#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
Unknown	0	hgsc.bcm.edu	37	1	13183341	13183341	+	IGR	SNP	C	C	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:13183341C>T								RP13-221M14.3 (18873 upstream) : PRAMEF26 (33014 downstream)																							TGAAGGTCATCTCCTTTCAGC	0.453																																					p.D178N		Atlas-SNP	.											.	.	.	.	0			c.G532A						.						96.0	67.0	76.0					1																	13183341		692	1591	2283	SO:0001628	intergenic_variant	0	exon2			GGTCATCTCCTTT																													chr1.hg19:g.13183341C>T		130.0	0.0		170.0	21.0	NM_001136561		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.453								
IPP	3652	hgsc.bcm.edu	37	1	46184955	46184955	+	Missense_Mutation	SNP	T	T	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:46184955T>G	ENST00000396478.3	-	6	1208	c.1106A>C	c.(1105-1107)cAg>cCg	p.Q369P		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	369						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					AGTTGTCCACTGTTTAGTAAC	0.363																																					p.Q369P		Atlas-SNP	.											.	IPP	66	.	0			c.A1106C						.						127.0	106.0	113.0					1																	46184955		2203	4300	6503	SO:0001583	missense	3652	exon6			GTCCACTGTTTAG	BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"""Kelch-like"", ""BTB/POZ domain containing"""	6108	protein-coding gene	gene with protein product	"""kelch-like family member 27"""	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.1106A>C	chr1.hg19:g.46184955T>G	ENSP00000379739:p.Gln369Pro	68.0	0.0		72.0	43.0	NM_001145349	A2A6V4|D3DQ11|Q8N5C3	Missense_Mutation	SNP	ENST00000396478.3	hg19	CCDS30702.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.061563	0.76187	.	.	ENSG00000197429	ENST00000359942;ENST00000396478	T;T	0.79141	-1.24;-1.24	5.84	5.84	0.93424	Galactose oxidase, beta-propeller (1);	0.107275	0.64402	D	0.000004	D	0.87051	0.6081	M	0.83953	2.67	0.80722	D	1	P;D	0.61080	0.832;0.989	P;P	0.58172	0.699;0.834	D	0.88807	0.3289	10	0.66056	D	0.02	.	16.216	0.82217	0.0:0.0:0.0:1.0	.	369;369	Q9Y573;A2A6V3	IPP_HUMAN;.	P	369	ENSP00000353024:Q369P;ENSP00000379739:Q369P	ENSP00000353024:Q369P	Q	-	2	0	IPP	45957542	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.597000	0.82733	2.228000	0.72767	0.482000	0.46254	CAG	.	.		0.363	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897	
LRRC7	57554	hgsc.bcm.edu	37	1	70505455	70505455	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:70505455A>G	ENST00000035383.5	+	19	3864	c.3834A>G	c.(3832-3834)atA>atG	p.I1278M	LRRC7_ENST00000415775.2_Missense_Mutation_p.I562M|LRRC7_ENST00000310961.5_Missense_Mutation_p.I1283M	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1278						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						TTAGACATATAGAAGCTAGAC	0.443																																					p.I1278M		Atlas-SNP	.											.	LRRC7	400	.	0			c.A3834G						.						92.0	91.0	91.0					1																	70505455		2203	4300	6503	SO:0001583	missense	57554	exon19			ACATATAGAAGCT		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.3834A>G	chr1.hg19:g.70505455A>G	ENSP00000035383:p.Ile1278Met	65.0	0.0		66.0	14.0	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	hg19	CCDS645.1	.	.	.	.	.	.	.	.	.	.	A	16.83	3.230527	0.58777	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.63255	0.17;-0.03;1.15	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.62036	0.2395	N	0.24115	0.695	0.49389	D	0.99978	D;D;D	0.89917	1.0;1.0;0.996	D;D;P	0.85130	0.991;0.997;0.823	T	0.69427	-0.5148	10	0.72032	D	0.01	.	15.9872	0.80168	1.0:0.0:0.0:0.0	.	562;1278;1278	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	M	1283;1278;562;1101	ENSP00000309245:I1283M;ENSP00000035383:I1278M;ENSP00000394867:I562M	ENSP00000035383:I1278M	I	+	3	3	LRRC7	70278043	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.530000	0.60595	2.367000	0.80283	0.528000	0.53228	ATA	.	.		0.443	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794	
SLC44A5	204962	hgsc.bcm.edu	37	1	75716965	75716965	+	Nonsense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:75716965A>T	ENST00000370855.5	-	7	388	c.275T>A	c.(274-276)tTg>tAg	p.L92*	SLC44A5_ENST00000469525.1_5'UTR|SLC44A5_ENST00000370859.3_Nonsense_Mutation_p.L92*|SLC44A5_ENST00000535611.1_5'UTR	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	92					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						AAAGTAAAACAAAATGGTCTT	0.398																																					p.L92X		Atlas-SNP	.											.	SLC44A5	231	.	0			c.T275A						.						106.0	94.0	98.0					1																	75716965		2203	4300	6503	SO:0001587	stop_gained	204962	exon7			TAAAACAAAATGG	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"""Solute carriers"""	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.275T>A	chr1.hg19:g.75716965A>T	ENSP00000359892:p.Leu92*	65.0	0.0		78.0	24.0	NM_001130058	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Nonsense_Mutation	SNP	ENST00000370855.5	hg19	CCDS667.1	.	.	.	.	.	.	.	.	.	.	A	34	5.322037	0.95708	.	.	ENSG00000137968	ENST00000370859;ENST00000536707;ENST00000370855;ENST00000535790	.	.	.	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.2814	13.9805	0.64301	1.0:0.0:0.0:0.0	.	.	.	.	X	92;131;92;85	.	ENSP00000359892:L92X	L	-	2	0	SLC44A5	75489553	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	6.972000	0.76110	2.094000	0.63399	0.528000	0.53228	TTG	.	.		0.398	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697	
CLCA2	9635	hgsc.bcm.edu	37	1	86919189	86919189	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:86919189C>A	ENST00000370565.4	+	13	2455	c.2293C>A	c.(2293-2295)Cca>Aca	p.P765T	CLCA2_ENST00000498802.1_3'UTR	NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	765					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TGATGTGTTTCCACCATGCAA	0.517																																					p.P765T	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.C2293A						.						89.0	91.0	90.0					1																	86919189		2203	4300	6503	SO:0001583	missense	9635	exon13			GTGTTTCCACCAT		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2293C>A	chr1.hg19:g.86919189C>A	ENSP00000359596:p.Pro765Thr	40.0	0.0		65.0	29.0	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	hg19	CCDS708.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.022242	0.75275	.	.	ENSG00000137975	ENST00000370565	T	0.07444	3.19	5.76	5.76	0.90799	.	0.209202	0.40385	N	0.001105	T	0.18923	0.0454	M	0.86028	2.79	0.37261	D	0.906973	D	0.59767	0.986	P	0.55785	0.784	T	0.00829	-1.1549	10	0.87932	D	0	-10.101	14.7385	0.69434	0.1448:0.8552:0.0:0.0	.	765	Q9UQC9	CLCA2_HUMAN	T	765	ENSP00000359596:P765T	ENSP00000359596:P765T	P	+	1	0	CLCA2	86691777	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.533000	0.53561	2.871000	0.98454	0.655000	0.94253	CCA	.	.		0.517	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
VAV3	10451	hgsc.bcm.edu	37	1	108152569	108152569	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:108152569A>T	ENST00000370056.4	-	22	2273	c.1999T>A	c.(1999-2001)Tat>Aat	p.Y667N	VAV3_ENST00000527011.1_Missense_Mutation_p.Y667N|VAV3_ENST00000415432.2_Missense_Mutation_p.Y107N|VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000544443.1_Missense_Mutation_p.Y71N	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	667	Sufficient for interaction with ROS1.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TGGCAAGAATAATCTACTGGT	0.363																																					p.Y667N		Atlas-SNP	.											.	VAV3	176	.	0			c.T1999A						.						99.0	95.0	96.0					1																	108152569		2203	4300	6503	SO:0001583	missense	10451	exon22			AAGAATAATCTAC	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12659	protein-coding gene	gene with protein product		605541	"""vav 3 oncogene"""				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.1999T>A	chr1.hg19:g.108152569A>T	ENSP00000359073:p.Tyr667Asn	93.0	0.0		114.0	43.0	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	hg19	CCDS785.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.035887	0.75617	.	.	ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000544443;ENST00000415432	T;D;T;T	0.92545	1.77;-3.06;1.77;1.77	5.14	5.14	0.70334	SH2 motif (1);	0.116765	0.64402	D	0.000012	D	0.95014	0.8386	M	0.80616	2.505	0.80722	D	1	D;D;D;D	0.89917	0.998;0.999;0.984;1.0	D;D;D;D	0.87578	0.991;0.988;0.95;0.998	D	0.94910	0.8064	10	0.48119	T	0.1	.	13.8104	0.63260	1.0:0.0:0.0:0.0	.	667;71;667;107	E9PQ97;B7Z3Z5;Q9UKW4;Q9UKW4-3	.;.;VAV3_HUMAN;.	N	667;667;71;107	ENSP00000359073:Y667N;ENSP00000432540:Y667N;ENSP00000446404:Y71N;ENSP00000394897:Y107N	ENSP00000359073:Y667N	Y	-	1	0	VAV3	107954092	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.368000	0.79567	2.074000	0.62210	0.477000	0.44152	TAT	.	.		0.363	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	
