352.2_RNA|DLX6-AS1_ENST00000452769.2_RNA|DLX6-AS1_ENST00000437541.1_RNA|DLX6-AS2_ENST00000606174.1_RNA|DLX6_ENST00000555308.1_5'Flank|DLX6-AS1_ENST00000430404.2_RNA|DLX6_ENST00000007660.5_Intron|DLX6-AS1_ENST00000605417.1_RNA|DLX6-AS1_ENST00000430027.3_RNA|DLX6-AS1_ENST00000437331.2_RNA|DLX6-AS1_ENST00000431497.2_RNA			P56179	DLX6_HUMAN	distal-less homeobox 6	0					anatomical structure formation involved in morphogenesis (GO:0048646)|embryonic limb morphogenesis (GO:0030326)|epithelial cell differentiation (GO:0030855)|head development (GO:0060322)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|palate development (GO:0060021)|positive regulation of epithelial cell proliferation (GO:0050679)|skeletal system development (GO:0001501)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(4)|ovary(2)|urinary_tract(1)	12	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					caacagcaacagccgccgccg	0.697																																					p.Q44P		Atlas-SNP	.											.,1	DLX6	37	.	0			c.A131C						.						2.0	3.0	3.0					7																	96635420		1105	2646	3751	SO:0001583	missense	1750	exon1			AGCAACAGCCGCC		CCDS47647.1, CCDS47647.2	7q21.3	2011-06-20	2005-12-22		ENSG00000006377	ENSG00000006377		"""Homeoboxes / ANTP class : NKL subclass"""	2919	protein-coding gene	gene with protein product		600030	"""distal-less homeo box 6"""			7907794	Standard	NM_005222		Approved		uc022ahu.1	P56179	OTTHUMG00000154201	ENST00000518156.2:c.131A>C	chr7.hg19:g.96635420A>C	ENSP00000428480:p.Gln44Pro	32.0	0.0		46.0	4.0	NM_005222	A4D1I2|B3KSQ0|J3KR92|Q3ZAR6|Q9UPL2	Missense_Mutation	SNP	ENST00000518156.2	hg19	CCDS47647.2	.	.	.	.	.	.	.	.	.	.	a	7.009	0.556463	0.13436	.	.	ENSG00000006377	ENST00000518156	D	0.92545	-3.06	2.89	-0.0314	0.13910	.	.	.	.	.	D	0.89653	0.6777	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.82739	-0.0308	6	0.32370	T	0.25	.	6.6539	0.22977	0.4411:0.5589:0.0:0.0	.	.	.	.	P	44	ENSP00000428480:Q44P	ENSP00000428480:Q44P	Q	+	2	0	DLX6	96473356	.	.	0.983000	0.44433	0.971000	0.66376	.	.	0.205000	0.20568	0.156000	0.16432	CAG	.	.		0.697	DLX6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334373.4	NM_005222	
COG5	10466	hgsc.bcm.edu	37	7	106898762	106898762	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr7:106898762C>A	ENST00000347053.3	-	15	1785	c.1735G>T	c.(1735-1737)Gca>Tca	p.A579S	COG5_ENST00000393603.2_Missense_Mutation_p.A579S|COG5_ENST00000297135.3_Missense_Mutation_p.A579S	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	579					intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						TTCACTACTGCCACATTTCTT	0.338																																					p.A579S		Atlas-SNP	.											.	COG5	78	.	0			c.G1735T						.						199.0	183.0	189.0					7																	106898762		2203	4300	6503	SO:0001583	missense	10466	exon15			CTACTGCCACATT	AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"""Components of oligomeric golgi complex"""	14857	protein-coding gene	gene with protein product		606821	"""golgi transport complex 1 (90 kDa subunit)"""	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.1735G>T	chr7.hg19:g.106898762C>A	ENSP00000334703:p.Ala579Ser	107.0	0.0		119.0	35.0	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	hg19	CCDS5743.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.348169	0.41599	.	.	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.58358	0.34;0.34;0.34	6.03	4.21	0.49690	.	0.271361	0.41500	N	0.000878	T	0.45013	0.1321	L	0.56199	1.76	0.39971	D	0.97479	B;B	0.27910	0.056;0.193	B;B	0.29942	0.028;0.109	T	0.29027	-1.0025	10	0.14252	T	0.57	-4.1358	10.409	0.44280	0.1349:0.7949:0.0:0.0702	.	579;579	Q9UP83;Q9UP83-2	COG5_HUMAN;.	S	579	ENSP00000334703:A579S;ENSP00000297135:A579S;ENSP00000377228:A579S	ENSP00000297135:A579S	A	-	1	0	COG5	106685998	0.998000	0.40836	0.999000	0.59377	0.979000	0.70002	3.080000	0.50112	0.860000	0.35481	-0.140000	0.14226	GCA	.	.		0.338	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4		
TMEM68	137695	hgsc.bcm.edu	37	8	56668880	56668880	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr8:56668880T>C	ENST00000434581.2	-	4	615	c.416A>G	c.(415-417)tAt>tGt	p.Y139C	TMEM68_ENST00000523073.1_Missense_Mutation_p.Y25C|TMEM68_ENST00000519784.1_Missense_Mutation_p.Y25C|TMEM68_ENST00000334667.2_Missense_Mutation_p.Y139C			Q96MH6	TMM68_HUMAN	transmembrane protein 68	139						integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups (GO:0016746)			NS(1)|kidney(1)|lung(2)|ovary(1)|skin(1)	6			Epithelial(17;0.000361)|all cancers(17;0.00326)			AGCCATGAAATAGTAAAAATC	0.323																																					p.Y139C		Atlas-SNP	.											.	TMEM68	25	.	0			c.A416G						.						50.0	54.0	53.0					8																	56668880		2202	4296	6498	SO:0001583	missense	137695	exon4			ATGAAATAGTAAA	AK056932	CCDS6161.1, CCDS75740.1, CCDS75741.1, CCDS75742.1	8q12.1	2011-12-12			ENSG00000167904	ENSG00000167904			26510	protein-coding gene	gene with protein product						12477932	Standard	XM_005251150		Approved	FLJ32370	uc003xsh.1	Q96MH6	OTTHUMG00000164293	ENST00000434581.2:c.416A>G	chr8.hg19:g.56668880T>C	ENSP00000395204:p.Tyr139Cys	108.0	0.0		92.0	27.0	NM_152417	Q658X6|Q8WUD2	Missense_Mutation	SNP	ENST00000434581.2	hg19		.	.	.	.	.	.	.	.	.	.	T	19.63	3.864066	0.71949	.	.	ENSG00000167904	ENST00000434581;ENST00000334667;ENST00000519784;ENST00000523073;ENST00000519780;ENST00000522090;ENST00000523423	D;D;D;D;D;D	0.97303	-3.22;-3.22;-3.22;-3.22;-4.33;-3.22	5.57	4.4	0.53042	Phospholipid/glycerol acyltransferase (2);	0.124094	0.56097	N	0.000028	D	0.98213	0.9409	M	0.84082	2.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	D	0.98223	1.0479	10	0.62326	D	0.03	-10.7085	11.8537	0.52425	0.1312:0.0:0.0:0.8688	.	139;139	Q96MH6-2;Q96MH6	.;TMM68_HUMAN	C	139;139;25;25;25;139;139	ENSP00000395204:Y139C;ENSP00000335416:Y139C;ENSP00000428688:Y25C;ENSP00000429026:Y25C;ENSP00000429667:Y25C;ENSP00000430542:Y139C	ENSP00000335416:Y139C	Y	-	2	0	TMEM68	56831434	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.015000	0.88690	0.919000	0.36945	0.482000	0.46254	TAT	.	.		0.323	TMEM68-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000378137.1	NM_152417	
CNBD1	168975	hgsc.bcm.edu	37	8	87951908	87951908	+	Silent	SNP	T	T	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr8:87951908T>C	ENST00000518476.1	+	4	408	c.357T>C	c.(355-357)caT>caC	p.H119H		NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	119										breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						AGAGAGCACATGGTGGCCATA	0.333																																					p.H119H		Atlas-SNP	.											.	CNBD1	206	.	0			c.T357C						.						78.0	75.0	76.0					8																	87951908		1818	4085	5903	SO:0001819	synonymous_variant	168975	exon4			AGCACATGGTGGC	AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571			26663	protein-coding gene	gene with protein product							Standard	NM_173538		Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.357T>C	chr8.hg19:g.87951908T>C		411.0	0.0		760.0	143.0	NM_173538		Silent	SNP	ENST00000518476.1	hg19	CCDS55259.1																																																																																			.	.		0.333	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538	
DCAF4L2	138009	hgsc.bcm.edu	37	8	88885852	88885852	+	Silent	SNP	C	C	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr8:88885852C>A	ENST00000319675.3	-	1	444	c.348G>T	c.(346-348)ccG>ccT	p.P116P		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	116										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						GGGTTTTGTGCGGGTATACCC	0.552																																					p.P116P		Atlas-SNP	.											.	DCAF4L2	187	.	0			c.G348T						.						128.0	124.0	125.0					8																	88885852		2203	4300	6503	SO:0001819	synonymous_variant	138009	exon1			TTTGTGCGGGTAT	AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"""WD repeat domain containing"""	26657	protein-coding gene	gene with protein product			"""WD repeat domain 21C"""	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.348G>T	chr8.hg19:g.88885852C>A		104.0	0.0		167.0	34.0	NM_152418		Silent	SNP	ENST00000319675.3	hg19	CCDS6245.1																																																																																			.	.		0.552	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418	
LRP12	29967	hgsc.bcm.edu	37	8	105503525	105503525	+	Silent	SNP	A	A	G			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr8:105503525A>G	ENST00000276654.5	-	7	2064	c.1956T>C	c.(1954-1956)tcT>tcC	p.S652S	LRP12_ENST00000424843.2_Silent_p.S633S|LRP12_ENST00000518375.1_5'UTR	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	652					endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CTGTATCATCAGACTCCACGG	0.478																																					p.S652S		Atlas-SNP	.											.	LRP12	124	.	0			c.T1956C						.						91.0	87.0	88.0					8																	105503525		2203	4300	6503	SO:0001819	synonymous_variant	29967	exon7			ATCATCAGACTCC	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"""Low density lipoprotein receptors"""	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.1956T>C	chr8.hg19:g.105503525A>G		104.0	0.0		160.0	100.0	NM_013437	A8K137|B4DRQ2	Silent	SNP	ENST00000276654.5	hg19	CCDS6303.1																																																																																			.	.		0.478	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437	
KLHL38	340359	hgsc.bcm.edu	37	8	124664210	124664210	+	Silent	SNP	C	C	G			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr8:124664210C>G	ENST00000325995.7	-	1	980	c.957G>C	c.(955-957)ccG>ccC	p.P319P	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	319										breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						ACAGCCGTGTCGGGAGTTTGG	0.592																																					p.P319P		Atlas-SNP	.											.	KLHL38	81	.	0			c.G957C						.						70.0	74.0	72.0					8																	124664210		2016	4164	6180	SO:0001819	synonymous_variant	340359	exon1			CCGTGTCGGGAGT		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.957G>C	chr8.hg19:g.124664210C>G		122.0	0.0		191.0	76.0	NM_001081675	A0PK12	Silent	SNP	ENST00000325995.7	hg19	CCDS43766.1																																																																																			.	.		0.592	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
PUF60	22827	hgsc.bcm.edu	37	8	144900554	144900554	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr8:144900554T>C	ENST00000526683.1	-	6	1054	c.499A>G	c.(499-501)Atg>Gtg	p.M167V	PUF60_ENST00000527197.1_Missense_Mutation_p.M121V|PUF60_ENST00000349157.6_Missense_Mutation_p.M150V|PUF60_ENST00000524570.1_5'UTR|PUF60_ENST00000313352.7_Missense_Mutation_p.M107V|PUF60_ENST00000453551.2_Missense_Mutation_p.M124V|PUF60_ENST00000456095.2_Missense_Mutation_p.M138V	NM_001271098.1|NM_078480.2	NP_001258027.1|NP_510965.1	Q9UHX1	PUF60_HUMAN	poly-U binding splicing factor 60KDa	167	Inhibits homodimerization.|Inhibits transcriptional repression, interaction with ERCC3 and apoptosis induction.|RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(3)|lung(7)|prostate(2)	14	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			TTGTGCTTCATGGTGACGGAG	0.647																																					p.M167V		Atlas-SNP	.											.	PUF60	26	.	0			c.A499G						.						46.0	51.0	49.0					8																	144900554		2097	4216	6313	SO:0001583	missense	22827	exon6			GCTTCATGGTGAC	AF114818	CCDS47933.1, CCDS47934.1, CCDS47935.1, CCDS59514.1, CCDS59515.1, CCDS59516.1	8q24.3	2013-02-12	2007-07-27		ENSG00000179950	ENSG00000179950		"""RNA binding motif (RRM) containing"""	17042	protein-coding gene	gene with protein product	"""siah binding protein 1"", ""FBP interacting repressor"", ""pyrimidine tract binding splicing factor"", ""Ro ribonucleoprotein binding protein 1"""	604819				10668799, 10882074, 17579712	Standard	NM_078480		Approved	FIR, SIAHBP1, RoBPI	uc003yzs.4	Q9UHX1	OTTHUMG00000165155	ENST00000526683.1:c.499A>G	chr8.hg19:g.144900554T>C	ENSP00000434359:p.Met167Val	108.0	0.0		195.0	117.0	NM_078480	A8K8K8|Q969E7|Q96D94|Q96H63|Q99628|Q9NZA0|Q9UJY7	Missense_Mutation	SNP	ENST00000526683.1	hg19	CCDS47934.1	.	.	.	.	.	.	.	.	.	.	T	16.55	3.154406	0.57259	.	.	ENSG00000179950	ENST00000526683;ENST00000453551;ENST00000313352;ENST00000456095;ENST00000349157;ENST00000527197;ENST00000526459;ENST00000529999;ENST00000531897;ENST00000533162	T;T;T;T;T;T;T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;3.39;-0.81;1.32	4.94	4.94	0.65067	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.043220	0.85682	D	0.000000	T	0.71333	0.3327	N	0.24115	0.695	0.80722	D	1	B;B;B	0.28233	0.047;0.17;0.204	B;B;B	0.43950	0.018;0.31;0.437	T	0.71220	-0.4657	10	0.44086	T	0.13	.	13.7722	0.63034	0.0:0.0:0.0:1.0	.	138;150;167	Q9UHX1-5;Q9UHX1-2;Q9UHX1	.;.;PUF60_HUMAN	V	167;124;107;138;150;121;149;187;187;204	ENSP00000434359:M167V;ENSP00000402953:M124V;ENSP00000322016:M107V;ENSP00000395417:M138V;ENSP00000322036:M150V;ENSP00000431960:M121V;ENSP00000432610:M149V;ENSP00000434863:M187V;ENSP00000437309:M187V;ENSP00000433403:M204V	ENSP00000322016:M107V	M	-	1	0	PUF60	144972542	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.939000	0.87685	1.860000	0.53959	0.482000	0.46254	ATG	.	.		0.647	PUF60-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382222.1	NM_014281	
KANK1	23189	hgsc.bcm.edu	37	9	711598	711598	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr9:711598G>C	ENST00000382303.1	+	7	1484	c.832G>C	c.(832-834)Gag>Cag	p.E278Q	KANK1_ENST00000382293.3_Missense_Mutation_p.E120Q|KANK1_ENST00000382297.2_Missense_Mutation_p.E278Q|KANK1_ENST00000489369.1_3'UTR	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	278					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GAAGGAGCTGGAGGAGCAGGT	0.562																																					p.E278Q		Atlas-SNP	.											.	KANK1	231	.	0			c.G832C						.						86.0	81.0	82.0					9																	711598		2203	4300	6503	SO:0001583	missense	23189	exon7			GAGCTGGAGGAGC	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.832G>C	chr9.hg19:g.711598G>C	ENSP00000371740:p.Glu278Gln	118.0	0.0		58.0	34.0	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	hg19	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.514496	0.85389	.	.	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.00940	5.52;5.52;5.52	5.82	5.82	0.92795	.	0.239747	0.29668	N	0.011505	T	0.07818	0.0196	M	0.84433	2.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.00492	-1.1707	10	0.87932	D	0	-0.0596	20.0953	0.97838	0.0:0.0:1.0:0.0	.	278;278	Q5W0W1;Q14678	.;KANK1_HUMAN	Q	278;278;278;120	ENSP00000371740:E278Q;ENSP00000371734:E278Q;ENSP00000371730:E120Q	ENSP00000346479:E278Q	E	+	1	0	KANK1	701598	1.000000	0.71417	0.990000	0.47175	0.987000	0.75469	9.363000	0.97131	2.767000	0.95098	0.655000	0.94253	GAG	.	.		0.562	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
PSIP1	11168	hgsc.bcm.edu	37	9	15469957	15469957	+	Nonsense_Mutation	SNP	T	T	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr9:15469957T>A	ENST00000380733.4	-	11	1355	c.1012A>T	c.(1012-1014)Aag>Tag	p.K338*	PSIP1_ENST00000380738.4_Nonsense_Mutation_p.K338*			O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1	338					establishment of integrated proviral latency (GO:0075713)|mRNA 5'-splice site recognition (GO:0000395)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to heat (GO:0009408)|response to oxidative stress (GO:0006979)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription coactivator activity (GO:0001105)|supercoiled DNA binding (GO:0097100)			breast(2)|endometrium(2)|kidney(1)|lung(3)|prostate(1)	9				GBM - Glioblastoma multiforme(50;2.38e-06)		TCCACTTTCTTAACTTCTGGC	0.308																																					p.K338X		Atlas-SNP	.											.	PSIP1	93	.	0			c.A1012T						.						101.0	99.0	100.0					9																	15469957		2203	4299	6502	SO:0001587	stop_gained	11168	exon11			CTTTCTTAACTTC	AF098482	CCDS6479.1, CCDS6480.1	9p22.2	2008-02-05	2004-02-24		ENSG00000164985	ENSG00000164985			9527	protein-coding gene	gene with protein product		603620	"""PC4 and SFRS1 interacting protein 2"""	PSIP2		9822615, 9885563	Standard	NM_033222		Approved	p52, LEDGF, p75	uc003zlw.4	O75475	OTTHUMG00000021021	ENST00000380733.4:c.1012A>T	chr9.hg19:g.15469957T>A	ENSP00000370109:p.Lys338*	40.0	0.0		13.0	5.0	NM_001128217	D3DRI9|O00256|O95368|Q6P391|Q86YB9|Q9NZI3|Q9UER6	Nonsense_Mutation	SNP	ENST00000380733.4	hg19	CCDS6479.1	.	.	.	.	.	.	.	.	.	.	T	39	7.782769	0.98486	.	.	ENSG00000164985	ENST00000380733;ENST00000380738	.	.	.	6.02	6.02	0.97574	.	0.042947	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.2108	0.82158	0.0:0.0:0.0:1.0	.	.	.	.	X	338	.	ENSP00000370109:K338X	K	-	1	0	PSIP1	15459957	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.429000	0.66495	2.299000	0.77371	0.528000	0.53228	AAG	.	.		0.308	PSIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055445.1	NM_033222	
DENND4C	55667	hgsc.bcm.edu	37	9	19316742	19316742	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr9:19316742C>T	ENST00000380432.2	+	8	1037	c.1004C>T	c.(1003-1005)gCg>gTg	p.A335V	DENND4C_ENST00000434457.2_Missense_Mutation_p.A571V|DENND4C_ENST00000602925.1_Missense_Mutation_p.A571V			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	335	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						CGCTTTATGGCGTCTATTTTA	0.418																																					p.A571V		Atlas-SNP	.											DENND4C,NS,carcinoma,-1,1	DENND4C	120	.	0			c.C1712T						.						122.0	136.0	132.0					9																	19316742		2203	4300	6503	SO:0001583	missense	55667	exon12			TTATGGCGTCTAT	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.1004C>T	chr9.hg19:g.19316742C>T	ENSP00000369797:p.Ala335Val	118.0	0.0		69.0	32.0	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	hg19		.	.	.	.	.	.	.	.	.	.	C	27.0	4.786761	0.90367	.	.	ENSG00000137145	ENST00000380437	.	.	.	5.13	5.13	0.70059	dDENN (3);	0.048658	0.85682	D	0.000000	T	0.79958	0.4536	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82004	-0.0672	9	0.87932	D	0	-17.9767	18.7716	0.91894	0.0:1.0:0.0:0.0	.	335	Q5VZ89	DEN4C_HUMAN	V	335	.	ENSP00000369802:A335V	A	+	2	0	DENND4C	19306742	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	7.599000	0.82757	2.672000	0.90937	0.460000	0.39030	GCG	.	.		0.418	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
KIAA1958	158405	hgsc.bcm.edu	37	9	115337110	115337110	+	Silent	SNP	T	T	G			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr9:115337110T>G	ENST00000337530.6	+	2	1046	c.750T>G	c.(748-750)gcT>gcG	p.A250A	KIAA1958_ENST00000374244.3_Silent_p.A250A|KIAA1958_ENST00000536272.1_Silent_p.A250A	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	250										endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						TAGGGTCTGCTAAACTGATTC	0.542																																					p.A250A		Atlas-SNP	.											.	KIAA1958	52	.	0			c.T750G						.						175.0	149.0	158.0					9																	115337110		2203	4300	6503	SO:0001819	synonymous_variant	158405	exon2			GTCTGCTAAACTG	AB075838	CCDS35108.1, CCDS69642.1	9q33.1	2009-09-22			ENSG00000165185	ENSG00000165185			23427	protein-coding gene	gene with protein product							Standard	NM_001287038		Approved	FLJ39294	uc004bgf.1	Q8N8K9	OTTHUMG00000020508	ENST00000337530.6:c.750T>G	chr9.hg19:g.115337110T>G		93.0	0.0		102.0	6.0	NM_133465	B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Silent	SNP	ENST00000337530.6	hg19	CCDS35108.1																																																																																			.	.		0.542	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465	
RAPGEF1	2889	hgsc.bcm.edu	37	9	134477527	134477527	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr9:134477527C>G	ENST00000372189.3	-	12	1987	c.1864G>C	c.(1864-1866)Gct>Cct	p.A622P	RAPGEF1_ENST00000372190.3_Missense_Mutation_p.A640P|RAPGEF1_ENST00000372195.1_Missense_Mutation_p.A639P	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	622					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		TCTTTCCCAGCCGGTGGCTCC	0.632																																					p.A640P		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.G1918C						.						27.0	31.0	30.0					9																	134477527		1948	4133	6081	SO:0001583	missense	2889	exon12			TCCCAGCCGGTGG	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"""guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"""	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.1864G>C	chr9.hg19:g.134477527C>G	ENSP00000361263:p.Ala622Pro	53.0	0.0		62.0	18.0	NM_198679	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	hg19	CCDS48047.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.571|5.571	0.290177|0.290177	0.10567|0.10567	.|.	.|.	ENSG00000107263|ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000398415;ENST00000437236;ENST00000372191;ENST00000357686;ENST00000431470;ENST00000545785|ENST00000414781	T;T;T|.	0.26518|.	1.73;1.74;1.74|.	5.11|5.11	1.02|1.02	0.19986|0.19986	.|.	0.819730|.	0.11592|.	N|.	0.548659|.	T|T	0.11750|0.11750	0.0286|0.0286	N|N	0.08118|0.08118	0|0	0.21064|0.21064	N|N	0.999793|0.999793	B;B;B;B;B;B;B;B|.	0.06786|.	0.001;0.001;0.001;0.0;0.0;0.0;0.0;0.001|.	B;B;B;B;B;B;B;B|.	0.09377|.	0.004;0.004;0.004;0.001;0.001;0.001;0.001;0.001|.	T|T	0.27706|0.27706	-1.0066|-1.0066	10|5	0.31617|.	T|.	0.26|.	.|.	2.0677|2.0677	0.03606|0.03606	0.2235:0.4494:0.1096:0.2174|0.2235:0.4494:0.1096:0.2174	.|.	122;456;219;602;583;639;622;640|.	E7ERR9;E9PDT1;Q5JUE7;C9JL20;Q13905-2;Q68DL3;Q13905;Q13905-3|.	.;.;.;.;.;.;RPGF1_HUMAN;.|.	P|A	622;639;568;622;640;602;600;67;206;456;639;122;36|49	ENSP00000361269:A639P;ENSP00000361263:A622P;ENSP00000361264:A640P|.	ENSP00000266110:A622P|.	A|G	-|-	1|2	0|0	RAPGEF1|RAPGEF1	133467348|133467348	0.054000|0.054000	0.20591|0.20591	0.829000|0.829000	0.32907|0.32907	0.041000|0.041000	0.13682|0.13682	0.204000|0.204000	0.17335|0.17335	-0.226000|-0.226000	0.09899|0.09899	-1.134000|-1.134000	0.01955|0.01955	GCT|GGC	.	.		0.632	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312	
SDCCAG3	10807	hgsc.bcm.edu	37	9	139301664	139301664	+	Missense_Mutation	SNP	T	T	C	rs527894531		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr9:139301664T>C	ENST00000357365.3	-	5	881	c.752A>G	c.(751-753)gAc>gGc	p.D251G	SDCCAG3_ENST00000371725.3_Missense_Mutation_p.D178G|SDCCAG3_ENST00000298537.7_Missense_Mutation_p.D228G|SDCCAG3_ENST00000461693.1_5'Flank	NM_001039707.1	NP_001034796.1	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	251						cytoplasm (GO:0005737)				NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	16		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)		AACCGCAAAGTCTGCGCTAGG	0.632																																					p.D251G		Atlas-SNP	.											.	SDCCAG3	41	.	0			c.A752G						.						32.0	34.0	34.0					9																	139301664		2004	4183	6187	SO:0001583	missense	10807	exon5			GCAAAGTCTGCGC	AF039688	CCDS6999.2, CCDS43903.1, CCDS43904.1	9q34.3	2010-10-27			ENSG00000165689	ENSG00000165689			10667	protein-coding gene	gene with protein product						9610721	Standard	XM_005266050		Approved	NY-CO-3	uc004chi.3	Q96C92	OTTHUMG00000020928	ENST00000357365.3:c.752A>G	chr9.hg19:g.139301664T>C	ENSP00000349929:p.Asp251Gly	120.0	0.0		122.0	40.0	NM_001039707	A6NCP1|O60525|Q5SXN1|Q5SXN2|Q5SXN3|Q5SXN4|Q5SXN8|Q6V704|Q9NVY5	Missense_Mutation	SNP	ENST00000357365.3	hg19	CCDS43904.1	.	.	.	.	.	.	.	.	.	.	T	14.96	2.690091	0.48097	.	.	ENSG00000165689	ENST00000357365;ENST00000298537;ENST00000371725;ENST00000371723	T;T;T;T	0.36157	2.31;2.34;2.33;1.27	5.4	4.19	0.49359	.	0.605936	0.17111	N	0.186623	T	0.33498	0.0865	L	0.57536	1.79	0.22142	N	0.999337	B;B;B	0.31077	0.089;0.307;0.307	B;B;B	0.30572	0.075;0.117;0.117	T	0.24404	-1.0161	10	0.46703	T	0.11	-3.4979	9.3005	0.37842	0.0:0.0:0.309:0.691	.	178;228;251	Q96C92-4;Q96C92-2;Q96C92	.;.;SDCG3_HUMAN	G	251;228;178;201	ENSP00000349929:D251G;ENSP00000298537:D228G;ENSP00000360790:D178G;ENSP00000360788:D201G	ENSP00000298537:D228G	D	-	2	0	SDCCAG3	138421485	0.717000	0.27966	0.282000	0.24776	0.881000	0.50899	1.050000	0.30404	2.039000	0.60335	0.533000	0.62120	GAC	.	.		0.632	SDCCAG3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055060.2	NM_006643	
SYNPO2L	79933	hgsc.bcm.edu	37	10	75407832	75407832	+	Silent	SNP	G	G	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr10:75407832G>T	ENST00000394810.2	-	4	1727	c.1578C>A	c.(1576-1578)ccC>ccA	p.P526P	SYNPO2L_ENST00000372873.4_Silent_p.P302P	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	526	Pro-rich.					cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					GCGCGTGGCTGGGAACCCCTG	0.687																																					p.P526P		Atlas-SNP	.											.	SYNPO2L	118	.	0			c.C1578A						.						8.0	10.0	10.0					10																	75407832		2185	4278	6463	SO:0001819	synonymous_variant	79933	exon4			GTGGCTGGGAACC	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.1578C>A	chr10.hg19:g.75407832G>T		121.0	0.0		74.0	4.0	NM_001114133	A5PKV9|Q68A20	Silent	SNP	ENST00000394810.2	hg19	CCDS44438.1																																																																																			.	.		0.687	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875	