LRIG2	9860	hgsc.bcm.edu	37	1	113657138	113657138	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:113657138G>A	ENST00000361127.5	+	15	2368	c.2170G>A	c.(2170-2172)Gcc>Acc	p.A724T	LRIG2_ENST00000492207.1_3'UTR	NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	724	Ig-like C2-type 3.				innervation (GO:0060384)|regulation of platelet-derived growth factor receptor signaling pathway (GO:0010640)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(10)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	31	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		AGGGAGTCCTGCCCCTCGTCT	0.493																																					p.A724T		Atlas-SNP	.											.	LRIG2	67	.	0			c.G2170A						.						99.0	91.0	94.0					1																	113657138		2203	4300	6503	SO:0001583	missense	9860	exon15			AGTCCTGCCCCTC	AB018349	CCDS30808.1	1p13.1	2013-01-11			ENSG00000198799	ENSG00000198799		"""Immunoglobulin superfamily / I-set domain containing"""	20889	protein-coding gene	gene with protein product		608869					Standard	XM_005271369		Approved	KIAA0806	uc001edf.1	O94898	OTTHUMG00000012133	ENST00000361127.5:c.2170G>A	chr1.hg19:g.113657138G>A	ENSP00000355396:p.Ala724Thr	57.0	0.0		69.0	21.0	NM_014813	Q9NSN2	Missense_Mutation	SNP	ENST00000361127.5	hg19	CCDS30808.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.505537	0.44558	.	.	ENSG00000198799	ENST00000361127	T	0.66099	-0.19	5.3	2.34	0.29019	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.173530	0.50627	D	0.000110	T	0.20333	0.0489	N	0.11341	0.13	0.42584	D	0.993225	B	0.09022	0.002	B	0.16722	0.016	T	0.04255	-1.0965	10	0.27785	T	0.31	.	8.1469	0.31117	0.1378:0.0:0.7352:0.127	.	724	O94898	LRIG2_HUMAN	T	724	ENSP00000355396:A724T	ENSP00000355396:A724T	A	+	1	0	LRIG2	113458661	0.997000	0.39634	0.962000	0.40283	0.950000	0.60333	2.272000	0.43373	0.593000	0.29745	0.561000	0.74099	GCC	.	.		0.493	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813	
RPTN	126638	hgsc.bcm.edu	37	1	152128332	152128332	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:152128332A>T	ENST00000316073.3	-	3	1307	c.1243T>A	c.(1243-1245)Tac>Aac	p.Y415N		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	415	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						ATCTGACTGTAGTGGGAACTC	0.517																																					p.Y415N		Atlas-SNP	.											.	RPTN	123	.	0			c.T1243A						.						784.0	679.0	711.0					1																	152128332		1568	3582	5150	SO:0001583	missense	126638	exon3			GACTGTAGTGGGA	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.1243T>A	chr1.hg19:g.152128332A>T	ENSP00000317895:p.Tyr415Asn	106.0	0.0		172.0	88.0	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	hg19	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	a	14.18	2.458554	0.43634	.	.	ENSG00000215853	ENST00000316073;ENST00000541545	T	0.11930	2.73	4.65	0.906	0.19314	.	.	.	.	.	T	0.03915	0.0110	M	0.78916	2.43	0.09310	N	1	P	0.50617	0.937	B	0.33392	0.163	T	0.37663	-0.9696	9	0.28530	T	0.3	.	4.3063	0.10949	0.4809:0.3424:0.1768:0.0	.	415	Q6XPR3	RPTN_HUMAN	N	415;70	ENSP00000317895:Y415N	ENSP00000317895:Y415N	Y	-	1	0	RPTN	150394956	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.330000	0.07925	-0.105000	0.12132	0.323000	0.21402	TAC	.	.		0.517	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
ACKR1	2532	hgsc.bcm.edu	37	1	159175433	159175433	+	Silent	SNP	C	C	T	rs375137235		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:159175433C>T	ENST00000368122.2	+	2	883	c.204C>T	c.(202-204)acC>acT	p.T68T	DARC_ENST00000537147.1_Silent_p.T68T|DARC_ENST00000368121.2_Silent_p.T70T|CTA-134P22.2_ENST00000609696.1_RNA	NM_002036.3	NP_002027.2	Q16570	ACKR1_HUMAN		68					chemokine-mediated signaling pathway (GO:0070098)|defense response (GO:0006952)|inflammatory response (GO:0006954)|regulation of chemokine production (GO:0032642)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-C chemokine binding (GO:0019957)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(2)|lung(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	8	all_hematologic(112;0.0429)					TCATCCTCACCAGTGTCCTGG	0.587																																					p.T70T		Atlas-SNP	.											.	DARC	76	.	0			c.C210T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	133.0	119.0	124.0		210,204	4.8	0.4	1		124	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DARC	NM_001122951.2,NM_002036.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	70/339,68/337	159175433	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2532	exon1			CCTCACCAGTGTC																												ENST00000368122.2:c.204C>T	chr1.hg19:g.159175433C>T		70.0	0.0		64.0	28.0	NM_001122951	A8YPG5|O75898|Q16300|Q8WWE3|Q9UJP0|Q9UKZ5|Q9UKZ6|Q9UQE1	Silent	SNP	ENST00000368122.2	hg19	CCDS1183.1																																																																																			.	.		0.587	DARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090338.2		
DUSP12	11266	hgsc.bcm.edu	37	1	161723027	161723027	+	Silent	SNP	T	T	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:161723027T>G	ENST00000367943.4	+	5	869	c.837T>G	c.(835-837)gcT>gcG	p.A279A		NM_007240.1	NP_009171.1	Q9UNI6	DUS12_HUMAN	dual specificity phosphatase 12	279					cellular protein modification process (GO:0006464)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of glucokinase activity (GO:0033133)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|lung(1)	5	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			TGGAATCTGCTTTGTTGGGAG	0.368																																					p.A279A		Atlas-SNP	.											.	DUSP12	20	.	0			c.T837G						.						247.0	204.0	219.0					1																	161723027		2203	4300	6503	SO:0001819	synonymous_variant	11266	exon5			ATCTGCTTTGTTG	AF119226	CCDS1234.1	1q21-q22	2011-06-09			ENSG00000081721	ENSG00000081721		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	3067	protein-coding gene	gene with protein product	"""serine/threonine specific protein phosphatase"", ""YVH1 protein-tyrosine phosphatase (S. cerevisiae) ortholog"""	604835				10446167	Standard	XM_005244862		Approved	YVH1, DUSP1	uc001gbo.3	Q9UNI6	OTTHUMG00000034540	ENST00000367943.4:c.837T>G	chr1.hg19:g.161723027T>G		88.0	0.0		94.0	35.0	NM_007240	Q5VXA8	Silent	SNP	ENST00000367943.4	hg19	CCDS1234.1																																																																																			.	.		0.368	DUSP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083588.1	NM_007240	