NRG3	10718	hgsc.bcm.edu	37	10	84118543	84118543	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr10:84118543G>T	ENST00000404547.1	+	2	872	c.872G>T	c.(871-873)cGa>cTa	p.R291L	NRG3_ENST00000372142.2_Missense_Mutation_p.R70L|NRG3_ENST00000556918.1_Missense_Mutation_p.R121L|NRG3_ENST00000372141.2_Missense_Mutation_p.R291L|NRG3_ENST00000404576.2_Missense_Mutation_p.R95L			P56975	NRG3_HUMAN	neuregulin 3	291	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		AAACCCTGCCGAGACAAGGAC	0.522																																					p.R291L		Atlas-SNP	.											.	NRG3	301	.	0			c.G872T						.						189.0	144.0	159.0					10																	84118543		2203	4300	6503	SO:0001583	missense	10718	exon2			CCTGCCGAGACAA	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.872G>T	chr10.hg19:g.84118543G>T	ENSP00000384796:p.Arg291Leu	158.0	0.0		163.0	48.0	NM_001165972	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	hg19	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	G	35	5.448643	0.96205	.	.	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287;ENST00000372142;ENST00000404576;ENST00000556918	T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3	5.72	4.72	0.59763	.	0.174915	0.27522	N	0.018988	T	0.14227	0.0344	N	0.01874	-0.695	0.80722	D	1	B;P;B	0.47191	0.431;0.891;0.312	B;B;B	0.43754	0.222;0.43;0.09	T	0.01697	-1.1293	10	0.29301	T	0.29	-12.557	5.3371	0.15963	0.2311:0.0:0.7689:0.0	.	291;70;291	B9EGV5;P56975-3;P56975-4	.;.;.	L	291;291;291;70;95;121	ENSP00000361214:R291L;ENSP00000384796:R291L;ENSP00000361215:R70L;ENSP00000385804:R95L;ENSP00000451376:R121L	ENSP00000361214:R291L	R	+	2	0	NRG3	84108523	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.063000	0.64332	2.711000	0.92665	0.655000	0.94253	CGA	.	.		0.522	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086	
INPP5A	3632	hgsc.bcm.edu	37	10	134595384	134595384	+	Missense_Mutation	SNP	G	G	A	rs374027590		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr10:134595384G>A	ENST00000368594.3	+	15	1455	c.1178G>A	c.(1177-1179)cGa>cAa	p.R393Q	RP11-288G11.3_ENST00000441365.2_lincRNA	NM_005539.3	NP_005530.3	Q14642	I5P1_HUMAN	inositol polyphosphate-5-phosphatase, 40kDa	393					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|PH domain binding (GO:0042731)			cervix(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)		CTGGCCTTCCGAATCATGCCC	0.612																																					p.R393Q	Pancreas(63;823 1267 11107 20380 51626)	Atlas-SNP	.											INPP5A_ENST00000445580,NS,carcinoma,+1,1	INPP5A	77	.	0			c.G1178A						.	G	GLN/ARG	1,4399	2.1+/-5.4	0,1,2199	107.0	122.0	117.0		1178	4.2	1.0	10		117	0,8582		0,0,4291	no	missense	INPP5A	NM_005539.3	43	0,1,6490	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	393/413	134595384	1,12981	2200	4291	6491	SO:0001583	missense	3632	exon15			CCTTCCGAATCAT	X77567	CCDS7669.2	10q26.3	2008-08-07	2002-08-29		ENSG00000068383	ENSG00000068383	3.1.3.56		6076	protein-coding gene	gene with protein product	"""CTCL tumor antigen HD-CL-02"", ""43 kDa inositol polyphosphate 5-phophatase"", ""inositol polyphosphate 5-phophatase, 40kDa"", ""InsP3 5-phosphatase"", ""type I inositol-1,4,5-trisphosphate 5-phosphatase"""	600106	"""inositol polyphosphate-5-phosphatase, 40kD"""			8013665	Standard	NM_005539		Approved	5PTASE	uc001llp.3	Q14642	OTTHUMG00000019293	ENST00000368594.3:c.1178G>A	chr10.hg19:g.134595384G>A	ENSP00000357583:p.Arg393Gln	133.0	0.0		106.0	36.0	NM_005539	D3DXI3|Q14640|Q5JSF1	Missense_Mutation	SNP	ENST00000368594.3	hg19	CCDS7669.2	.	.	.	.	.	.	.	.	.	.	G	28.6	4.932221	0.92389	2.27E-4	0.0	ENSG00000068383	ENST00000368594;ENST00000416326;ENST00000432898;ENST00000445580	T;D	0.95342	0.95;-3.68	4.15	4.15	0.48705	Endonuclease/exonuclease/phosphatase (1);Inositol polyphosphate-related phosphatase (1);	0.098789	0.43579	D	0.000552	D	0.96497	0.8857	M	0.66939	2.045	0.80722	D	1	P;D	0.76494	0.868;0.999	B;D	0.72625	0.294;0.978	D	0.96365	0.9269	10	0.45353	T	0.12	-4.1261	16.8306	0.85943	0.0:0.0:1.0:0.0	.	336;393	F5GWM1;Q14642	.;I5P1_HUMAN	Q	393;336;310;75	ENSP00000357583:R393Q;ENSP00000390749:R75Q	ENSP00000357583:R393Q	R	+	2	0	INPP5A	134445374	1.000000	0.71417	0.967000	0.41034	0.939000	0.58152	8.586000	0.90806	2.044000	0.60594	0.455000	0.32223	CGA	.	.		0.612	INPP5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051085.1	NM_005539	
MUC5B	727897	hgsc.bcm.edu	37	11	1262639	1262639	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr11:1262639C>A	ENST00000529681.1	+	31	4587	c.4529C>A	c.(4528-4530)aCa>aAa	p.T1510K	MUC5B_ENST00000447027.1_Missense_Mutation_p.T1513K|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1510	7 X Cys-rich subdomain repeats.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		TGTCAGTGGACAGAGTGGTTT	0.632																																					p.T1510K		Atlas-SNP	.											.	MUC5B	473	.	0			c.C4529A						.						48.0	58.0	55.0					11																	1262639		2090	4213	6303	SO:0001583	missense	727897	exon31			AGTGGACAGAGTG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.4529C>A	chr11.hg19:g.1262639C>A	ENSP00000436812:p.Thr1510Lys	143.0	0.0		144.0	52.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	c	13.52	2.261126	0.39995	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.26660	1.72;1.72	5.01	5.01	0.66863	.	.	.	.	.	T	0.55016	0.1894	M	0.81341	2.54	0.38443	D	0.946766	D;D	0.76494	0.999;0.999	D;D	0.72982	0.979;0.979	T	0.64799	-0.6322	9	0.87932	D	0	.	18.3736	0.90428	0.0:1.0:0.0:0.0	.	2203;1513	A7Y9J9;E9PBJ0	.;.	K	1510;1513;1511;1580	ENSP00000436812:T1510K;ENSP00000415793:T1513K	ENSP00000343037:T1511K	T	+	2	0	MUC5B	1219215	0.915000	0.31059	0.882000	0.34594	0.337000	0.28794	3.324000	0.52022	2.341000	0.79615	0.299000	0.19835	ACA	.	.		0.632	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
NLRP14	338323	hgsc.bcm.edu	37	11	7064609	7064609	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr11:7064609G>T	ENST00000299481.4	+	4	1698	c.1352G>T	c.(1351-1353)gGg>gTg	p.G451V		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	451	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		AGAAGGCTTGGGTTAACTCAA	0.433																																					p.G451V		Atlas-SNP	.											.	NLRP14	187	.	0			c.G1352T						.						125.0	129.0	128.0					11																	7064609		2201	4296	6497	SO:0001583	missense	338323	exon4			GGCTTGGGTTAAC	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.1352G>T	chr11.hg19:g.7064609G>T	ENSP00000299481:p.Gly451Val	135.0	0.0		133.0	54.0	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	hg19	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	G	12.36	1.913891	0.33815	.	.	ENSG00000158077	ENST00000299481	D	0.86769	-2.17	4.34	2.42	0.29668	.	0.132021	0.35096	N	0.003447	D	0.89897	0.6848	M	0.88105	2.93	0.41912	D	0.990478	D	0.58268	0.982	P	0.53450	0.726	D	0.88525	0.3099	10	0.72032	D	0.01	.	3.7282	0.08482	0.2303:0.2084:0.5613:0.0	.	451	Q86W24	NAL14_HUMAN	V	451	ENSP00000299481:G451V	ENSP00000299481:G451V	G	+	2	0	NLRP14	7021185	0.003000	0.15002	0.881000	0.34555	0.440000	0.31957	0.267000	0.18552	1.156000	0.42514	0.655000	0.94253	GGG	.	.		0.433	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
VWCE	220001	hgsc.bcm.edu	37	11	61032665	61032665	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr11:61032665G>A	ENST00000335613.5	-	17	2371	c.1985C>T	c.(1984-1986)tCc>tTc	p.S662F	VWCE_ENST00000535710.1_Missense_Mutation_p.S127F	NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	662	VWFC 5. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						GTCCACGGGGGAACAGGCCAC	0.627																																					p.S662F		Atlas-SNP	.											.	VWCE	84	.	0			c.C1985T						.						44.0	36.0	38.0					11																	61032665		2181	4275	6456	SO:0001583	missense	220001	exon17			ACGGGGGAACAGG	AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.1985C>T	chr11.hg19:g.61032665G>A	ENSP00000334186:p.Ser662Phe	325.0	0.0		341.0	102.0	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Missense_Mutation	SNP	ENST00000335613.5	hg19	CCDS8002.1	.	.	.	.	.	.	.	.	.	.	G	19.89	3.910841	0.72983	.	.	ENSG00000167992	ENST00000335613;ENST00000535710	T;T	0.72835	-0.69;-0.69	4.88	4.88	0.63580	von Willebrand factor, type C (4);	0.000000	0.34802	N	0.003677	T	0.80297	0.4597	L	0.49699	1.58	0.41527	D	0.988433	D	0.76494	0.999	D	0.91635	0.999	T	0.80569	-0.1324	10	0.46703	T	0.11	.	16.2196	0.82251	0.0:0.0:1.0:0.0	.	662	Q96DN2	VWCE_HUMAN	F	662;127	ENSP00000334186:S662F;ENSP00000442570:S127F	ENSP00000334186:S662F	S	-	2	0	VWCE	60789241	1.000000	0.71417	0.934000	0.37439	0.987000	0.75469	4.669000	0.61575	2.421000	0.82119	0.555000	0.69702	TCC	.	.		0.627	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718	
DAGLA	747	hgsc.bcm.edu	37	11	61511843	61511843	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr11:61511843C>A	ENST00000257215.5	+	20	3127	c.3011C>A	c.(3010-3012)aCg>aAg	p.T1004K	RP11-467L20.10_ENST00000536405.1_lincRNA	NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	1004					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		ATGGACCTGACGCCCACGGGC	0.667																																					p.T1004K		Atlas-SNP	.											.	DAGLA	109	.	0			c.C3011A						.						47.0	51.0	50.0					11																	61511843		2202	4298	6500	SO:0001583	missense	747	exon20			ACCTGACGCCCAC	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"""neural stem cell-derived dendrite regulator"""	614015	"""chromosome 11 open reading frame 11"""	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.3011C>A	chr11.hg19:g.61511843C>A	ENSP00000257215:p.Thr1004Lys	156.0	0.0		138.0	51.0	NM_006133	A7E233|Q6WQJ0	Missense_Mutation	SNP	ENST00000257215.5	hg19	CCDS31578.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.393229	0.62066	.	.	ENSG00000134780	ENST00000257215	T	0.27402	1.67	4.03	3.03	0.35002	.	0.190106	0.45867	D	0.000339	T	0.21427	0.0516	N	0.24115	0.695	0.46185	D	0.998919	B	0.15141	0.012	B	0.13407	0.009	T	0.12604	-1.0541	10	0.72032	D	0.01	-11.1783	12.6053	0.56519	0.1665:0.8335:0.0:0.0	.	1004	Q9Y4D2	DGLA_HUMAN	K	1004	ENSP00000257215:T1004K	ENSP00000257215:T1004K	T	+	2	0	DAGLA	61268419	0.996000	0.38824	0.990000	0.47175	0.990000	0.78478	3.539000	0.53604	1.979000	0.57680	0.462000	0.41574	ACG	.	.		0.667	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
KIRREL3	84623	hgsc.bcm.edu	37	11	126316746	126316746	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr11:126316746G>A	ENST00000525144.2	-	9	1282	c.1033C>T	c.(1033-1035)Ctc>Ttc	p.L345F	KIRREL3_ENST00000525704.2_Missense_Mutation_p.L345F|KIRREL3_ENST00000529097.2_Missense_Mutation_p.L345F	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	345	Ig-like C2-type 4.				hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		AGATCCACGAGCAAGGATTGG	0.612																																					p.L345F		Atlas-SNP	.											.	KIRREL3	183	.	0			c.C1033T						.						41.0	44.0	43.0					11																	126316746		2069	4197	6266	SO:0001583	missense	84623	exon9			CCACGAGCAAGGA	AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.1033C>T	chr11.hg19:g.126316746G>A	ENSP00000435466:p.Leu345Phe	58.0	0.0		95.0	29.0	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Missense_Mutation	SNP	ENST00000525144.2	hg19	CCDS53723.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.408497	0.62399	.	.	ENSG00000149571	ENST00000525144;ENST00000529097;ENST00000525704	T;T;T	0.67171	-0.25;-0.25;-0.25	4.55	2.64	0.31445	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.086699	0.47852	D	0.000214	T	0.60792	0.2296	L	0.28014	0.82	0.80722	D	1	D;D;P	0.59767	0.986;0.971;0.953	P;P;P	0.55303	0.563;0.773;0.718	T	0.58578	-0.7612	10	0.54805	T	0.06	.	6.6942	0.23189	0.084:0.0:0.6016:0.3145	.	345;345;345	Q8IZU9-2;E9PRX9;Q8IZU9	.;.;KIRR3_HUMAN	F	345	ENSP00000435466:L345F;ENSP00000434081:L345F;ENSP00000435094:L345F	ENSP00000435466:L345F	L	-	1	0	KIRREL3	125821956	1.000000	0.71417	0.465000	0.27155	0.906000	0.53458	2.233000	0.43027	0.335000	0.23614	0.297000	0.19635	CTC	.	.		0.612	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531	