RGS4	5999	hgsc.bcm.edu	37	1	163043349	163043349	+	Silent	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:163043349T>A	ENST00000367909.6	+	4	655	c.315T>A	c.(313-315)tcT>tcA	p.S105S	RGS4_ENST00000491263.1_3'UTR|RGS4_ENST00000527809.1_Silent_p.S87S|RGS4_ENST00000367906.3_Silent_p.S87S|RGS4_ENST00000367908.4_Intron|RGS4_ENST00000531057.1_Silent_p.S105S|RGS4_ENST00000421743.2_Silent_p.S202S	NM_001113380.1|NM_005613.5	NP_001106851.1|NP_005604.1	P49798	RGS4_HUMAN	regulator of G-protein signaling 4	105	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				inactivation of MAPK activity (GO:0000188)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)	21						AATCACCATCTAAACTAAGTC	0.368																																					p.S202S	Ovarian(76;1257 1738 3039 6086)	Atlas-SNP	.											.	RGS4	97	.	0			c.T606A						.						103.0	95.0	98.0					1																	163043349		2203	4300	6503	SO:0001819	synonymous_variant	5999	exon5			ACCATCTAAACTA	BC051869	CCDS1243.1, CCDS44270.1, CCDS44271.1, CCDS44272.1	1q23.3	2008-05-14	2007-08-14		ENSG00000117152	ENSG00000117152		"""Regulators of G-protein signaling"""	10000	protein-coding gene	gene with protein product		602516	"""regulator of G-protein signalling 4"", ""schizophrenia disorder 9"""	SCZD9		8602223, 8756726	Standard	NM_001102445		Approved		uc001gcl.4	P49798	OTTHUMG00000034417	ENST00000367909.6:c.315T>A	chr1.hg19:g.163043349T>A		242.0	0.0		259.0	101.0	NM_001102445	A7XA56|A7XA58|A7XA59|A7YVV7|B1APZ3	Silent	SNP	ENST00000367909.6	hg19	CCDS1243.1																																																																																			.	.		0.368	RGS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083197.2	NM_005613	
ASTN1	460	hgsc.bcm.edu	37	1	176838062	176838062	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:176838062G>A	ENST00000367654.3	-	22	3800	c.3589C>T	c.(3589-3591)Cac>Tac	p.H1197Y	ASTN1_ENST00000367657.3_Missense_Mutation_p.H1189Y|ASTN1_ENST00000424564.2_Missense_Mutation_p.H1189Y|ASTN1_ENST00000361833.2_Missense_Mutation_p.H1189Y	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	1197					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						AGGACCCGGTGTAAGGTGGGG	0.488																																					p.H1189Y		Atlas-SNP	.											.	ASTN1	314	.	0			c.C3565T						.						157.0	147.0	151.0					1																	176838062		2203	4300	6503	SO:0001583	missense	460	exon22			CCCGGTGTAAGGT	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.3589C>T	chr1.hg19:g.176838062G>A	ENSP00000356626:p.His1197Tyr	174.0	0.0		204.0	68.0	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	hg19		.	.	.	.	.	.	.	.	.	.	G	14.25	2.480535	0.44044	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.11495	2.77;3.18;3.18;2.77	5.7	5.7	0.88788	.	0.042709	0.85682	D	0.000000	T	0.11367	0.0277	L	0.27053	0.805	0.80722	D	1	B;B	0.34103	0.437;0.232	B;B	0.40375	0.327;0.248	T	0.09400	-1.0676	10	0.07644	T	0.81	-17.1324	19.4429	0.94831	0.0:0.0:1.0:0.0	.	1189;1189	O14525-2;B1AJS1	.;.	Y	1189;1189;1197;1189;1189	ENSP00000356629:H1189Y;ENSP00000354536:H1189Y;ENSP00000356626:H1197Y;ENSP00000395041:H1189Y	ENSP00000354536:H1189Y	H	-	1	0	ASTN1	175104685	1.000000	0.71417	0.507000	0.27676	0.142000	0.21351	7.782000	0.85680	2.698000	0.92095	0.655000	0.94253	CAC	.	.		0.488	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
TDRD5	163589	hgsc.bcm.edu	37	1	179600021	179600021	+	Silent	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:179600021A>T	ENST00000367614.1	+	7	1451	c.1092A>T	c.(1090-1092)ctA>ctT	p.L364L	TDRD5_ENST00000294848.8_Silent_p.L364L|TDRD5_ENST00000444136.1_Silent_p.L364L	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	364	HTH OST-type 3. {ECO:0000255|PROSITE- ProRule:PRU00975}.				DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						AAGACTTACTAGTGTTTGATG	0.398																																					p.L364L		Atlas-SNP	.											.	TDRD5	149	.	0			c.A1092T						.						137.0	128.0	131.0					1																	179600021		2203	4300	6503	SO:0001819	synonymous_variant	163589	exon7			CTTACTAGTGTTT	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"""Tudor domain containing"""	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.1092A>T	chr1.hg19:g.179600021A>T		275.0	0.0		286.0	104.0	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Silent	SNP	ENST00000367614.1	hg19	CCDS1332.1																																																																																			.	.		0.398	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
KIAA1614	57710	hgsc.bcm.edu	37	1	180904396	180904396	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:180904396C>A	ENST00000367588.4	+	5	1406	c.1351C>A	c.(1351-1353)Cgc>Agc	p.R451S	KIAA1614_ENST00000367587.1_Missense_Mutation_p.R72S	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	451										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						GTCGCACGTGCGCTTTGAGGA	0.701																																					p.R451S		Atlas-SNP	.											.	KIAA1614	75	.	0			c.C1351A						.						9.0	12.0	11.0					1																	180904396		2054	4152	6206	SO:0001583	missense	57710	exon5			CACGTGCGCTTTG	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.1351C>A	chr1.hg19:g.180904396C>A	ENSP00000356560:p.Arg451Ser	39.0	0.0		66.0	26.0	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	hg19	CCDS41442.1	.	.	.	.	.	.	.	.	.	.	c	18.39	3.612668	0.66672	.	.	ENSG00000135835	ENST00000367588;ENST00000367587	T;T	0.63744	0.22;-0.06	4.83	4.83	0.62350	.	0.137394	0.49305	D	0.000150	T	0.76463	0.3991	L	0.61218	1.895	0.28098	N	0.9315370000000001	D	0.89917	1.0	D	0.91635	0.999	T	0.79276	-0.1870	9	0.51188	T	0.08	-22.1444	16.0625	0.80847	0.0:1.0:0.0:0.0	.	451	Q5VZ46	K1614_HUMAN	S	451;72	ENSP00000356560:R451S;ENSP00000356559:R72S	ENSP00000356559:R72S	R	+	1	0	KIAA1614	179171019	0.997000	0.39634	0.748000	0.31131	0.120000	0.20174	3.946000	0.56644	2.383000	0.81215	0.457000	0.33378	CGC	.	.		0.701	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
CACNA1E	777	hgsc.bcm.edu	37	1	181689967	181689967	+	Silent	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:181689967T>A	ENST00000367573.2	+	15	1932	c.1932T>A	c.(1930-1932)ccT>ccA	p.P644P	CACNA1E_ENST00000357570.5_Silent_p.P595P|CACNA1E_ENST00000358338.5_Silent_p.P595P|CACNA1E_ENST00000367567.4_Silent_p.P251P|CACNA1E_ENST00000367570.1_Silent_p.P644P|CACNA1E_ENST00000526775.1_Silent_p.P644P|CACNA1E_ENST00000360108.3_Silent_p.P644P	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	644					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						ATACCTTCCCTGCAGCCATCA	0.428																																					p.P644P		Atlas-SNP	.											.	CACNA1E	778	.	0			c.T1932A						.						69.0	67.0	68.0					1																	181689967		1894	4125	6019	SO:0001819	synonymous_variant	777	exon15			CTTCCCTGCAGCC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.1932T>A	chr1.hg19:g.181689967T>A		27.0	0.0		46.0	13.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	hg19	CCDS55664.1																																																																																			.	.		0.428	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
CACNA1E	777	hgsc.bcm.edu	37	1	181702886	181702886	+	Splice_Site	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:181702886A>T	ENST00000367573.2	+	21	3262	c.3262A>T	c.(3262-3264)Att>Ttt	p.I1088F	CACNA1E_ENST00000357570.5_Splice_Site_p.I1039F|CACNA1E_ENST00000358338.5_Splice_Site_p.I1020F|CACNA1E_ENST00000367567.4_Splice_Site_p.I695F|CACNA1E_ENST00000367570.1_Splice_Site_p.I1088F|CACNA1E_ENST00000526775.1_Splice_Site_p.I1069F|CACNA1E_ENST00000360108.3_Splice_Site_p.I1069F	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1088					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CGTGGTGCACAGTGAGAGCAC	0.622																																					p.I1088F		Atlas-SNP	.											.	CACNA1E	778	.	0			c.A3262T						.						32.0	35.0	34.0					1																	181702886		2136	4221	6357	SO:0001630	splice_region_variant	777	exon21			GTGCACAGTGAGA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.3262+1A>T	chr1.hg19:g.181702886A>T		114.0	0.0		160.0	61.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	A	14.05	2.420767	0.42918	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.96427	-3.95;-3.95;-3.96;-3.95;-4.01;-3.96;-3.96	4.88	4.88	0.63580	.	0.604131	0.19018	N	0.124893	D	0.92325	0.7565	N	0.08118	0	0.49687	D	0.99981	P;P;P	0.50819	0.775;0.939;0.557	B;P;B	0.47299	0.256;0.543;0.221	D	0.93529	0.6868	10	0.66056	D	0.02	.	14.1472	0.65357	1.0:0.0:0.0:0.0	.	1069;1088;1088	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	F	1088;1069;1039;1020;695;1069;1088	ENSP00000356542:I1088F;ENSP00000434814:I1069F;ENSP00000350183:I1039F;ENSP00000351101:I1020F;ENSP00000356539:I695F;ENSP00000353222:I1069F;ENSP00000356545:I1088F	ENSP00000350183:I1039F	I	+	1	0	CACNA1E	179969509	1.000000	0.71417	1.000000	0.80357	0.438000	0.31896	5.000000	0.63940	1.832000	0.53329	0.459000	0.35465	ATT	.	.		0.622	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	Missense_Mutation