COL2A1	1280	hgsc.bcm.edu	37	12	48388212	48388212	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr12:48388212G>T	ENST00000380518.3	-	12	975	c.811C>A	c.(811-813)Cct>Act	p.P271T	COL2A1_ENST00000337299.6_Missense_Mutation_p.P202T	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	271	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	TTTACCTGAGGACCAGGCGGA	0.542																																					p.P271T		Atlas-SNP	.											.	COL2A1	368	.	0			c.C811A						.						130.0	107.0	115.0					12																	48388212		2203	4300	6503	SO:0001583	missense	1280	exon12			CCTGAGGACCAGG	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"""Collagens"""	2200	protein-coding gene	gene with protein product		120140	"""collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)"", ""arthroophthalmopathy, progressive (Stickler syndrome)"""	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.811C>A	chr12.hg19:g.48388212G>T	ENSP00000369889:p.Pro271Thr	110.0	0.0		163.0	47.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Missense_Mutation	SNP	ENST00000380518.3	hg19	CCDS41778.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.262627	0.59431	.	.	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	D;D	0.96856	-4.15;-4.15	3.91	3.91	0.45181	.	0.000000	0.85682	D	0.000000	D	0.97501	0.9182	M	0.65975	2.015	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.83275	0.993;0.996	D	0.97305	0.9933	10	0.49607	T	0.09	.	15.8912	0.79299	0.0:0.0:1.0:0.0	.	202;271	P02458-1;P02458	.;CO2A1_HUMAN	T	271;202;202	ENSP00000369889:P271T;ENSP00000338213:P202T	ENSP00000338213:P202T	P	-	1	0	COL2A1	46674479	1.000000	0.71417	1.000000	0.80357	0.768000	0.43524	9.323000	0.96364	2.478000	0.83669	0.561000	0.74099	CCT	.	.		0.542	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
NAV3	89795	hgsc.bcm.edu	37	12	78515815	78515815	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr12:78515815T>C	ENST00000397909.2	+	16	4018	c.3845T>C	c.(3844-3846)tTa>tCa	p.L1282S	NAV3_ENST00000228327.6_Missense_Mutation_p.L1282S|NAV3_ENST00000266692.7_Intron|NAV3_ENST00000536525.2_Missense_Mutation_p.L1282S			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1282	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						AGTACCACATTAGCGCGGCAA	0.562										HNSCC(70;0.22)																											p.L1282S		Atlas-SNP	.											.	NAV3	506	.	0			c.T3845C						.						53.0	52.0	52.0					12																	78515815		2076	4224	6300	SO:0001583	missense	89795	exon16			CCACATTAGCGCG	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.3845T>C	chr12.hg19:g.78515815T>C	ENSP00000381007:p.Leu1282Ser	124.0	0.0		122.0	41.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.	.	.	.	.	.	.	.	.	.	T	16.44	3.124623	0.56613	.	.	ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327	T;T;T	0.30981	1.52;1.51;1.51	5.96	5.96	0.96718	.	0.000000	0.31859	U	0.006956	T	0.43010	0.1228	N	0.22421	0.69	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.997;0.998;0.999	T	0.33189	-0.9878	10	0.44086	T	0.13	-10.6382	16.4338	0.83864	0.0:0.0:0.0:1.0	.	1282;1282;1282	E7EUC6;Q8IVL0;Q8IVL0-2	.;NAV3_HUMAN;.	S	1282	ENSP00000446132:L1282S;ENSP00000381007:L1282S;ENSP00000228327:L1282S	ENSP00000228327:L1282S	L	+	2	0	NAV3	77039946	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.806000	0.86020	2.270000	0.75569	0.533000	0.62120	TTA	.	.		0.562	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
MED13L	23389	hgsc.bcm.edu	37	12	116413042	116413042	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr12:116413042T>C	ENST00000281928.3	-	25	5871	c.5665A>G	c.(5665-5667)Atg>Gtg	p.M1889V		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1889						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		AGAGATGTCATTTGGACAATC	0.443																																					p.M1889V		Atlas-SNP	.											.	MED13L	193	.	0			c.A5665G						.						90.0	84.0	86.0					12																	116413042		2203	4300	6503	SO:0001583	missense	23389	exon25			ATGTCATTTGGAC	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.5665A>G	chr12.hg19:g.116413042T>C	ENSP00000281928:p.Met1889Val	130.0	0.0		152.0	63.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	hg19	CCDS9177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.55|16.55	3.154616|3.154616	0.57259|0.57259	.|.	.|.	ENSG00000123066|ENSG00000123066	ENST00000281928|ENST00000552447	D|.	0.82803|.	-1.65|.	5.78|5.78	4.63|4.63	0.57726|0.57726	.|.	0.074656|.	0.85682|.	N|.	0.000000|.	T|T	0.57666|0.57666	0.2069|0.2069	L|L	0.44542|0.44542	1.39|1.39	0.48511|0.48511	D|D	0.999661|0.999661	B|.	0.12013|.	0.005|.	B|.	0.14578|.	0.011|.	T|T	0.53697|0.53697	-0.8402|-0.8402	10|5	0.36615|.	T|.	0.2|.	.|.	11.8979|11.8979	0.52665|0.52665	0.0:0.0682:0.0:0.9318|0.0:0.0682:0.0:0.9318	.|.	1889|.	Q71F56|.	MD13L_HUMAN|.	V|S	1889|93	ENSP00000281928:M1889V|.	ENSP00000281928:M1889V|.	M|N	-|-	1|2	0|0	MED13L|MED13L	114897425|114897425	1.000000|1.000000	0.71417|0.71417	0.961000|0.961000	0.40146|0.40146	0.998000|0.998000	0.95712|0.95712	4.801000|4.801000	0.62532|0.62532	1.120000|1.120000	0.41904|0.41904	0.482000|0.482000	0.46254|0.46254	ATG|AAT	.	.		0.443	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
PPP2R5E	5529	hgsc.bcm.edu	37	14	63881864	63881864	+	Silent	SNP	T	T	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr14:63881864T>C	ENST00000337537.3	-	5	1145	c.543A>G	c.(541-543)gtA>gtG	p.V181V	PPP2R5E_ENST00000553266.1_5'UTR|PPP2R5E_ENST00000422769.2_Silent_p.V105V|PPP2R5E_ENST00000555899.1_Silent_p.V181V	NM_001282179.1|NM_001282180.1|NM_001282181.1|NM_001282182.1|NM_006246.2	NP_001269108.1|NP_001269109.1|NP_001269110.1|NP_001269111.1|NP_006237.1	Q16537	2A5E_HUMAN	protein phosphatase 2, regulatory subunit B', epsilon isoform	181					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)	15				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		TTACCTGTAATACAAATTTCT	0.308																																					p.V181V		Atlas-SNP	.											.	PPP2R5E	43	.	0			c.A543G						.						88.0	90.0	90.0					14																	63881864		2202	4297	6499	SO:0001819	synonymous_variant	5529	exon5			CTGTAATACAAAT	L76703	CCDS9758.1, CCDS61467.1, CCDS61468.1	14q23.2	2010-06-18	2007-01-22		ENSG00000154001	ENSG00000154001		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9313	protein-coding gene	gene with protein product		601647	"""protein phosphatase 2, regulatory subunit B (B56), epsilon isoform"""			7592815	Standard	NM_006246		Approved		uc001xgd.1	Q16537	OTTHUMG00000140341	ENST00000337537.3:c.543A>G	chr14.hg19:g.63881864T>C		205.0	0.0		196.0	62.0	NM_006246	A4FU37|B7ZAW5|B7ZKK8|B7ZKK9|J3KQN6|Q52LW4	Silent	SNP	ENST00000337537.3	hg19	CCDS9758.1																																																																																			.	.		0.308	PPP2R5E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276973.1	NM_006246	
STON2	85439	hgsc.bcm.edu	37	14	81743600	81743600	+	Silent	SNP	G	G	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr14:81743600G>A	ENST00000267540.2	-	4	2255	c.2055C>T	c.(2053-2055)acC>acT	p.T685T	STON2_ENST00000556280.1_5'Flank|STON2_ENST00000555447.1_Silent_p.T685T	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	685	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		TGAAAGGCAAGGTCTTCTCAG	0.537																																					p.T685T		Atlas-SNP	.											STON2,right_upper_lobe,carcinoma,0,1	STON2	94	.	0			c.C2055T						.						124.0	117.0	119.0					14																	81743600		2203	4300	6503	SO:0001819	synonymous_variant	85439	exon6			AGGCAAGGTCTTC	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"""stoned B homolog 2 (Drosophila)"""	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.2055C>T	chr14.hg19:g.81743600G>A		169.0	0.0		150.0	93.0	NM_001256430	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Silent	SNP	ENST00000267540.2	hg19	CCDS9875.1																																																																																			.	.		0.537	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104	
EMP2	2013	hgsc.bcm.edu	37	16	10631932	10631932	+	Splice_Site	SNP	C	C	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr16:10631932C>A	ENST00000359543.3	-	4	379		c.e4-1		EMP2_ENST00000536829.1_Splice_Site	NM_001424.4	NP_001415.1	P54851	EMP2_HUMAN	epithelial membrane protein 2						cell proliferation (GO:0008283)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|regulation of glomerular filtration (GO:0003093)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	integrin binding (GO:0005178)			NS(1)|endometrium(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6						GTGGAGTACTCTGCGGGAAAA	0.622																																					.	GBM(158;2021 2691 14714 39478)	Atlas-SNP	.											.	EMP2	21	.	0			c.170-1G>T						.						107.0	98.0	101.0					16																	10631932		2197	4300	6497	SO:0001630	splice_region_variant	2013	exon5			AGTACTCTGCGGG	U52100	CCDS10541.1	16p13.2	2008-08-01			ENSG00000213853	ENSG00000213853			3334	protein-coding gene	gene with protein product		602334				8996089, 10331954, 16216233	Standard	NM_001424		Approved	XMP	uc002czx.3	P54851	OTTHUMG00000129752	ENST00000359543.3:c.170-1G>T	chr16.hg19:g.10631932C>A		106.0	0.0		108.0	42.0	NM_001424	B2R7V6|D3DUF8	Splice_Site	SNP	ENST00000359543.3	hg19	CCDS10541.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.839259	0.51057	.	.	ENSG00000213853	ENST00000359543;ENST00000536829	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6338	0.91370	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	EMP2	10539433	1.000000	0.71417	0.600000	0.28864	0.011000	0.07611	4.741000	0.62095	2.620000	0.88729	0.655000	0.94253	.	.	.		0.622	EMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251965.1	NM_001424	Intron
ZNF469	84627	hgsc.bcm.edu	37	16	88494565	88494565	+	Silent	SNP	C	C	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr16:88494565C>A	ENST00000437464.1	+	1	687	c.687C>A	c.(685-687)gcC>gcA	p.A229A	ZNF469_ENST00000565624.1_Silent_p.A229A	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	229	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						AATACCAGGCCAGTGGGGCCG	0.682																																					p.A229A		Atlas-SNP	.											.	ZNF469	121	.	0			c.C687A						.						5.0	7.0	6.0					16																	88494565		682	1574	2256	SO:0001819	synonymous_variant	84627	exon1			CCAGGCCAGTGGG	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.687C>A	chr16.hg19:g.88494565C>A		205.0	0.0		229.0	93.0	NM_001127464		Silent	SNP	ENST00000437464.1	hg19	CCDS45544.1																																																																																			.	.		0.682	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
PLD2	5338	hgsc.bcm.edu	37	17	4719981	4719981	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr17:4719981G>A	ENST00000263088.6	+	15	1653	c.1522G>A	c.(1522-1524)Ggc>Agc	p.G508S	PLD2_ENST00000572940.1_Missense_Mutation_p.G508S	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	508	Catalytic.				cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)	31					Choline(DB00122)	CTTCTGGCTGGGCAAGGACTA	0.617																																					p.G508S		Atlas-SNP	.											.	PLD2	138	.	0			c.G1522A						.						146.0	139.0	142.0					17																	4719981		2203	4300	6503	SO:0001583	missense	5338	exon15			TGGCTGGGCAAGG	AF035483	CCDS11057.1, CCDS58507.1	17p13.3	2008-04-14			ENSG00000129219	ENSG00000129219	3.1.4.4		9068	protein-coding gene	gene with protein product	"""choline phosphatase 2"""	602384				9858823, 9582313	Standard	NM_002663		Approved		uc002fzc.3	O14939	OTTHUMG00000090779	ENST00000263088.6:c.1522G>A	chr17.hg19:g.4719981G>A	ENSP00000263088:p.Gly508Ser	136.0	0.0		90.0	44.0	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	hg19	CCDS11057.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.901737	0.92035	.	.	ENSG00000129219	ENST00000263088	T	0.13657	2.57	4.62	4.62	0.57501	.	0.050614	0.85682	N	0.000000	T	0.45756	0.1358	H	0.95079	3.62	0.80722	D	1	P;P;P	0.47106	0.489;0.87;0.89	B;P;P	0.57548	0.066;0.823;0.671	T	0.61535	-0.7043	10	0.87932	D	0	-19.7883	14.9669	0.71201	0.0:0.0:1.0:0.0	.	365;508;508	B7Z905;O14939-2;O14939	.;.;PLD2_HUMAN	S	508	ENSP00000263088:G508S	ENSP00000263088:G508S	G	+	1	0	PLD2	4666947	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.084000	0.94076	2.392000	0.81423	0.561000	0.74099	GGC	.	.		0.617	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	
TP53	7157	hgsc.bcm.edu	37	17	7578555	7578555	+	Splice_Site	SNP	C	C	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr17:7578555C>T	ENST00000269305.4	-	5	565		c.e5-1		TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|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 core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(39)|p.0?(8)|p.V73fs*9(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CAGGGGAGTACTGTAGGAAGA	0.552		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											.	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000545858,NS,carcinoma,0,58	TP53	33396	.	51	Unknown(39)|Whole gene deletion(8)|Deletion - Frameshift(3)|Insertion - In frame(1)	ovary(9)|pancreas(6)|bone(5)|upper_aerodigestive_tract(4)|liver(4)|lung(4)|breast(4)|large_intestine(3)|central_nervous_system(3)|oesophagus(3)|haematopoietic_and_lymphoid_tissue(2)|stomach(1)|endometrium(1)|urinary_tract(1)|autonomic_ganglia(1)	c.376-1G>A						.						42.0	42.0	42.0					17																	7578555		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGAGTACTGTAGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.376-1G>A	chr17.hg19:g.7578555C>T		93.0	0.0		57.0	30.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.431133	0.62844	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591	.	.	.	4.87	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4246	0.50003	0.0:0.9094:0.0:0.0906	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7519280	1.000000	0.71417	0.999000	0.59377	0.918000	0.54935	7.639000	0.83342	1.359000	0.45940	0.655000	0.94253	.	.	.		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron
MYH13	8735	hgsc.bcm.edu	37	17	10206563	10206563	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr17:10206563C>T	ENST00000418404.3	-	38	5780	c.5617G>A	c.(5617-5619)Gac>Aac	p.D1873N	MYH13_ENST00000252172.4_Missense_Mutation_p.D1873N|RP11-401O9.4_ENST00000609088.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1873					cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						TGCAGCTTGTCCACCAGGTCC	0.587																																					p.D1873N		Atlas-SNP	.											.	MYH13	533	.	0			c.G5617A						.						150.0	157.0	155.0					17																	10206563		2151	4268	6419	SO:0001583	missense	8735	exon39			GCTTGTCCACCAG	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.5617G>A	chr17.hg19:g.10206563C>T	ENSP00000404570:p.Asp1873Asn	104.0	0.0		80.0	30.0	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	hg19	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.284484	0.80803	.	.	ENSG00000006788	ENST00000252172	D	0.85013	-1.93	3.81	3.81	0.43845	Myosin tail (1);	.	.	.	.	D	0.92384	0.7583	H	0.97440	4.005	0.45852	D	0.998717	B	0.24823	0.112	B	0.37387	0.248	D	0.93707	0.7020	9	0.87932	D	0	.	16.2342	0.82361	0.0:1.0:0.0:0.0	.	1873	Q9UKX3	MYH13_HUMAN	N	1873	ENSP00000252172:D1873N	ENSP00000252172:D1873N	D	-	1	0	MYH13	10147288	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.855000	0.69510	2.107000	0.64212	0.561000	0.74099	GAC	.	.		0.587	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	
SPECC1	92521	hgsc.bcm.edu	37	17	20135682	20135682	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr17:20135682G>A	ENST00000261503.5	+	7	2366	c.2315G>A	c.(2314-2316)gGc>gAc	p.G772D	SPECC1_ENST00000395529.3_Missense_Mutation_p.G772D|SPECC1_ENST00000584527.1_Missense_Mutation_p.G190D|SPECC1_ENST00000395530.2_Missense_Mutation_p.G691D|SPECC1_ENST00000395525.3_Missense_Mutation_p.G691D|SPECC1_ENST00000395527.4_Missense_Mutation_p.G772D|SPECC1_ENST00000472876.1_3'UTR|SPECC1_ENST00000395522.2_Missense_Mutation_p.G691D|SPECC1_ENST00000536879.1_Missense_Mutation_p.G112D|AC004702.2_ENST00000580225.1_lincRNA	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	772					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		GATGTGCAGGGCCACGGCAGG	0.632																																					p.G772D		Atlas-SNP	.											.	SPECC1	100	.	0			c.G2315A						.						23.0	24.0	23.0					17																	20135682		2202	4300	6502	SO:0001583	missense	92521	exon7			TGCAGGGCCACGG	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"""sperm antigen HCMOGT 1"", ""cytokinesis and spindle organization B"", ""cytospin B"""	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.2315G>A	chr17.hg19:g.20135682G>A	ENSP00000261503:p.Gly772Asp	98.0	0.0		84.0	27.0	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	hg19	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.104481	0.56291	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529;ENST00000536879;ENST00000395522;ENST00000395527;ENST00000395525	T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6	4.22	3.23	0.37069	.	0.147651	0.64402	D	0.000008	T	0.60547	0.2277	L	0.60455	1.87	0.58432	D	0.999996	P;D;D;D;P	0.61697	0.658;0.99;0.99;0.99;0.923	B;P;P;P;P	0.57324	0.283;0.628;0.818;0.818;0.493	T	0.59994	-0.7349	10	0.35671	T	0.21	-13.791	12.2339	0.54503	0.0:0.1737:0.8263:0.0	.	772;691;691;772;772	A8MV89;Q5M775-4;Q5M775-3;Q5M775-2;Q5M775	.;.;.;.;CYTSB_HUMAN	D	772;772;772;112;691;691;691	ENSP00000261503:G772D;ENSP00000378900:G772D;ENSP00000438294:G112D;ENSP00000378893:G691D;ENSP00000378896:G691D	ENSP00000261503:G772D	G	+	2	0	SPECC1	20076274	1.000000	0.71417	0.961000	0.40146	0.908000	0.53690	3.352000	0.52239	1.336000	0.45506	0.655000	0.94253	GGC	.	.		0.632	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
SLC46A1	113235	hgsc.bcm.edu	37	17	26731821	26731821	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr17:26731821G>T	ENST00000440501.1	-	2	989	c.894C>A	c.(892-894)tgC>tgA	p.C298*	SLC46A1_ENST00000321666.5_Nonsense_Mutation_p.C298*|SLC46A1_ENST00000584729.1_5'UTR|CTD-2350C19.1_ENST00000583956.1_RNA|CTD-2350C19.2_ENST00000580714.1_RNA	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	298					cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	TGGAGTCCCAGCAGAGGGGTG	0.547																																					p.C298X		Atlas-SNP	.											.	SLC46A1	17	.	0			c.C894A						.						101.0	110.0	107.0					17																	26731821		2028	4184	6212	SO:0001587	stop_gained	113235	exon2			GTCCCAGCAGAGG	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"""Solute carriers"""	30521	protein-coding gene	gene with protein product	"""heme carrier protein 1"", ""proton-coupled folate transporter"""	611672	"""solute carrier family 46, member 1"""			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.894C>A	chr17.hg19:g.26731821G>T	ENSP00000395653:p.Cys298*	195.0	0.0		285.0	143.0	NM_001242366	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Nonsense_Mutation	SNP	ENST00000440501.1	hg19		.	.	.	.	.	.	.	.	.	.	G	33	5.212205	0.95069	.	.	ENSG00000076351	ENST00000440501;ENST00000321666	.	.	.	5.15	4.19	0.49359	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-23.5089	10.8105	0.46545	0.1519:0.0:0.8481:0.0	.	.	.	.	X	298	.	ENSP00000318828:C298X	C	-	3	2	SLC46A1	23755948	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	6.417000	0.73337	1.177000	0.42855	-0.251000	0.11542	TGC	.	.		0.547	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669	
KIAA0100	9703	hgsc.bcm.edu	37	17	26946763	26946763	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr17:26946763G>C	ENST00000528896.2	-	31	5625	c.5551C>G	c.(5551-5553)Ctg>Gtg	p.L1851V	KIAA0100_ENST00000389003.3_Missense_Mutation_p.L1708V|KIAA0100_ENST00000544884.1_Missense_Mutation_p.L1708V|KIAA0100_ENST00000579924.2_5'UTR|SPAG5-AS1_ENST00000414744.1_RNA|SPAG5-AS1_ENST00000424210.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	1851						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					AGGTCAAGCAGATTCTCATTC	0.488																																					p.L1851V		Atlas-SNP	.											.	KIAA0100	175	.	0			c.C5551G						.						114.0	89.0	97.0					17																	26946763		2203	4300	6503	SO:0001583	missense	9703	exon31			CAAGCAGATTCTC	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"""cancer/testis antigen 101"", ""breast cancer overexpressed gene 1"""	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.5551C>G	chr17.hg19:g.26946763G>C	ENSP00000436773:p.Leu1851Val	87.0	0.0		109.0	31.0	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	G	16.74	3.206762	0.58343	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T;T	0.50813	0.73;1.54;1.56	5.75	2.68	0.31781	FMP27,  C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.56426	0.1984	L	0.51422	1.61	0.58432	D	0.999993	D	0.69078	0.997	D	0.85130	0.997	T	0.49952	-0.8884	10	0.24483	T	0.36	.	9.1525	0.36971	0.2952:0.0:0.7048:0.0	.	1851	Q14667	K0100_HUMAN	V	1851;1821;1851;1708	ENSP00000467716:L1821V;ENSP00000436773:L1851V;ENSP00000446443:L1708V	ENSP00000005905:L1851V	L	-	1	2	KIAA0100	23970890	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.120000	0.41968	0.758000	0.33059	0.655000	0.94253	CTG	.	.		0.488	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680	
TEX14	56155	hgsc.bcm.edu	37	17	56707834	56707834	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr17:56707834T>A	ENST00000240361.8	-	3	303	c.218A>T	c.(217-219)gAt>gTt	p.D73V	U3_ENST00000390893.1_RNA|TEX14_ENST00000389934.3_Missense_Mutation_p.D73V|TEX14_ENST00000349033.5_Missense_Mutation_p.D73V			Q8IWB6	TEX14_HUMAN	testis expressed 14	73					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.D73G(1)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CACCAGAACATCAACGAATTT	0.378																																					p.D73V		Atlas-SNP	.											TEX14,NS,NS,0,1	TEX14	343	.	1	Substitution - Missense(1)	pancreas(1)	c.A218T						.						96.0	80.0	85.0					17																	56707834		2203	4300	6503	SO:0001583	missense	56155	exon3			AGAACATCAACGA	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.218A>T	chr17.hg19:g.56707834T>A	ENSP00000240361:p.Asp73Val	138.0	2.0		329.0	68.0	NM_198393	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	hg19	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.246914	0.80024	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.65549	-0.16;-0.16;-0.16	5.7	5.7	0.88788	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000010	T	0.69700	0.3140	L	0.28504	0.86	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.79784	0.993;0.988;0.988	T	0.73442	-0.3981	10	0.87932	D	0	-8.114	14.844	0.70246	0.0:0.0:0.0:1.0	.	73;73;73	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	V	73	ENSP00000240361:D73V;ENSP00000374584:D73V;ENSP00000268910:D73V	ENSP00000240361:D73V	D	-	2	0	TEX14	54062833	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	3.667000	0.54547	2.190000	0.69967	0.456000	0.33151	GAT	.	.		0.378	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
NDUFV2	4729	hgsc.bcm.edu	37	18	9117876	9117876	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr18:9117876A>G	ENST00000318388.6	+	2	209	c.95A>G	c.(94-96)aAt>aGt	p.N32S	NDUFV2_ENST00000400033.1_Missense_Mutation_p.N35S|RP11-143J12.3_ENST00000579467.1_RNA|RP11-21J18.1_ENST00000579126.1_RNA	NM_021074.4	NP_066552.2	P19404	NDUV2_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa	32					cardiac muscle tissue development (GO:0048738)|cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|nervous system development (GO:0007399)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|lung(4)|ovary(1)|stomach(1)	7						GTTATGCAAAATGGAGCTGGA	0.279																																					p.N32S		Atlas-SNP	.											.	NDUFV2	17	.	0			c.A95G						.						61.0	67.0	65.0					18																	9117876		2203	4296	6499	SO:0001583	missense	4729	exon2			TGCAAAATGGAGC	X84421	CCDS11842.1	18p11.22	2011-07-04	2002-08-29		ENSG00000178127	ENSG00000178127	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7717	protein-coding gene	gene with protein product	"""complex I 24kDa subunit"", ""NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial"""	600532	"""NADH dehydrogenase (ubiquinone) flavoprotein 2 (24kD)"""			9763677, 7607668	Standard	NM_021074		Approved	CI-24k	uc002knu.3	P19404	OTTHUMG00000131593	ENST00000318388.6:c.95A>G	chr18.hg19:g.9117876A>G	ENSP00000327268:p.Asn32Ser	356.0	0.0		366.0	101.0	NM_021074	Q9BV41	Missense_Mutation	SNP	ENST00000318388.6	hg19	CCDS11842.1	.	.	.	.	.	.	.	.	.	.	A	6.981	0.551073	0.13374	.	.	ENSG00000178127	ENST00000318388;ENST00000400033	T;T	0.40756	1.02;1.03	5.55	4.38	0.52667	.	0.281089	0.47093	D	0.000247	T	0.22044	0.0531	N	0.12961	0.28	0.31897	N	0.616514	B	0.09022	0.002	B	0.04013	0.001	T	0.16217	-1.0410	10	0.08381	T	0.77	-25.8517	10.4518	0.44526	0.8762:0.0:0.1238:0.0	.	32	P19404	NDUV2_HUMAN	S	32;35	ENSP00000327268:N32S;ENSP00000382908:N35S	ENSP00000327268:N32S	N	+	2	0	NDUFV2	9107876	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	1.699000	0.37804	2.238000	0.73509	0.477000	0.44152	AAT	.	.		0.279	NDUFV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254475.2	NM_021074	
DSC3	1825	hgsc.bcm.edu	37	18	28598662	28598662	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr18:28598662A>C	ENST00000360428.4	-	8	1127	c.1047T>G	c.(1045-1047)aaT>aaG	p.N349K	DSC3_ENST00000434452.1_Missense_Mutation_p.N349K	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	349	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			GTGCATTATCATTTGAATCTG	0.308																																					p.N349K		Atlas-SNP	.											.	DSC3	225	.	0			c.T1047G						.						177.0	169.0	172.0					18																	28598662		2203	4300	6503	SO:0001583	missense	1825	exon8			ATTATCATTTGAA	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"""Cadherins / Major cadherins"""	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.1047T>G	chr18.hg19:g.28598662A>C	ENSP00000353608:p.Asn349Lys	53.0	0.0		51.0	15.0	NM_024423	A6NN35|Q14200|Q9HAZ9	Missense_Mutation	SNP	ENST00000360428.4	hg19	CCDS32810.1	.	.	.	.	.	.	.	.	.	.	A	18.63	3.666011	0.67700	.	.	ENSG00000134762	ENST00000360428;ENST00000434452	T;T	0.77750	-1.12;-1.12	5.25	1.53	0.23141	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.35407	N	0.003228	D	0.91442	0.7299	H	0.99042	4.41	0.58432	D	0.999998	D;D	0.89917	0.999;1.0	D;D	0.83275	0.991;0.996	D	0.90723	0.4636	10	0.87932	D	0	.	9.2457	0.37525	0.7853:0.0:0.2147:0.0	.	349;349	Q14574;Q14574-2	DSC3_HUMAN;.	K	349	ENSP00000353608:N349K;ENSP00000392068:N349K	ENSP00000353608:N349K	N	-	3	2	DSC3	26852660	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	1.791000	0.38744	0.475000	0.27415	-0.341000	0.08007	AAT	.	.		0.308	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423	