LAMC2	3918	hgsc.bcm.edu	37	1	183207463	183207463	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:183207463C>A	ENST00000264144.4	+	19	2841	c.2776C>A	c.(2776-2778)Cgt>Agt	p.R926S	LAMC2_ENST00000493293.1_Missense_Mutation_p.R926S	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	926	Domain II and I.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						GCTGCTTTCCCGTGCCAATCT	0.413																																					p.R926S		Atlas-SNP	.											LAMC2,colon,carcinoma,0,1	LAMC2	113	.	0			c.C2776A						.						132.0	122.0	125.0					1																	183207463		2203	4300	6503	SO:0001583	missense	3918	exon19			CTTTCCCGTGCCA	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.2776C>A	chr1.hg19:g.183207463C>A	ENSP00000264144:p.Arg926Ser	37.0	0.0		84.0	35.0	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	hg19	CCDS1352.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.280939	0.80692	.	.	ENSG00000058085	ENST00000493293;ENST00000537180;ENST00000264144	T;T	0.17854	2.4;2.25	5.19	4.21	0.49690	.	0.000000	0.64402	D	0.000002	T	0.42921	0.1224	M	0.83483	2.645	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.73708	0.956;0.956;0.981	T	0.41698	-0.9494	10	0.62326	D	0.03	.	12.8485	0.57844	0.1627:0.8373:0.0:0.0	.	926;926;926	Q2M1N2;Q13753;Q13753-2	.;LAMC2_HUMAN;.	S	926	ENSP00000432063:R926S;ENSP00000264144:R926S	ENSP00000264144:R926S	R	+	1	0	LAMC2	181474086	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.525000	0.53502	2.558000	0.86282	0.655000	0.94253	CGT	.	.		0.413	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562	
SWT1	54823	hgsc.bcm.edu	37	1	185137519	185137519	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:185137519A>T	ENST00000367500.4	+	4	378	c.213A>T	c.(211-213)caA>caT	p.Q71H	SWT1_ENST00000367501.3_Missense_Mutation_p.Q71H	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	71										breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						AAAGAAGACAAGGACTGAAAA	0.234																																					p.Q71H		Atlas-SNP	.											.	SWT1	88	.	0			c.A213T						.						31.0	37.0	35.0					1																	185137519		2169	4271	6440	SO:0001583	missense	54823	exon4			AAGACAAGGACTG	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 26"""	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.213A>T	chr1.hg19:g.185137519A>T	ENSP00000356470:p.Gln71His	274.0	0.0		357.0	173.0	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	hg19	CCDS1367.1	.	.	.	.	.	.	.	.	.	.	A	2.824	-0.244237	0.05906	.	.	ENSG00000116668	ENST00000367501;ENST00000367500;ENST00000450350	T;T;T	0.46819	2.21;2.21;0.86	4.7	-3.61	0.04556	.	0.717261	0.12541	N	0.459923	T	0.29749	0.0743	L	0.43152	1.355	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.18808	-1.0325	10	0.41790	T	0.15	.	1.8988	0.03263	0.3507:0.1518:0.3588:0.1387	.	71	Q5T5J6	SWT1_HUMAN	H	71	ENSP00000356471:Q71H;ENSP00000356470:Q71H;ENSP00000401413:Q71H	ENSP00000356470:Q71H	Q	+	3	2	SWT1	183404142	0.933000	0.31639	0.023000	0.16930	0.050000	0.14768	0.106000	0.15354	-0.574000	0.05990	0.459000	0.35465	CAA	.	.		0.234	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	
RGS18	64407	hgsc.bcm.edu	37	1	192129516	192129516	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:192129516C>T	ENST00000367460.3	+	3	411	c.230C>T	c.(229-231)cCt>cTt	p.P77L	RGS18_ENST00000481707.1_3'UTR	NM_130782.2	NP_570138.1	Q9NS28	RGS18_HUMAN	regulator of G-protein signaling 18	77					G-protein coupled receptor signaling pathway (GO:0007186)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			kidney(1)|large_intestine(2)|lung(15)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AGAGTCTCCCCTGAAGAGGCA	0.358																																					p.P77L		Atlas-SNP	.											.	RGS18	54	.	0			c.C230T						.						110.0	101.0	104.0					1																	192129516		2203	4300	6503	SO:0001583	missense	64407	exon3			TCTCCCCTGAAGA	AF268036	CCDS1374.1	1q31.2	2008-02-05	2007-08-14		ENSG00000150681	ENSG00000150681		"""Regulators of G-protein signaling"""	14261	protein-coding gene	gene with protein product		607192	"""regulator of G-protein signalling 18"""			11042171	Standard	NM_130782		Approved	RGS13	uc001gsg.3	Q9NS28	OTTHUMG00000035592	ENST00000367460.3:c.230C>T	chr1.hg19:g.192129516C>T	ENSP00000356430:p.Pro77Leu	115.0	0.0		133.0	58.0	NM_130782	B2RD23	Missense_Mutation	SNP	ENST00000367460.3	hg19	CCDS1374.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.477014	0.44044	.	.	ENSG00000150681	ENST00000367460	T	0.62498	0.02	5.91	4.01	0.46588	Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.142711	0.64402	N	0.000004	T	0.53802	0.1819	L	0.52364	1.645	0.80722	D	1	B	0.15930	0.015	B	0.18871	0.023	T	0.46555	-0.9183	10	0.31617	T	0.26	.	10.3565	0.43967	0.1349:0.7942:0.0:0.071	.	77	Q9NS28	RGS18_HUMAN	L	77	ENSP00000356430:P77L	ENSP00000356430:P77L	P	+	2	0	RGS18	190396139	1.000000	0.71417	0.991000	0.47740	0.984000	0.73092	3.383000	0.52471	0.797000	0.33971	0.655000	0.94253	CCT	.	.		0.358	RGS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086382.1	NM_130782	
PLXNA2	5362	hgsc.bcm.edu	37	1	208252776	208252776	+	Silent	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:208252776T>A	ENST00000367033.3	-	12	3172	c.2415A>T	c.(2413-2415)gcA>gcT	p.A805A		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	805			A -> G (in dbSNP:rs17011882).		axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.A805A(1)		NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CCCGCTGGGCTGCACACTTGT	0.587																																					p.A805A		Atlas-SNP	.											PLXNA2,NS,carcinoma,0,1	PLXNA2	178	.	1	Substitution - coding silent(1)	lung(1)	c.A2415T						.						20.0	21.0	21.0					1																	208252776		2202	4300	6502	SO:0001819	synonymous_variant	5362	exon12			CTGGGCTGCACAC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.2415A>T	chr1.hg19:g.208252776T>A		72.0	0.0		85.0	33.0	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	hg19	CCDS31013.1																																																																																			.	.		0.587	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
FAM71A	149647	hgsc.bcm.edu	37	1	212798434	212798434	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:212798434G>C	ENST00000294829.3	+	1	646	c.215G>C	c.(214-216)gGc>gCc	p.G72A	RP11-338C15.5_ENST00000427949.1_RNA	NM_153606.3	NP_705834.2	Q8IYT1	FA71A_HUMAN	family with sequence similarity 71, member A	72						nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(12)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(81;0.00631)|all cancers(67;0.00981)|GBM - Glioblastoma multiforme(131;0.0715)|Epithelial(68;0.094)		GTGACCATGGGCATTGCACGT	0.542																																					p.G72A		Atlas-SNP	.											.	FAM71A	87	.	0			c.G215C						.						149.0	125.0	133.0					1																	212798434		2203	4300	6503	SO:0001583	missense	149647	exon1			CCATGGGCATTGC		CCDS1507.1	1q32.3	2008-02-05			ENSG00000162771	ENSG00000162771			26541	protein-coding gene	gene with protein product						12477932	Standard	NM_153606		Approved	FLJ32796	uc010pth.1	Q8IYT1	OTTHUMG00000041084	ENST00000294829.3:c.215G>C	chr1.hg19:g.212798434G>C	ENSP00000294829:p.Gly72Ala	93.0	0.0		105.0	36.0	NM_153606	Q5VTZ1	Missense_Mutation	SNP	ENST00000294829.3	hg19	CCDS1507.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.527504	0.27299	.	.	ENSG00000162771	ENST00000294829	T	0.12774	2.65	4.41	3.46	0.39613	.	0.182460	0.34245	N	0.004134	T	0.30792	0.0776	M	0.66439	2.03	0.35263	D	0.779787	D	0.61080	0.989	D	0.67548	0.952	T	0.41215	-0.9521	10	0.59425	D	0.04	-31.17	10.2591	0.43416	0.0:0.2011:0.7989:0.0	.	72	Q8IYT1	FA71A_HUMAN	A	72	ENSP00000294829:G72A	ENSP00000294829:G72A	G	+	2	0	FAM71A	210865057	1.000000	0.71417	0.996000	0.52242	0.383000	0.30230	2.912000	0.48782	1.176000	0.42840	0.460000	0.39030	GGC	.	.		0.542	FAM71A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098529.1	NM_153606	
EXOC8	149371	hgsc.bcm.edu	37	1	231471360	231471360	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:231471360G>C	ENST00000360394.2	-	1	2218	c.2132C>G	c.(2131-2133)tCt>tGt	p.S711C	SPRTN_ENST00000391858.4_5'Flank|EXOC8_ENST00000366645.1_Missense_Mutation_p.S707C|SPRTN_ENST00000295050.7_5'Flank|SPRTN_ENST00000008440.9_5'Flank	NM_175876.3	NP_787072.2	Q8IYI6	EXOC8_HUMAN	exocyst complex component 8	711					cellular protein localization (GO:0034613)|cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(2)|endometrium(1)|large_intestine(2)|liver(1)|lung(5)|prostate(1)|skin(1)|stomach(1)	14	Breast(184;0.0871)	all_cancers(173;0.151)|Prostate(94;0.183)				AATAAGTCTAGATGCATTCCT	0.403																																					p.S711C		Atlas-SNP	.											.	EXOC8	42	.	0			c.C2132G						.						155.0	145.0	148.0					1																	231471360		2203	4300	6503	SO:0001583	missense	149371	exon1			AGTCTAGATGCAT	AL117352	CCDS1593.1	1q42.2	2013-01-22			ENSG00000116903	ENSG00000116903			24659	protein-coding gene	gene with protein product		615283				12477932	Standard	NM_175876		Approved	SEC84, EXO84, Exo84p	uc001huq.3	Q8IYI6	OTTHUMG00000038025	ENST00000360394.2:c.2132C>G	chr1.hg19:g.231471360G>C	ENSP00000353564:p.Ser711Cys	145.0	0.0		203.0	72.0	NM_175876	B3KU33|Q5TE82	Missense_Mutation	SNP	ENST00000360394.2	hg19	CCDS1593.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.689005	0.88735	.	.	ENSG00000116903	ENST00000360394;ENST00000366645	T;T	0.78364	-1.17;-1.16	5.43	5.43	0.79202	.	0.062472	0.64402	D	0.000004	T	0.72162	0.3426	N	0.19112	0.55	0.80722	D	1	P	0.50943	0.94	P	0.46975	0.533	T	0.72950	-0.4136	10	0.38643	T	0.18	-15.1838	19.5966	0.95541	0.0:0.0:1.0:0.0	.	711	Q8IYI6	EXOC8_HUMAN	C	711;707	ENSP00000353564:S711C;ENSP00000355605:S707C	ENSP00000353564:S711C	S	-	2	0	EXOC8	229537983	1.000000	0.71417	0.237000	0.24090	0.994000	0.84299	9.378000	0.97191	2.698000	0.92095	0.655000	0.94253	TCT	.	.		0.403	EXOC8-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_175876	
RYR2	6262	hgsc.bcm.edu	37	1	237804197	237804197	+	Splice_Site	SNP	T	T	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:237804197T>G	ENST00000366574.2	+	47	7433	c.7116T>G	c.(7114-7116)ctT>ctG	p.L2372L	RYR2_ENST00000360064.6_Splice_Site_p.L2370L|RYR2_ENST00000542537.1_Splice_Site_p.L2356L	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2372	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTCATGAAAGTGACACAGAGG	0.428																																					p.L2372L		Atlas-SNP	.											.	RYR2	1273	.	0			c.T7116G						.						121.0	115.0	117.0					1																	237804197		2011	4196	6207	SO:0001630	splice_region_variant	6262	exon47			TGAAAGTGACACA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.7116-1T>G	chr1.hg19:g.237804197T>G		26.0	0.0		35.0	6.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.428	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	Silent
PXDN	7837	hgsc.bcm.edu	37	2	1652347	1652347	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:1652347C>A	ENST00000252804.4	-	17	3255	c.3205G>T	c.(3205-3207)Gcc>Tcc	p.A1069S		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1069					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.A1069T(1)		breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		AACCTGAAGGCCGCGGTGGCG	0.597																																					p.A1069S		Atlas-SNP	.											PXDN,NS,carcinoma,0,1	PXDN	255	.	1	Substitution - Missense(1)	kidney(1)	c.G3205T						.						54.0	66.0	62.0					2																	1652347		2189	4280	6469	SO:0001583	missense	7837	exon17			TGAAGGCCGCGGT	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"""Immunoglobulin superfamily / I-set domain containing"""	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.3205G>T	chr2.hg19:g.1652347C>A	ENSP00000252804:p.Ala1069Ser	46.0	0.0		41.0	19.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	hg19	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	C	17.97	3.519345	0.64634	.	.	ENSG00000130508	ENST00000252804	T	0.79940	-1.32	5.72	4.84	0.62591	.	0.000000	0.85682	D	0.000000	D	0.93900	0.8048	H	0.98542	4.26	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.96345	0.9254	10	0.87932	D	0	-37.893	16.2512	0.82489	0.1337:0.8663:0.0:0.0	.	1069	Q92626	PXDN_HUMAN	S	1069	ENSP00000252804:A1069S	ENSP00000252804:A1069S	A	-	1	0	PXDN	1631354	1.000000	0.71417	0.953000	0.39169	0.341000	0.28922	5.896000	0.69822	1.411000	0.46957	0.650000	0.86243	GCC	.	.		0.597	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
PLB1	151056	hgsc.bcm.edu	37	2	28752185	28752185	+	Splice_Site	SNP	C	C	A	rs542670180		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:28752185C>A	ENST00000327757.5	+	7	371	c.327C>A	c.(325-327)gtC>gtA	p.V109V	PLB1_ENST00000422425.2_Splice_Site_p.V109V	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	109	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					TCTCTTTAGTCCTTTCAGACA	0.502																																					p.V109V		Atlas-SNP	.											.	PLB1	255	.	0			c.C327A						.						173.0	151.0	158.0					2																	28752185		2203	4300	6503	SO:0001630	splice_region_variant	151056	exon7			TTTAGTCCTTTCA		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.326-1C>A	chr2.hg19:g.28752185C>A		44.0	0.0		44.0	18.0	NM_001170585	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	hg19	CCDS33168.1	.	.	.	.	.	.	.	.	.	.	C	9.578	1.122947	0.20959	.	.	ENSG00000163803	ENST00000404858	.	.	.	5.49	2.26	0.28386	.	.	.	.	.	T	0.53514	0.1801	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44832	-0.9302	4	.	.	.	.	5.7636	0.18213	0.0:0.6184:0.0:0.3816	.	.	.	.	Y	108	.	.	S	+	2	0	PLB1	28605689	0.995000	0.38212	0.998000	0.56505	0.566000	0.35808	0.403000	0.20982	0.668000	0.31126	0.655000	0.94253	TCC	.	.		0.502	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		Silent
FAM179A	165186	hgsc.bcm.edu	37	2	29226440	29226440	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:29226440C>T	ENST00000379558.4	+	6	1073	c.722C>T	c.(721-723)cCa>cTa	p.P241L	FAM179A_ENST00000403861.2_Missense_Mutation_p.P241L	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	241										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CCACCCATCCCAAAGGCCAGG	0.647																																					p.P241L		Atlas-SNP	.											.	FAM179A	106	.	0			c.C722T						.						37.0	43.0	41.0					2																	29226440		2051	4171	6222	SO:0001583	missense	165186	exon6			CCATCCCAAAGGC	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.722C>T	chr2.hg19:g.29226440C>T	ENSP00000368876:p.Pro241Leu	118.0	0.0		178.0	14.0	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	hg19	CCDS1769.2	.	.	.	.	.	.	.	.	.	.	C	3.463	-0.109477	0.06924	.	.	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.14766	2.98;2.48	5.16	0.17	0.15021	.	.	.	.	.	T	0.07458	0.0188	N	0.19112	0.55	0.09310	N	1	B;B	0.29301	0.241;0.041	B;B	0.29598	0.104;0.028	T	0.38067	-0.9678	9	0.32370	T	0.25	.	4.2617	0.10744	0.1483:0.5091:0.0:0.3426	.	241;241	F8W8E4;Q6ZUX3	.;F179A_HUMAN	L	241	ENSP00000368876:P241L;ENSP00000384699:P241L	ENSP00000368876:P241L	P	+	2	0	FAM179A	29079944	0.009000	0.17119	0.004000	0.12327	0.003000	0.03518	0.234000	0.17930	-0.030000	0.13804	-0.424000	0.05967	CCA	.	.		0.647	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