ST8SIA5	29906	hgsc.bcm.edu	37	18	44268787	44268787	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr18:44268787G>T	ENST00000315087.7	-	4	1067	c.407C>A	c.(406-408)aCc>aAc	p.T136N	ST8SIA5_ENST00000590497.1_5'UTR|ST8SIA5_ENST00000536490.1_Missense_Mutation_p.T105N|ST8SIA5_ENST00000538168.1_Missense_Mutation_p.T172N	NM_013305.4	NP_037437.2	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	136					carbohydrate metabolic process (GO:0005975)|glycosphingolipid biosynthetic process (GO:0006688)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialyltransferase activity (GO:0008373)			kidney(1)|large_intestine(10)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	22						GATGCCACTGGTGTCCACCTC	0.597																																					p.T136N		Atlas-SNP	.											.	ST8SIA5	57	.	0			c.C407A						.						194.0	165.0	175.0					18																	44268787		2203	4300	6503	SO:0001583	missense	29906	exon4			CCACTGGTGTCCA	U91641	CCDS11930.1	18q12.3	2013-03-01	2003-01-14	2005-02-07	ENSG00000101638	ENSG00000101638		"""Sialyltransferases"""	17827	protein-coding gene	gene with protein product	"""ST8Sia V"""	607162	"""sialyltransferase 8E (alpha-2, 8-polysialytransferase)"""	SIAT8E		9199191	Standard	XM_005258250		Approved		uc002lcj.1	O15466	OTTHUMG00000132643	ENST00000315087.7:c.407C>A	chr18.hg19:g.44268787G>T	ENSP00000321343:p.Thr136Asn	82.0	0.0		115.0	61.0	NM_013305	B7Z1K9|Q6IAW7	Missense_Mutation	SNP	ENST00000315087.7	hg19	CCDS11930.1	.	.	.	.	.	.	.	.	.	.	G	11.11	1.541740	0.27563	.	.	ENSG00000101638	ENST00000315087;ENST00000538168;ENST00000536490	T;T;T	0.29142	1.58;1.58;1.58	5.59	2.78	0.32641	.	0.156981	0.56097	N	0.000025	T	0.16514	0.0397	N	0.16368	0.405	0.52501	D	0.999951	B;B;B	0.20261	0.002;0.0;0.043	B;B;B	0.19666	0.006;0.003;0.026	T	0.08146	-1.0736	10	0.24483	T	0.36	.	7.643	0.28305	0.0656:0.1207:0.6884:0.1254	.	105;172;136	F5H8D1;B7Z1K9;O15466	.;.;SIA8E_HUMAN	N	136;172;105	ENSP00000321343:T136N;ENSP00000445492:T172N;ENSP00000443683:T105N	ENSP00000321343:T136N	T	-	2	0	ST8SIA5	42522785	1.000000	0.71417	0.990000	0.47175	0.964000	0.63967	5.323000	0.65858	0.293000	0.22520	-0.224000	0.12420	ACC	.	.		0.597	ST8SIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255892.1	NM_013305	
CRB3	92359	hgsc.bcm.edu	37	19	6464770	6464770	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr19:6464770C>G	ENST00000598494.1	+	2	589	c.58C>G	c.(58-60)Cgc>Ggc	p.R20G	CRB3_ENST00000356762.3_Missense_Mutation_p.R20G|CRB3_ENST00000308243.7_Missense_Mutation_p.R20G|CRB3_ENST00000600229.1_Missense_Mutation_p.R20G			Q9BUF7	CRUM3_HUMAN	crumbs family member 3	20					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|protein localization to plasma membrane (GO:0072659)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)|SH3 domain binding (GO:0017124)			endometrium(1)|large_intestine(1)|lung(1)	3						CCTGCTGGCCCGCTGGGGCCG	0.701																																					p.R20G		Atlas-SNP	.											.	CRB3	8	.	0			c.C58G						.						4.0	5.0	4.0					19																	6464770		1714	3666	5380	SO:0001583	missense	92359	exon2			CTGGCCCGCTGGG	AF503290	CCDS12166.1, CCDS12167.1	19p13.3	2014-02-06	2014-02-06		ENSG00000130545	ENSG00000130545			20237	protein-coding gene	gene with protein product		609737	"""crumbs homolog 3 (Drosophila)"""				Standard	XM_005259680		Approved	MGC17303	uc002mez.3	Q9BUF7	OTTHUMG00000181828	ENST00000598494.1:c.58C>G	chr19.hg19:g.6464770C>G	ENSP00000469707:p.Arg20Gly	39.0	0.0		26.0	12.0	NM_174881	A8KA91|D6W643|Q8N0V8|Q8WVA0	Missense_Mutation	SNP	ENST00000598494.1	hg19	CCDS12167.1	.	.	.	.	.	.	.	.	.	.	C	10.99	1.508142	0.27036	.	.	ENSG00000130545	ENST00000356762;ENST00000308243	.	.	.	4.01	0.0923	0.14472	.	0.494583	0.19462	N	0.113675	T	0.27663	0.0680	L	0.57536	1.79	0.22266	N	0.999249	B;B	0.09022	0.002;0.002	B;B	0.10450	0.005;0.005	T	0.26815	-1.0092	9	0.06625	T	0.88	-1.0174	3.6067	0.08045	0.0:0.506:0.2192:0.2748	.	20;20	Q9BUF7-2;Q9BUF7	.;CRUM3_HUMAN	G	20	.	ENSP00000310123:R20G	R	+	1	0	CRB3	6415770	0.000000	0.05858	0.901000	0.35422	0.300000	0.27592	-0.827000	0.04424	0.275000	0.22094	0.462000	0.41574	CGC	.	.		0.701	CRB3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457837.1		
CPAMD8	27151	hgsc.bcm.edu	37	19	17017877	17017877	+	Silent	SNP	C	C	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr19:17017877C>T	ENST00000443236.1	-	30	4084	c.4053G>A	c.(4051-4053)gcG>gcA	p.A1351A	RN7SL835P_ENST00000579920.1_RNA	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1304						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						TGGCCAGGGGCGCAGCAGACT	0.657																																					p.A1351A		Atlas-SNP	.											.	CPAMD8	192	.	0			c.G4053A						.						34.0	42.0	39.0					19																	17017877		2154	4254	6408	SO:0001819	synonymous_variant	27151	exon30			CAGGGGCGCAGCA	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.4053G>A	chr19.hg19:g.17017877C>T		131.0	0.0		108.0	57.0	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	hg19	CCDS42519.1	.	.	.	.	.	.	.	.	.	.	C	0.039	-1.291064	0.01375	.	.	ENSG00000160111	ENST00000443236	.	.	.	3.07	-6.14	0.02111	.	.	.	.	.	T	0.24392	0.0591	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.26643	-1.0097	4	.	.	.	.	5.792	0.18365	0.0:0.3732:0.2202:0.4065	.	.	.	.	H	1362	.	.	R	-	2	0	CPAMD8	16878877	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.852000	0.01667	-1.644000	0.01517	-1.607000	0.00807	CGC	.	.		0.657	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
RPL18A	6142	hgsc.bcm.edu	37	19	17972267	17972267	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr19:17972267G>T	ENST00000222247.5	+	2	265	c.184G>T	c.(184-186)Gtc>Ttc	p.V62F	RPL18A_ENST00000599870.1_Missense_Mutation_p.V33F|RPL18A_ENST00000600147.1_Missense_Mutation_p.V62F|SNORA68_ENST00000384437.1_RNA|RPL18A_ENST00000599898.1_Missense_Mutation_p.V23F	NM_000980.3	NP_000971.1	Q02543	RL18A_HUMAN	ribosomal protein L18a	62					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|upper_aerodigestive_tract(1)	5						AGGGGAGATTGTCTACTGTGG	0.512																																					p.V62F		Atlas-SNP	.											.	RPL18A	15	.	0			c.G184T						.						32.0	33.0	32.0					19																	17972267		2203	4300	6503	SO:0001583	missense	6142	exon2			GAGATTGTCTACT	AB007175	CCDS12367.1	19p13.11	2011-04-06			ENSG00000105640	ENSG00000105640		"""L ribosomal proteins"""	10311	protein-coding gene	gene with protein product	"""60S ribosomal protein L18a"", ""ribosomal protein L18a-like protein"""	604178				9582194	Standard	NM_000980		Approved	L18A	uc002nhp.3	Q02543		ENST00000222247.5:c.184G>T	chr19.hg19:g.17972267G>T	ENSP00000222247:p.Val62Phe	60.0	0.0		32.0	12.0	NM_000980		Missense_Mutation	SNP	ENST00000222247.5	hg19	CCDS12367.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.203390	0.58234	.	.	ENSG00000105640	ENST00000420197;ENST00000222247	.	.	.	4.11	4.11	0.48088	Ribosomal protein L18a/LX (1);	0.138713	0.47852	U	0.000207	D	0.83760	0.5324	M	0.90082	3.085	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	D	0.87704	0.2562	9	0.87932	D	0	.	14.229	0.65879	0.0:0.0:1.0:0.0	.	62	Q02543	RL18A_HUMAN	F	62	.	ENSP00000222247:V62F	V	+	1	0	RPL18A	17833267	1.000000	0.71417	0.896000	0.35187	0.068000	0.16541	9.415000	0.97375	2.019000	0.59389	0.563000	0.77884	GTC	.	.		0.512	RPL18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466679.1	NM_000980	
ZNF208	7757	hgsc.bcm.edu	37	19	22156515	22156515	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr19:22156515T>C	ENST00000397126.4	-	4	1469	c.1321A>G	c.(1321-1323)Atg>Gtg	p.M441V	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	441					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TTATGTTCCATAAGGTTTGAG	0.373																																					p.M441V		Atlas-SNP	.											.	ZNF208	817	.	0			c.A1321G						.						82.0	89.0	87.0					19																	22156515		2119	4251	6370	SO:0001583	missense	7757	exon4			GTTCCATAAGGTT	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.1321A>G	chr19.hg19:g.22156515T>C	ENSP00000380315:p.Met441Val	122.0	0.0		149.0	29.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	hg19	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	T	0.029	-1.346276	0.01266	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.16897	2.31	2.83	-3.15	0.05233	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10809	0.0264	.	.	.	0.09310	N	1	B	0.22346	0.068	B	0.34346	0.18	T	0.46624	-0.9178	8	0.23302	T	0.38	.	5.9142	0.19045	0.1678:0.573:0.0:0.2592	.	441	O43345	ZN208_HUMAN	V	441	ENSP00000380315:M441V	ENSP00000380315:M441V	M	-	1	0	ZNF208	21948355	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.193000	0.01244	-0.302000	0.08869	0.254000	0.18369	ATG	.	.		0.373	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
RYR1	6261	hgsc.bcm.edu	37	19	39034235	39034235	+	Silent	SNP	A	A	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr19:39034235A>C	ENST00000359596.3	+	86	11842	c.11842A>C	c.(11842-11844)Agg>Cgg	p.R3948R	RYR1_ENST00000355481.4_Silent_p.R3943R|RYR1_ENST00000360985.3_Silent_p.R3943R			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3948					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GCAGGGCAAGAGGAACTTCTC	0.602																																					p.R3948R		Atlas-SNP	.											.	RYR1	708	.	0			c.A11842C						.						90.0	84.0	86.0					19																	39034235		2203	4300	6503	SO:0001819	synonymous_variant	6261	exon86			GGCAAGAGGAACT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.11842A>C	chr19.hg19:g.39034235A>C		94.0	0.0		112.0	17.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.602	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
PSG3	5671	hgsc.bcm.edu	37	19	43236995	43236995	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr19:43236995C>T	ENST00000327495.5	-	3	834	c.650G>A	c.(649-651)tGt>tAt	p.C217Y	PSG3_ENST00000595140.1_Missense_Mutation_p.C217Y|PSG3_ENST00000490592.1_5'Flank	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	217	Ig-like C2-type 1.				defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				CCGTATTTCACATTCATAGGG	0.517																																					p.C217Y		Atlas-SNP	.											.	PSG3	82	.	0			c.G650A						.						230.0	236.0	234.0					19																	43236995		2203	4298	6501	SO:0001583	missense	5671	exon3			ATTTCACATTCAT		CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.650G>A	chr19.hg19:g.43236995C>T	ENSP00000332215:p.Cys217Tyr	73.0	0.0		145.0	88.0	NM_021016	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	SNP	ENST00000327495.5	hg19	CCDS12611.1	.	.	.	.	.	.	.	.	.	.	-	12.33	1.904323	0.33628	.	.	ENSG00000221826	ENST00000327495	T	0.58940	0.3	1.59	1.59	0.23543	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.78304	0.4262	M	0.93507	3.425	0.28060	N	0.933025	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.979	T	0.66452	-0.5920	9	0.87932	D	0	.	6.5812	0.22596	0.0:1.0:0.0:0.0	.	195;217	Q08266;Q16557	.;PSG3_HUMAN	Y	217	ENSP00000332215:C217Y	ENSP00000332215:C217Y	C	-	2	0	PSG3	47928835	0.064000	0.20934	0.284000	0.24805	0.019000	0.09904	0.781000	0.26774	0.871000	0.35750	0.393000	0.25936	TGT	.	.		0.517	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016	
NKPD1	284353	hgsc.bcm.edu	37	19	45656158	45656158	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr19:45656158C>A	ENST00000438936.2	-	3	1082	c.871G>T	c.(871-873)Gat>Tat	p.D291Y	AC005757.7_ENST00000589594.1_lincRNA|NKPD1_ENST00000429338.1_Missense_Mutation_p.D291Y|NKPD1_ENST00000317951.4_Missense_Mutation_p.D513Y|NKPD1_ENST00000589776.1_Missense_Mutation_p.D291Y			Q17RQ9	NKPD1_HUMAN	NTPase, KAP family P-loop domain containing 1	291	KAP NTPase.					integral component of membrane (GO:0016021)				endometrium(1)|lung(4)|prostate(2)|urinary_tract(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)		TAGCCGTTATCGGCCGTGCCC	0.637																																					p.D513Y		Atlas-SNP	.											.	NKPD1	46	.	0			c.G1537T						.						11.0	14.0	13.0					19																	45656158		2085	4208	6293	SO:0001583	missense	284353	exon4			CGTTATCGGCCGT	AK090919		19q13.32	2012-07-02		2012-07-02	ENSG00000179846	ENSG00000179846			24739	protein-coding gene	gene with protein product						14702039	Standard	NM_198478		Approved	FLJ33600	uc010xxi.2	Q17RQ9	OTTHUMG00000160521	ENST00000438936.2:c.871G>T	chr19.hg19:g.45656158C>A	ENSP00000401739:p.Asp291Tyr	129.0	0.0		152.0	80.0	NM_198478	B7ZLG6|D6RH15|Q8N2A2	Missense_Mutation	SNP	ENST00000438936.2	hg19		.	.	.	.	.	.	.	.	.	.	C	15.05	2.717980	0.48622	.	.	ENSG00000179846	ENST00000317951;ENST00000438936;ENST00000429338	T;T;T	0.32753	1.44;1.44;1.44	5.3	5.3	0.74995	KAP P-loop (1);	0.051073	0.85682	D	0.000000	T	0.52549	0.1741	L	0.56769	1.78	0.49130	D	0.999752	D	0.89917	1.0	D	0.91635	0.999	T	0.50432	-0.8829	10	0.51188	T	0.08	-43.981	16.4297	0.83837	0.0:1.0:0.0:0.0	.	291	Q17RQ9	NKPD1_HUMAN	Y	513;291;291	ENSP00000321976:D513Y;ENSP00000401739:D291Y;ENSP00000404706:D291Y	ENSP00000321976:D513Y	D	-	1	0	NKPD1	50347998	1.000000	0.71417	1.000000	0.80357	0.626000	0.37791	5.687000	0.68219	2.476000	0.83614	0.462000	0.41574	GAT	.	.		0.637	NKPD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000360950.2	NM_198478	