EML4	27436	hgsc.bcm.edu	37	2	42530527	42530527	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:42530527A>T	ENST00000318522.5	+	16	2102	c.1840A>T	c.(1840-1842)Agg>Tgg	p.R614W	EML4_ENST00000401738.3_Missense_Mutation_p.R625W|EML4_ENST00000453191.2_De_novo_Start_OutOfFrame|EML4_ENST00000402711.2_Missense_Mutation_p.R556W	NM_019063.3	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	614					microtubule-based process (GO:0007017)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|mitotic spindle (GO:0072686)			EML4/ALK(543)	NS(2)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	12						TGCTCAGGACAGGCAGGTGTG	0.468			T	ALK	NSCLC																																p.R614W		Atlas-SNP	.		Dom	yes		2	2p21	27436	echinoderm microtubule associated protein like 4		E	.	EML4	92	.	0			c.A1840T						.						131.0	121.0	124.0					2																	42530527		2203	4300	6503	SO:0001583	missense	27436	exon16			CAGGACAGGCAGG	AF177377	CCDS1807.1, CCDS46266.1	2p21	2013-01-10		2002-02-15	ENSG00000143924	ENSG00000143924		"""WD repeat domain containing"""	1316	protein-coding gene	gene with protein product		607442		C2orf2			Standard	NM_019063		Approved	ROPP120, ELP120	uc002rsi.3	Q9HC35	OTTHUMG00000128603	ENST00000318522.5:c.1840A>T	chr2.hg19:g.42530527A>T	ENSP00000320663:p.Arg614Trp	125.0	0.0		143.0	62.0	NM_019063	A6H8Y6|B2RBK3|B2RTW7|B5MCW9|Q3SWW0|Q53R29|Q53TW8|Q6PJ45|Q9NV40	Missense_Mutation	SNP	ENST00000318522.5	hg19	CCDS1807.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.072079	0.76415	.	.	ENSG00000143924	ENST00000318522;ENST00000402711;ENST00000401738	T;T;T	0.61742	0.08;0.08;0.08	5.01	3.83	0.44106	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.083457	0.85682	D	0.000000	T	0.79275	0.4418	M	0.93062	3.375	0.80722	D	1	D;D;D	0.76494	0.992;0.999;0.996	D;D;D	0.72625	0.949;0.978;0.97	T	0.82497	-0.0428	10	0.72032	D	0.01	-12.6355	11.2629	0.49093	0.8467:0.1533:0.0:0.0	.	556;625;614	B5MCW9;B5MBZ0;Q9HC35	.;.;EMAL4_HUMAN	W	614;556;625	ENSP00000320663:R614W;ENSP00000385059:R556W;ENSP00000384939:R625W	ENSP00000320663:R614W	R	+	1	2	EML4	42384031	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.387000	0.52501	0.905000	0.36596	0.528000	0.53228	AGG	.	.		0.468	EML4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250463.3	NM_019063	
USP34	9736	hgsc.bcm.edu	37	2	61520656	61520656	+	Silent	SNP	T	T	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:61520656T>C	ENST00000398571.2	-	33	4567	c.4491A>G	c.(4489-4491)ttA>ttG	p.L1497L		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1497					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			AAATTTCTAATAACTGTTGAA	0.348																																					p.L1497L		Atlas-SNP	.											.	USP34	334	.	0			c.A4491G						.						84.0	76.0	79.0					2																	61520656		1814	4075	5889	SO:0001819	synonymous_variant	9736	exon33			TTCTAATAACTGT	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.4491A>G	chr2.hg19:g.61520656T>C		177.0	0.0		235.0	50.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	hg19	CCDS42686.1																																																																																			.	.		0.348	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
ARHGAP25	9938	hgsc.bcm.edu	37	2	69034418	69034418	+	Silent	SNP	G	G	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:69034418G>A	ENST00000295381.3	+	5	896	c.477G>A	c.(475-477)caG>caA	p.Q159Q	ARHGAP25_ENST00000497079.1_Silent_p.Q153Q|ARHGAP25_ENST00000544262.1_Silent_p.Q134Q|ARHGAP25_ENST00000409030.3_Silent_p.Q152Q|ARHGAP25_ENST00000409220.1_Silent_p.Q153Q|ARHGAP25_ENST00000456116.2_3'UTR|ARHGAP25_ENST00000467265.1_Silent_p.Q120Q|ARHGAP25_ENST00000409202.3_Silent_p.Q160Q	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	159	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						TGTTTGGCCAGCGCTTGGATG	0.527																																					p.Q160Q		Atlas-SNP	.											.	ARHGAP25	175	.	0			c.G480A						.						90.0	84.0	86.0					2																	69034418		2203	4300	6503	SO:0001819	synonymous_variant	9938	exon5			TGGCCAGCGCTTG	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.477G>A	chr2.hg19:g.69034418G>A		196.0	0.0		186.0	72.0	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Silent	SNP	ENST00000295381.3	hg19		.	.	.	.	.	.	.	.	.	.	G	9.044	0.990388	0.18966	.	.	ENSG00000163219	ENST00000497259	.	.	.	4.88	4.01	0.46588	.	.	.	.	.	T	0.64649	0.2617	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66972	-0.5788	5	0.87932	D	0	.	8.3561	0.32331	0.2439:0.0:0.7561:0.0	.	.	.	.	N	19	.	ENSP00000420427:S92N	S	+	2	0	ARHGAP25	68887922	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	3.082000	0.50128	1.301000	0.44836	-0.234000	0.12200	AGC	.	.		0.527	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	
ZNF638	27332	hgsc.bcm.edu	37	2	71650150	71650150	+	Missense_Mutation	SNP	C	C	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:71650150C>G	ENST00000409544.1	+	22	4136	c.3506C>G	c.(3505-3507)aCt>aGt	p.T1169S	ZNF638_ENST00000264447.4_Missense_Mutation_p.T1169S|ZNF638_ENST00000355812.3_Intron|ZNF638_ENST00000409407.1_Missense_Mutation_p.T109S	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1169	Glu-rich.				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						GAGCTTGAAACTCAAGGAGAG	0.418																																					p.T1169S		Atlas-SNP	.											.	ZNF638	179	.	0			c.C3506G						.						95.0	94.0	94.0					2																	71650150		2203	4300	6503	SO:0001583	missense	27332	exon22			TTGAAACTCAAGG	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.3506C>G	chr2.hg19:g.71650150C>G	ENSP00000386433:p.Thr1169Ser	102.0	0.0		133.0	45.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	hg19	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	C	1.044	-0.677871	0.03378	.	.	ENSG00000075292	ENST00000394137;ENST00000264447;ENST00000409544;ENST00000409407;ENST00000462695	T;T;T	0.28895	1.59;1.59;1.92	5.69	2.66	0.31614	.	0.584093	0.16588	N	0.207891	T	0.16128	0.0388	L	0.27053	0.805	0.43673	D	0.996101	B;B;B	0.22346	0.068;0.017;0.01	B;B;B	0.15484	0.006;0.013;0.006	T	0.06058	-1.0848	10	0.12430	T	0.62	-3.8445	5.5923	0.17307	0.3903:0.5178:0.0:0.092	.	1169;1169;1169	A8K583;Q14966-3;Q14966	.;.;ZN638_HUMAN	S	748;1169;1169;109;109	ENSP00000264447:T1169S;ENSP00000386433:T1169S;ENSP00000386813:T109S	ENSP00000264447:T1169S	T	+	2	0	ZNF638	71503658	0.007000	0.16637	0.998000	0.56505	0.127000	0.20565	0.361000	0.20267	1.469000	0.48083	0.655000	0.94253	ACT	.	.		0.418	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
DNAH6	1768	hgsc.bcm.edu	37	2	84880551	84880551	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:84880551G>C	ENST00000237449.6	+	33	5195	c.5187G>C	c.(5185-5187)gaG>gaC	p.E1729D	DNAH6_ENST00000389394.3_Missense_Mutation_p.E1729D|DNAH6_ENST00000398278.2_Missense_Mutation_p.E1729D			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1729	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTCAGCCTGAGATGTGTATGG	0.393																																					p.E1729D		Atlas-SNP	.											.	DNAH6	194	.	0			c.G5187C						.						56.0	49.0	51.0					2																	84880551		692	1591	2283	SO:0001583	missense	1768	exon34			GCCTGAGATGTGT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.5187G>C	chr2.hg19:g.84880551G>C	ENSP00000237449:p.Glu1729Asp	84.0	0.0		95.0	38.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.594698	0.28445	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.40476	1.03;1.03;1.03	5.03	2.2	0.27929	.	.	.	.	.	T	0.31231	0.0790	L	0.39467	1.215	0.20926	N	0.999824	P	0.37955	0.612	B	0.33846	0.171	T	0.08493	-1.0719	9	0.44086	T	0.13	.	9.6334	0.39793	0.2407:0.0:0.7593:0.0	.	1729	Q9C0G6	DYH6_HUMAN	D	1729	ENSP00000374045:E1729D;ENSP00000381326:E1729D;ENSP00000237449:E1729D	ENSP00000237449:E1729D	E	+	3	2	DNAH6	84734062	0.186000	0.23225	0.592000	0.28758	0.991000	0.79684	0.314000	0.19432	0.526000	0.28541	0.544000	0.68410	GAG	.	.		0.393	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
GLI2	2736	hgsc.bcm.edu	37	2	121728098	121728099	+	Missense_Mutation	DNP	CC	CC	AA			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:121728098_121728099CC>AA	ENST00000452319.1	+	7	1035_1036	c.975_976CC>AA	c.(973-978)gcCCag>gcAAag	p.Q326K	GLI2_ENST00000361492.4_Missense_Mutation_p.Q326K|GLI2_ENST00000314490.11_5'UTR|GLI2_ENST00000435313.2_3'UTR					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				CCTTCCTGGCCCAGCAGCCCAT	0.639																																					p.A325A|p.Q326K		Atlas-SNP	.											.	GLI2	187	.	0			c.C975A|c.C976A						.																																			SO:0001583	missense	2736	exon6			CCTGGCCCAGCAG|CTGGCCCAGCAGC		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	Exception_encountered	chr2.hg19:g.121728098_121728099delinsAA	ENSP00000390436:p.Gln326Lys	98.0|95.0	0.0		126.0|125.0	57.0	NM_005270		Silent|Missense_Mutation	SNP	ENST00000452319.1	hg19	CCDS33283.1																																																																																			.	.		0.639	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
ACVR2A	92	hgsc.bcm.edu	37	2	148653868	148653868	+	Splice_Site	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:148653868A>T	ENST00000241416.7	+	2	691		c.e2-1		ACVR2A_ENST00000535787.1_Intron|ACVR2A_ENST00000404590.1_Splice_Site	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA						activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		ATTATCTTATAGGTGCTATAC	0.323																																					.		Atlas-SNP	.											.	ACVR2A	125	.	0			c.56-2A>T						.						65.0	70.0	68.0					2																	148653868		2203	4299	6502	SO:0001630	splice_region_variant	92	exon2			TCTTATAGGTGCT		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"""activin A receptor, type II"""	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.56-1A>T	chr2.hg19:g.148653868A>T		49.0	0.0		72.0	35.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Splice_Site	SNP	ENST00000241416.7	hg19	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.113429	0.77210	.	.	ENSG00000121989	ENST00000241416;ENST00000404590	.	.	.	5.17	5.17	0.71159	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0153	0.71578	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACVR2A	148370338	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	9.280000	0.95786	1.942000	0.56320	0.533000	0.62120	.	.	.		0.323	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616	Intron
ACVR2A	92	hgsc.bcm.edu	37	2	148653987	148653987	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:148653987G>C	ENST00000241416.7	+	2	809	c.173G>C	c.(172-174)cGg>cCg	p.R58P	ACVR2A_ENST00000535787.1_5'UTR|AC009480.3_ENST00000402410.2_RNA|ACVR2A_ENST00000404590.1_Missense_Mutation_p.R58P	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	58					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		GATAAACGGCGGCATTGTTTT	0.393																																					p.R58P		Atlas-SNP	.											.	ACVR2A	125	.	0			c.G173C						.						176.0	173.0	174.0					2																	148653987		2203	4300	6503	SO:0001583	missense	92	exon2			AACGGCGGCATTG		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"""activin A receptor, type II"""	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.173G>C	chr2.hg19:g.148653987G>C	ENSP00000241416:p.Arg58Pro	73.0	0.0		96.0	25.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Missense_Mutation	SNP	ENST00000241416.7	hg19	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	G	16.41	3.115003	0.56505	.	.	ENSG00000121989	ENST00000241416;ENST00000404590	D;D	0.98313	-4.86;-4.86	5.58	5.58	0.84498	TGF-beta receptor/activin receptor, type I/II (1);	0.064020	0.64402	D	0.000006	D	0.95007	0.8384	N	0.24115	0.695	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	D	0.91890	0.5523	10	0.29301	T	0.29	.	14.4061	0.67083	0.0:0.0:0.8524:0.1476	.	58	P27037	AVR2A_HUMAN	P	58	ENSP00000241416:R58P;ENSP00000384338:R58P	ENSP00000241416:R58P	R	+	2	0	ACVR2A	148370457	1.000000	0.71417	0.990000	0.47175	0.876000	0.50452	5.554000	0.67294	2.619000	0.88677	0.655000	0.94253	CGG	.	.		0.393	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616	
ZNF804A	91752	hgsc.bcm.edu	37	2	185800725	185800725	+	Missense_Mutation	SNP	G	G	T	rs371202844		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:185800725G>T	ENST00000302277.6	+	4	1196	c.602G>T	c.(601-603)gGg>gTg	p.G201V		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	201							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						AACCAAGTTGGGGATCAAGCC	0.408																																					p.G201V		Atlas-SNP	.											.	ZNF804A	322	.	0			c.G602T						.						65.0	68.0	67.0					2																	185800725		2203	4300	6503	SO:0001583	missense	91752	exon4			AAGTTGGGGATCA	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.602G>T	chr2.hg19:g.185800725G>T	ENSP00000303252:p.Gly201Val	109.0	0.0		128.0	40.0	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	hg19	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	G	11.86	1.763984	0.31228	.	.	ENSG00000170396	ENST00000302277	T	0.07216	3.21	5.32	2.48	0.30137	.	0.225677	0.31102	N	0.008252	T	0.08670	0.0215	M	0.65975	2.015	0.45205	D	0.998216	B	0.28512	0.214	B	0.23852	0.049	T	0.16100	-1.0414	10	0.87932	D	0	-1.7274	3.1123	0.06363	0.1506:0.1409:0.5623:0.1462	.	201	Q7Z570	Z804A_HUMAN	V	201	ENSP00000303252:G201V	ENSP00000303252:G201V	G	+	2	0	ZNF804A	185508970	1.000000	0.71417	0.018000	0.16275	0.986000	0.74619	3.921000	0.56454	0.219000	0.20840	0.467000	0.42956	GGG	.	.		0.408	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
ZSWIM2	151112	hgsc.bcm.edu	37	2	187697904	187697904	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:187697904T>A	ENST00000295131.2	-	7	923	c.884A>T	c.(883-885)tAc>tTc	p.Y295F		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	295					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			AGTATCTATGTATTTTACAAC	0.308																																					p.Y295F		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.A884T						.						117.0	111.0	113.0					2																	187697904		2198	4294	6492	SO:0001583	missense	151112	exon7			TCTATGTATTTTA	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.884A>T	chr2.hg19:g.187697904T>A	ENSP00000295131:p.Tyr295Phe	169.0	0.0		193.0	65.0	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	hg19	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	T	0.789	-0.759367	0.03019	.	.	ENSG00000163012	ENST00000295131	T	0.22945	1.93	5.44	0.537	0.17144	.	0.638228	0.13952	N	0.351408	T	0.19127	0.0459	L	0.42245	1.32	0.09310	N	1	B	0.25007	0.116	B	0.22880	0.042	T	0.18871	-1.0323	10	0.34782	T	0.22	-1.0638	7.8676	0.29545	0.0:0.3365:0.0:0.6635	.	295	Q8NEG5	ZSWM2_HUMAN	F	295	ENSP00000295131:Y295F	ENSP00000295131:Y295F	Y	-	2	0	ZSWIM2	187406149	0.233000	0.23772	0.003000	0.11579	0.086000	0.17979	0.368000	0.20399	0.075000	0.16796	0.477000	0.44152	TAC	.	.		0.308	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
PLCL1	5334	hgsc.bcm.edu	37	2	198948585	198948585	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:198948585T>A	ENST00000428675.1	+	2	742	c.344T>A	c.(343-345)aTg>aAg	p.M115K	PLCL1_ENST00000437704.2_Missense_Mutation_p.M17K	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	115	Interaction with PPP1C.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	ATCAGCTTCATGCAAGCTGGC	0.453																																					p.M115K		Atlas-SNP	.											.	PLCL1	358	.	0			c.T344A						.						78.0	73.0	75.0					2																	198948585		2203	4300	6503	SO:0001583	missense	5334	exon2			GCTTCATGCAAGC	D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"""phospholipase C related, but catalytically inactive protein"", ""protein phosphatase 1, regulatory subunit 127"""	600597	"""phospholipase C, epsilon"""	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.344T>A	chr2.hg19:g.198948585T>A	ENSP00000402861:p.Met115Lys	105.0	0.0		90.0	34.0	NM_006226	Q3MJ90|Q53SD3|Q7Z3S3	Missense_Mutation	SNP	ENST00000428675.1	hg19	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	T	25.8	4.674636	0.88445	.	.	ENSG00000115896	ENST00000428675;ENST00000437704	T;T	0.64260	-0.09;-0.09	5.67	5.67	0.87782	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	D	0.82967	0.5152	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.99;0.999	D	0.86392	0.1736	9	.	.	.	.	16.215	0.82206	0.0:0.0:0.0:1.0	.	115;41	Q15111;B4DYZ4	PLCL1_HUMAN;.	K	115;17	ENSP00000402861:M115K;ENSP00000414138:M17K	.	M	+	2	0	PLCL1	198656830	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.986000	0.88173	2.288000	0.76882	0.533000	0.62120	ATG	.	.		0.453	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226	