SULF2	55959	hgsc.bcm.edu	37	20	46365492	46365492	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr20:46365492T>C	ENST00000359930.4	-	3	1221	c.370A>G	c.(370-372)Agc>Ggc	p.S124G	SULF2_ENST00000478766.1_5'UTR|SULF2_ENST00000467815.1_Missense_Mutation_p.S124G|SULF2_ENST00000361612.4_Missense_Mutation_p.S124G|SULF2_ENST00000484875.1_Missense_Mutation_p.S124G	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	124					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						AAGGTGCGGCTCTCGTGCTGT	0.622																																					p.S124G		Atlas-SNP	.											.	SULF2	131	.	0			c.A370G						.						181.0	130.0	147.0					20																	46365492		2203	4300	6503	SO:0001583	missense	55959	exon3			TGCGGCTCTCGTG	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.370A>G	chr20.hg19:g.46365492T>C	ENSP00000353007:p.Ser124Gly	88.0	0.0		91.0	36.0	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	hg19	CCDS13408.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.813584	0.50527	.	.	ENSG00000196562	ENST00000359930;ENST00000484875;ENST00000361612;ENST00000467815;ENST00000437955	D;D;D;D;D	0.98602	-5.02;-5.02;-5.02;-5.02;-5.02	5.34	1.82	0.25136	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.247613	0.47852	N	0.000218	D	0.95354	0.8492	L	0.34521	1.04	0.28885	N	0.894179	B;B;B	0.27971	0.027;0.048;0.196	B;B;B	0.33521	0.041;0.041;0.165	D	0.91927	0.5552	10	0.66056	D	0.02	-15.8801	8.9188	0.35599	0.0:0.2169:0.0:0.7831	.	124;124;124	G3XAE6;Q8IWU5-2;Q8IWU5	.;.;SULF2_HUMAN	G	124	ENSP00000353007:S124G;ENSP00000418290:S124G;ENSP00000354662:S124G;ENSP00000418442:S124G;ENSP00000410026:S124G	ENSP00000353007:S124G	S	-	1	0	SULF2	45798899	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	2.543000	0.45752	0.326000	0.23384	0.459000	0.35465	AGC	.	.		0.622	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837	
PCNT	5116	hgsc.bcm.edu	37	21	47851867	47851867	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr21:47851867G>T	ENST00000359568.5	+	38	8596	c.8489G>T	c.(8488-8490)tGt>tTt	p.C2830F	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2830					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CAGAAGCACTGTGAGGCGCTC	0.567																																					p.C2830F		Atlas-SNP	.											.	PCNT	283	.	0			c.G8489T						.						65.0	58.0	61.0					21																	47851867		2203	4300	6503	SO:0001583	missense	5116	exon38			AGCACTGTGAGGC	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.8489G>T	chr21.hg19:g.47851867G>T	ENSP00000352572:p.Cys2830Phe	104.0	0.0		53.0	26.0	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	G	10.17	1.275595	0.23307	.	.	ENSG00000160299	ENST00000359568	T	0.01548	4.78	5.21	4.31	0.51392	.	0.217433	0.23700	N	0.045428	T	0.03651	0.0104	L	0.32530	0.975	0.09310	N	1	D;D	0.65815	0.995;0.991	P;P	0.58172	0.834;0.687	T	0.52859	-0.8519	10	0.19590	T	0.45	.	12.5238	0.56075	0.1353:0.0:0.8647:0.0	.	2712;2830	O95613-2;O95613	.;PCNT_HUMAN	F	2830	ENSP00000352572:C2830F	ENSP00000352572:C2830F	C	+	2	0	PCNT	46676295	0.000000	0.05858	0.065000	0.19835	0.056000	0.15407	0.400000	0.20932	2.606000	0.88127	0.655000	0.94253	TGT	.	.		0.567	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
C22orf29	79680	hgsc.bcm.edu	37	22	19839750	19839750	+	Missense_Mutation	SNP	C	C	T	rs9618711		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr22:19839750C>T	ENST00000405640.1	-	2	703	c.35G>A	c.(34-36)cGc>cAc	p.R12H	GNB1L_ENST00000405009.1_Intron|GNB1L_ENST00000329517.6_Intron|GNB1L_ENST00000403325.1_Intron|C22orf29_ENST00000328554.4_Missense_Mutation_p.R12H|C22orf29_ENST00000484072.1_Intron|GNB1L_ENST00000460402.1_Intron|C22orf29_ENST00000407472.1_Missense_Mutation_p.R12H			Q7L3V2	BOP_HUMAN	chromosome 22 open reading frame 29	12					mitochondrial outer membrane permeabilization (GO:0097345)|regulation of mitochondrial membrane potential (GO:0051881)	mitochondrion (GO:0005739)		p.R12H(1)		NS(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	7	Colorectal(54;0.0993)					GATGGGAATGCGAGGGCCCTG	0.637																																					p.R12H		Atlas-SNP	.											C22orf29,NS,carcinoma,-1,1	C22orf29	23	.	1	Substitution - Missense(1)	large_intestine(1)	c.G35A						.	C	HIS/ARG,	0,4406		0,0,2203	56.0	56.0	56.0		35,	-2.1	0.0	22	dbSNP_119	56	1,8589		0,1,4294	no	missense,intron	GNB1L,C22orf29	NM_024627.5,NM_053004.2	29,	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,	12/365,	19839750	1,12995	2203	4295	6498	SO:0001583	missense	79680	exon3			GGAATGCGAGGGC	BX640998	CCDS13769.1	22q11.21	2006-07-05			ENSG00000215012	ENSG00000215012			26112	protein-coding gene	gene with protein product						12477932	Standard	NM_024627		Approved	FLJ21125	uc002zqh.3	Q7L3V2	OTTHUMG00000030314	ENST00000405640.1:c.35G>A	chr22.hg19:g.19839750C>T	ENSP00000384924:p.Arg12His	127.0	0.0		132.0	42.0	NM_024627	A8K5E7|D3DX21|Q6MZM8|Q6N000|Q9H7A0	Missense_Mutation	SNP	ENST00000405640.1	hg19	CCDS13769.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.920401	0.33908	0.0	1.16E-4	ENSG00000215012	ENST00000407472;ENST00000328554;ENST00000405640;ENST00000416337	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	3.69	-2.1	0.07210	.	.	.	.	.	T	0.12220	0.0297	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.23226	-1.0194	9	0.33940	T	0.23	-0.2253	3.3818	0.07257	0.1819:0.3924:0.0:0.4257	rs9618711	12	Q7L3V2	CV029_HUMAN	H	12	ENSP00000386111:R12H;ENSP00000330596:R12H;ENSP00000384924:R12H;ENSP00000392994:R12H	ENSP00000330596:R12H	R	-	2	0	C22orf29	18219750	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.577000	0.05847	-0.296000	0.08947	-0.136000	0.14681	CGC	.	.		0.637	C22orf29-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317290.2	NM_024627	
AMELX	265	hgsc.bcm.edu	37	X	11316227	11316227	+	Intron	SNP	C	C	G			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chrX:11316227C>G	ENST00000380714.3	+	4	170				ARHGAP6_ENST00000337414.4_Intron|AMELX_ENST00000348912.4_Intron|AMELX_ENST00000380712.3_Nonsense_Mutation_p.S36*|ARHGAP6_ENST00000380718.1_Intron|ARHGAP6_ENST00000380732.3_Intron|ARHGAP6_ENST00000413512.3_Intron|ARHGAP6_ENST00000380736.1_Intron	NM_001142.2	NP_001133.1	Q99217	AMELX_HUMAN	amelogenin, X-linked						biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|enamel mineralization (GO:0070166)|epithelial to mesenchymal transition (GO:0001837)|ion homeostasis (GO:0050801)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of tooth mineralization (GO:0070172)|signal transduction (GO:0007165)|tooth mineralization (GO:0034505)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|hydroxyapatite binding (GO:0046848)|identical protein binding (GO:0042802)|structural constituent of tooth enamel (GO:0030345)			endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	15						TTGTAGAACTCACATTCTCAG	0.358																																					p.S36X		Atlas-SNP	.											.	AMELX	31	.	0			c.C107G						.						236.0	226.0	229.0					X																	11316227		2203	4300	6503	SO:0001627	intron_variant	265	exon4			AGAACTCACATTC		CCDS14144.1, CCDS14145.1, CCDS14146.1	Xp22.31-p22.1	2010-04-20	2010-04-20		ENSG00000125363	ENSG00000125363			461	protein-coding gene	gene with protein product	"""amelogenesis imperfecta 1"""	300391	"""amelogenin (X chromosome, amelogenesis imperfecta 1)"""	AMG, AIH1		1734713	Standard	NM_182680		Approved		uc004cus.3	Q99217	OTTHUMG00000021130	ENST00000380714.3:c.103-129C>G	chrX.hg19:g.11316227C>G		151.0	0.0		215.0	88.0	NM_182680	Q96NW6|Q9UCA7	Nonsense_Mutation	SNP	ENST00000380714.3	hg19	CCDS14144.1	.	.	.	.	.	.	.	.	.	.	C	17.46	3.394290	0.62066	.	.	ENSG00000125363	ENST00000380712	.	.	.	4.56	2.73	0.32206	.	0.000000	0.29198	N	0.012860	.	.	.	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	4.5126	4.7718	0.13160	0.2125:0.6733:0.0:0.1142	.	.	.	.	X	36	.	ENSP00000370088:S36X	S	+	2	0	AMELX	11226148	0.261000	0.24063	0.029000	0.17559	0.933000	0.57130	0.431000	0.21444	0.458000	0.26988	0.459000	0.35465	TCA	.	.		0.358	AMELX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055746.1	NM_001142	
TLR8	51311	hgsc.bcm.edu	37	X	12940017	12940017	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chrX:12940017G>C	ENST00000218032.6	+	2	2945	c.2858G>C	c.(2857-2859)aGc>aCc	p.S953T	TLR8_ENST00000311912.5_Missense_Mutation_p.S971T	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	953	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	TATGCAAAAAGCTGGAACTTT	0.403																																					p.S953T		Atlas-SNP	.											.	TLR8	134	.	0			c.G2858C						.						63.0	61.0	62.0					X																	12940017		2203	4299	6502	SO:0001583	missense	51311	exon2			CAAAAAGCTGGAA	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.2858G>C	chrX.hg19:g.12940017G>C	ENSP00000218032:p.Ser953Thr	223.0	0.0		398.0	318.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	hg19	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	G	5.474	0.272429	0.10349	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.05025	3.51;3.51	5.7	-1.87	0.07737	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.146640	0.31188	N	0.008086	T	0.09335	0.0230	L	0.58428	1.81	0.29378	N	0.863525	D;D	0.53462	0.96;0.96	P;P	0.49799	0.622;0.622	T	0.14643	-1.0465	10	0.06891	T	0.86	.	15.475	0.75471	0.2651:0.0:0.7349:0.0	.	953;971	Q9NR97;D1CS70	TLR8_HUMAN;.	T	953;971	ENSP00000218032:S953T;ENSP00000312082:S971T	ENSP00000218032:S953T	S	+	2	0	TLR8	12849938	0.727000	0.28069	0.041000	0.18516	0.902000	0.53008	0.278000	0.18753	-0.805000	0.04404	-0.191000	0.12829	AGC	.	.		0.403	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
PRPS1	5631	hgsc.bcm.edu	37	X	106890949	106890949	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chrX:106890949A>G	ENST00000372435.4	+	6	940	c.818A>G	c.(817-819)aAt>aGt	p.N273S	PRPS1_ENST00000372418.1_Missense_Mutation_p.N173S|PRPS1_ENST00000372428.4_Missense_Mutation_p.N206S|PRPS1_ENST00000543248.1_Missense_Mutation_p.N273S	NM_002764.3	NP_002755.1	P60891	PRPS1_HUMAN	phosphoribosyl pyrophosphate synthetase 1	273					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|hypoxanthine biosynthetic process (GO:0046101)|nervous system development (GO:0007399)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|pyrimidine nucleotide biosynthetic process (GO:0006221)|ribonucleoside monophosphate biosynthetic process (GO:0009156)|small molecule metabolic process (GO:0044281)|urate biosynthetic process (GO:0034418)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)			breast(3)|endometrium(2)|kidney(3)|large_intestine(3)|lung(11)|upper_aerodigestive_tract(1)	23						GTAGTCACCAATACCATACCT	0.453																																					p.N273S		Atlas-SNP	.											.	PRPS1	33	.	0			c.A818G						.						139.0	113.0	122.0					X																	106890949		2203	4300	6503	SO:0001583	missense	5631	exon6			TCACCAATACCAT	X15331	CCDS14529.1, CCDS76007.1	Xq22.3	2014-09-17			ENSG00000147224	ENSG00000147224	2.7.6.1		9462	protein-coding gene	gene with protein product	"""PRS I"", ""ribose-phosphate diphosphokinase 1"""	311850	"""deafness, X-linked 2, perceptive, congenital"""	DFN2		1962753, 20021999	Standard	NM_002764		Approved	CMTX5, DFNX1	uc004ene.4	P60891	OTTHUMG00000022167	ENST00000372435.4:c.818A>G	chrX.hg19:g.106890949A>G	ENSP00000361512:p.Asn273Ser	106.0	0.0		101.0	5.0	NM_002764	B1ALA8|B2R6T7|B4DNL6|D3DUX6|P09329	Missense_Mutation	SNP	ENST00000372435.4	hg19	CCDS14529.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.159280	0.78226	.	.	ENSG00000147224	ENST00000372435;ENST00000372428;ENST00000543248;ENST00000372418	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	3.76	3.76	0.43208	.	0.000000	0.85682	D	0.000000	D	0.88976	0.6584	M	0.93420	3.415	0.54753	D	0.999987	D;D	0.76494	0.999;0.999	D;D	0.62955	0.909;0.909	D	0.91190	0.4983	10	0.87932	D	0	.	11.5863	0.50920	1.0:0.0:0.0:0.0	.	273;273	Q53FW2;P60891	.;PRPS1_HUMAN	S	273;206;273;173	ENSP00000361512:N273S;ENSP00000361505:N206S;ENSP00000443185:N273S;ENSP00000361495:N173S	ENSP00000361495:N173S	N	+	2	0	PRPS1	106777605	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.576000	0.90770	1.699000	0.51192	0.486000	0.48141	AAT	.	.		0.453	PRPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057840.1		
GPR101	83550	hgsc.bcm.edu	37	X	136112559	136112559	+	Silent	SNP	C	C	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chrX:136112559C>T	ENST00000298110.1	-	1	1274	c.1275G>A	c.(1273-1275)gtG>gtA	p.V425V		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	425						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					TTTCGACATCCACCCACACGG	0.507																																					p.V425V		Atlas-SNP	.											.	GPR101	96	.	0			c.G1275A						.						88.0	76.0	80.0					X																	136112559		2203	4300	6503	SO:0001819	synonymous_variant	83550	exon1			GACATCCACCCAC	AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"""GPCR / Class A : Orphans"""	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.1275G>A	chrX.hg19:g.136112559C>T		82.0	0.0		63.0	48.0	NM_054021	Q5JSM8|Q8NG93	Silent	SNP	ENST00000298110.1	hg19	CCDS14662.1																																																																																			.	.		0.507	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1		
PLXNB3	5365	hgsc.bcm.edu	37	X	153033156	153033156	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chrX:153033156G>T	ENST00000361971.5	+	3	988	c.874G>T	c.(874-876)Gcc>Tcc	p.A292S	PLXNB3_ENST00000538543.1_Intron|PLXNB3_ENST00000538776.1_Intron|PLXNB3_ENST00000538282.1_Intron|U52111.14_ENST00000416854.1_RNA|U52111.14_ENST00000434284.1_RNA|PLXNB3_ENST00000538966.1_Missense_Mutation_p.A315S	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	292	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CATCCAGGCCGCCTTCCTTGC	0.706																																					p.A315S		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G943T						.						12.0	11.0	12.0					X																	153033156		2172	4254	6426	SO:0001583	missense	5365	exon4			CAGGCCGCCTTCC	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.874G>T	chrX.hg19:g.153033156G>T	ENSP00000355378:p.Ala292Ser	111.0	0.0		95.0	72.0	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	hg19	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	G	12.93	2.084675	0.36758	.	.	ENSG00000198753	ENST00000538966;ENST00000361971	T;T	0.14266	2.52;2.52	5.1	4.23	0.50019	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.236856	0.21888	N	0.067630	T	0.41096	0.1144	M	0.86502	2.82	0.24828	N	0.992549	D;D	0.89917	1.0;0.973	D;P	0.80764	0.994;0.796	T	0.36480	-0.9746	10	0.44086	T	0.13	.	13.1238	0.59342	0.0:0.0:0.8386:0.1614	.	315;292	F5H773;Q9ULL4	.;PLXB3_HUMAN	S	315;292	ENSP00000442736:A315S;ENSP00000355378:A292S	ENSP00000355378:A292S	A	+	1	0	PLXNB3	152686350	1.000000	0.71417	0.040000	0.18447	0.077000	0.17291	6.946000	0.75953	0.932000	0.37266	-0.351000	0.07748	GCC	.	.		0.706	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
PHF20L1	51105	hgsc.bcm.edu	37	8	133806672	133806673	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr8:133806672_133806673insA	ENST00000395386.2	+	3	399_400	c.100_101insA	c.(100-102)gaafs	p.E34fs	PHF20L1_ENST00000395379.1_Frame_Shift_Ins_p.E34fs|PHF20L1_ENST00000395390.2_Frame_Shift_Ins_p.E34fs|PHF20L1_ENST00000395376.1_Frame_Shift_Ins_p.E34fs|PHF20L1_ENST00000220847.7_5'UTR|PHF20L1_ENST00000337920.4_Frame_Shift_Ins_p.E34fs	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	34	Tudor 1.						zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			ATCACGAATTGAAAAAATTGAC	0.351																																					p.E34fs		Atlas-INDEL	.											.	PHF20L1	129	.	0			c.100_101insA						.																																			SO:0001589	frameshift_variant	51105	exon3			.	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	24280	protein-coding gene	gene with protein product	"""tudor domain containing 20B"""					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.106dupA	chr8.hg19:g.133806678_133806678dupA	ENSP00000378784:p.Glu34fs	163.0	0.0		271.0	95.0	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Frame_Shift_Ins	INS	ENST00000395386.2	hg19	CCDS6367.2																																																																																			.	.		0.351	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018	
TMEM247	388946	hgsc.bcm.edu	37	2	46707883	46707884	+	Frame_Shift_Ins	INS	-	-	GG	rs201742486		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:46707883_46707884insGG	ENST00000434431.1	+	2	457_458	c.457_458insGG	c.(457-459)caafs	p.Q153fs		NM_001145051.2	NP_001138523.1	A6NEH6	TM247_HUMAN	transmembrane protein 247	153						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											GCAGCTGCAGCAAGAGGCGGCG	0.678																																					p.Q153fs		Atlas-INDEL	.											ENSG00000187600_ENST00000434431,NS,carcinoma,-1,2	.	.	.	0			c.457_458insGG						.																																			SO:0001589	frameshift_variant	388946	exon2			.		CCDS56117.1	2p21	2012-04-11			ENSG00000187600	ENSG00000187600			42967	protein-coding gene	gene with protein product							Standard	NM_001145051		Approved		uc010yod.3	A6NEH6	OTTHUMG00000153137	Exception_encountered	chr2.hg19:g.46707883_46707884insGG	ENSP00000388684:p.Gln153fs	129.0	0.0		119.0	27.0	NM_001145051		Frame_Shift_Ins	INS	ENST00000434431.1	hg19	CCDS56117.1																																																																																			.	.		0.678	TMEM247-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329726.1	NM_001145051	
ZNF638	27332	hgsc.bcm.edu	37	2	71576746	71576746	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:71576746delA	ENST00000409544.1	+	2	1292	c.662delA	c.(661-663)gaafs	p.E221fs	ZNF638_ENST00000377802.2_Frame_Shift_Del_p.E221fs|ZNF638_ENST00000264447.4_Frame_Shift_Del_p.E221fs|ZNF638_ENST00000355812.3_Frame_Shift_Del_p.E221fs|ZNF638_ENST00000410075.1_3'UTR	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	221					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						GGCTACACAGAAGATCCACTT	0.383																																					p.E221fs		Atlas-INDEL	.											.	ZNF638	179	.	0			c.661delG						.						99.0	96.0	97.0					2																	71576746		2203	4300	6503	SO:0001589	frameshift_variant	27332	exon2			.	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.662delA	chr2.hg19:g.71576746delA	ENSP00000386433:p.Glu221fs	116.0	0.0		138.0	37.0	NM_001252612	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Frame_Shift_Del	DEL	ENST00000409544.1	hg19	CCDS1917.1																																																																																			.	.		0.383	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
CAST	831	hgsc.bcm.edu	37	5	96062545	96062546	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr5:96062545_96062546insA	ENST00000341926.3	+	3	231_232	c.69_70insA	c.(70-72)aaafs	p.K24fs	CAST_ENST00000511049.1_Frame_Shift_Ins_p.K10fs|CAST_ENST00000511782.1_Frame_Shift_Ins_p.K10fs|CAST_ENST00000504465.1_Intron|CAST_ENST00000508830.1_Frame_Shift_Ins_p.K107fs|CAST_ENST00000508608.1_Intron|CAST_ENST00000359176.4_Frame_Shift_Ins_p.K107fs|CAST_ENST00000509903.1_Intron|CAST_ENST00000395813.1_Frame_Shift_Ins_p.K107fs|CAST_ENST00000325674.7_Intron|CAST_ENST00000395812.2_Intron|CAST_ENST00000309190.5_Intron|CAST_ENST00000510756.1_Intron|CAST_ENST00000338252.3_Frame_Shift_Ins_p.K24fs			P20810	ICAL_HUMAN	calpastatin	24					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	22		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		TTCCTAACAAGAAAAAACACAA	0.396																																					p.K23fs		Atlas-INDEL	.											.	CAST	58	.	0			c.69_70insA						.																																			SO:0001589	frameshift_variant	831	exon5			.	AF327443	CCDS4082.1, CCDS54882.1, CCDS54883.1, CCDS75279.1	5q15	2012-09-20			ENSG00000153113	ENSG00000153113			1515	protein-coding gene	gene with protein product		114090				8340353, 14685690, 15820218	Standard	NM_173060		Approved		uc003klx.3	P20810	OTTHUMG00000128413	ENST00000341926.3:c.75dupA	chr5.hg19:g.96062551_96062551dupA	ENSP00000339914:p.Lys24fs	157.0	0.0		75.0	40.0	NM_001190442	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Frame_Shift_Ins	INS	ENST00000341926.3	hg19																																																																																				.	.		0.396	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062	
APC	324	hgsc.bcm.edu	37	5	112175951	112175952	+	Frame_Shift_Ins	INS	-	-	A	rs587783031		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr5:112175951_112175952insA	ENST00000457016.1	+	16	5040_5041	c.4660_4661insA	c.(4660-4662)gaafs	p.E1554fs	APC_ENST00000257430.4_Frame_Shift_Ins_p.E1554fs|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Frame_Shift_Ins_p.E1554fs			P25054	APC_HUMAN	adenomatous polyposis coli	1554	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.T1556fs*3(42)|p.E1554fs*5(2)|p.E1554fs*3(1)|p.?(1)|p.T1556fs*9(1)|p.?fs(1)|p.K1192fs*3(1)|p.E1554*(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAAAGAGGCAGAAAAAACTATT	0.342		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.E1554fs	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-INDEL	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,colon,carcinoma,-1,58	APC	4158	.	50	Insertion - Frameshift(45)|Deletion - Frameshift(3)|Substitution - Nonsense(1)|Unknown(1)	large_intestine(45)|stomach(3)|soft_tissue(1)|skin(1)	c.4660_4661insA						.																																			SO:0001589	frameshift_variant	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	.	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4666dupA	chr5.hg19:g.112175957_112175957dupA	ENSP00000413133:p.Glu1554fs	269.0	0.0		155.0	62.0	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Ins	INS	ENST00000457016.1	hg19	CCDS4107.1																																																																																			.	.		0.342	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
OTOF	9381	hgsc.bcm.edu	37	2	26693553	26693554	+	In_Frame_Ins	INS	-	-	CTT	rs368148603		TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr2:26693553_26693554insCTT	ENST00000272371.2	-	32	4056_4057	c.3930_3931insAAG	c.(3928-3933)aagggc>aagAAGggc	p.1310_1311insK	OTOF_ENST00000339598.3_In_Frame_Ins_p.543_544insK|OTOF_ENST00000402415.3_In_Frame_Ins_p.620_621insK|OTOF_ENST00000338581.6_In_Frame_Ins_p.543_544insK|OTOF_ENST00000403946.3_In_Frame_Ins_p.1310_1311insK	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1310	Poly-Lys.				membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCGCAGTGCCcttcttcttct	0.579																																					p.G1311delinsKG	GBM(102;732 1451 20652 24062 31372)	Atlas-INDEL	.											.	OTOF	524	.	0			c.3931_3932insAAG						.																																			SO:0001652	inframe_insertion	9381	exon32			.	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.3928_3930dupAAG	chr2.hg19:g.26693560_26693562dupCTT	ENSP00000272371:p.Lys1310_Lys1310dup	50.0	0.0		47.0	14.0	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	In_Frame_Ins	INS	ENST00000272371.2	hg19	CCDS1725.1																																																																																			.	.		0.579	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
ATR	545	hgsc.bcm.edu	37	3	142188996	142188997	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DD-AADC-01A-11D-A40R-10	TCGA-DD-AADC-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bce9063-4ae3-4e6b-864c-dcc9f551beb5	64941a85-6c7d-475d-b59f-9457c23db2ee	g.chr3:142188996_142188997insA	ENST00000350721.4	-	37	6371_6372	c.6250_6251insT	c.(6250-6252)tatfs	p.Y2084fs	ATR_ENST00000383101.3_Frame_Shift_Ins_p.Y2020fs|RP11-383G6.3_ENST00000460977.1_RNA	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2084	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CATTGACTGATATATGAACTGA	0.302								Other conserved DNA damage response genes																													p.Y2084fs		Atlas-INDEL	.											.	ATR	285	.	0			c.6251_6252insT						.																																			SO:0001589	frameshift_variant	545	exon37			.	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.6251dupT	chr3.hg19:g.142188997_142188997dupA	ENSP00000343741:p.Tyr2084fs	89.0	0.0		109.0	31.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Frame_Shift_Ins	INS	ENST00000350721.4	hg19	CCDS3124.1																																																																																			.	.		0.302	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