CNTN4	152330	hgsc.bcm.edu	37	3	3084827	3084827	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:3084827A>T	ENST00000397461.1	+	21	3062	c.2678A>T	c.(2677-2679)aAt>aTt	p.N893I	CNTN4-AS1_ENST00000442749.2_RNA|CNTN4_ENST00000448906.2_Missense_Mutation_p.N565I|CNTN4_ENST00000358480.3_Missense_Mutation_p.N674I|CNTN4_ENST00000427331.1_Missense_Mutation_p.N893I|CNTN4_ENST00000397459.2_Missense_Mutation_p.N565I|CNTN4_ENST00000418658.1_Missense_Mutation_p.N893I	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	893	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		GCAACAGTCAATGTGACAACC	0.433																																					p.N893I		Atlas-SNP	.											.	CNTN4	335	.	0			c.A2678T						.						82.0	80.0	81.0					3																	3084827		2203	4300	6503	SO:0001583	missense	152330	exon22			CAGTCAATGTGAC	AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.2678A>T	chr3.hg19:g.3084827A>T	ENSP00000380602:p.Asn893Ile	480.0	1.0		424.0	108.0	NM_175607	B2RAX3|Q8IX14|Q8TC35	Missense_Mutation	SNP	ENST00000397461.1	hg19	CCDS43041.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.374002	0.82573	.	.	ENSG00000144619	ENST00000418658;ENST00000397461;ENST00000427331;ENST00000358480;ENST00000397459;ENST00000448906	T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63	5.22	5.22	0.72569	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.58595	0.2133	L	0.54908	1.71	0.80722	D	1	B;P	0.40731	0.309;0.728	P;P	0.53809	0.677;0.735	T	0.55679	-0.8103	9	.	.	.	.	15.3899	0.74735	1.0:0.0:0.0:0.0	.	892;893	Q8IWV2-3;Q8IWV2	.;CNTN4_HUMAN	I	893;893;893;674;565;565	ENSP00000396010:N893I;ENSP00000380602:N893I;ENSP00000413642:N893I;ENSP00000351267:N674I;ENSP00000380600:N565I;ENSP00000392077:N565I	.	N	+	2	0	CNTN4	3059827	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.219000	0.78000	2.106000	0.64143	0.533000	0.62120	AAT	.	.		0.433	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2		
CACNA2D3	55799	hgsc.bcm.edu	37	3	54880437	54880437	+	Nonsense_Mutation	SNP	T	T	A	rs368852689		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:54880437T>A	ENST00000474759.1	+	17	1617	c.1569T>A	c.(1567-1569)taT>taA	p.Y523*	CACNA2D3_ENST00000490478.1_Nonsense_Mutation_p.Y429*|CACNA2D3_ENST00000288197.5_Nonsense_Mutation_p.Y523*|CACNA2D3_ENST00000415676.2_Nonsense_Mutation_p.Y523*	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	523	Cache.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	TTCACGGTTATGCCTTTGCAA	0.408																																					p.Y523X		Atlas-SNP	.											.	CACNA2D3	159	.	0			c.T1569A						.						90.0	84.0	86.0					3																	54880437		1882	4108	5990	SO:0001587	stop_gained	55799	exon17			CGGTTATGCCTTT	AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"""Calcium channel subunits"""	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.1569T>A	chr3.hg19:g.54880437T>A	ENSP00000419101:p.Tyr523*	50.0	0.0		60.0	14.0	NM_018398	B2RPL6|Q9NY16|Q9NY18	Nonsense_Mutation	SNP	ENST00000474759.1	hg19	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	T	37	6.197801	0.97367	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624;ENST00000438476	.	.	.	5.47	4.27	0.50696	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.3557	10.3003	0.43648	0.0:0.076:0.0:0.924	.	.	.	.	X	523;523;523;429;429;422	.	ENSP00000288197:Y523X	Y	+	3	2	CACNA2D3	54855477	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.958000	0.29227	0.859000	0.35456	0.454000	0.30748	TAT	.	.		0.408	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1		
IL17RD	54756	hgsc.bcm.edu	37	3	57148802	57148802	+	Silent	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:57148802A>T	ENST00000296318.7	-	3	316	c.228T>A	c.(226-228)gcT>gcA	p.A76A	IL17RD_ENST00000479825.1_5'UTR|IL17RD_ENST00000320057.5_5'UTR|IL17RD_ENST00000463523.1_5'UTR|IL17RD_ENST00000427856.2_Silent_p.A52A	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	76					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		TCTGGGCGTCAGCAATCACAT	0.453																																					p.A76A		Atlas-SNP	.											.	IL17RD	93	.	0			c.T228A						.						72.0	73.0	72.0					3																	57148802		1937	4144	6081	SO:0001819	synonymous_variant	54756	exon3			GGCGTCAGCAATC	AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"""Interleukins and interleukin receptors"""	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.228T>A	chr3.hg19:g.57148802A>T		53.0	0.0		65.0	35.0	NM_017563	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Silent	SNP	ENST00000296318.7	hg19	CCDS2880.2																																																																																			.	.		0.453	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563	
PRICKLE2	166336	hgsc.bcm.edu	37	3	64084768	64084768	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:64084768T>A	ENST00000295902.6	-	8	3079	c.2494A>T	c.(2494-2496)Agc>Tgc	p.S832C	PRICKLE2-AS1_ENST00000460946.1_RNA|PRICKLE2-AS1_ENST00000476308.1_RNA|RP11-129B22.1_ENST00000482609.1_RNA|PRICKLE2_ENST00000564377.1_Missense_Mutation_p.S888C	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	832					establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		CTTTTCCTGCTGTGCAACTGT	0.468																																					p.S832C		Atlas-SNP	.											.	PRICKLE2	88	.	0			c.A2494T						.						107.0	105.0	106.0					3																	64084768		2203	4300	6503	SO:0001583	missense	166336	exon8			TCCTGCTGTGCAA	AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637			20340	protein-coding gene	gene with protein product		608501	"""prickle-like 2 (Drosophila)"""			12525887	Standard	NM_198859		Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000295902.6:c.2494A>T	chr3.hg19:g.64084768T>A	ENSP00000295902:p.Ser832Cys	86.0	0.0		75.0	15.0	NM_198859	Q0VF44	Missense_Mutation	SNP	ENST00000295902.6	hg19	CCDS2902.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.962224	0.53400	.	.	ENSG00000163637	ENST00000295902	D	0.86432	-2.12	5.83	3.44	0.39384	.	0.059918	0.64402	D	0.000002	D	0.83963	0.5368	L	0.44542	1.39	0.42333	D	0.9923	D	0.57899	0.981	P	0.46796	0.527	T	0.82851	-0.0253	10	0.72032	D	0.01	-26.1787	10.3142	0.43727	0.0:0.1304:0.0:0.8696	.	832	Q7Z3G6	PRIC2_HUMAN	C	832	ENSP00000295902:S832C	ENSP00000295902:S832C	S	-	1	0	PRICKLE2	64059808	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.660000	0.46749	0.474000	0.27392	0.533000	0.62120	AGC	.	.		0.468	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859	
OR5H6	79295	hgsc.bcm.edu	37	3	97983418	97983418	+	Missense_Mutation	SNP	T	T	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:97983418T>G	ENST00000383696.2	+	1	331	c.290T>G	c.(289-291)aTg>aGg	p.M97R	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005479.1	NP_001005479.1	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H, member 6 (gene/pseudogene)	97						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						ACTCCGAAGATGCTGATCAAC	0.408																																					p.M97R		Atlas-SNP	.											.	OR5H6	89	.	0			c.T290G						.						141.0	146.0	144.0					3																	97983418		2203	4300	6503	SO:0001583	missense	79295	exon1			CGAAGATGCTGAT	BK004374	CCDS33800.1	3q12.1	2013-10-10	2013-10-10		ENSG00000230301	ENSG00000230301		"""GPCR / Class A : Olfactory receptors"""	14767	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily H, member 6"""				Standard	NM_001005479		Approved		uc003dsi.1	Q8NGV6	OTTHUMG00000160078	ENST00000383696.2:c.290T>G	chr3.hg19:g.97983418T>G	ENSP00000373196:p.Met97Arg	137.0	0.0		122.0	30.0	NM_001005479	Q6IF88	Missense_Mutation	SNP	ENST00000383696.2	hg19	CCDS33800.1	.	.	.	.	.	.	.	.	.	.	-	12.86	2.065491	0.36470	.	.	ENSG00000230301	ENST00000383696	T	0.06068	3.35	2.19	0.902	0.19290	GPCR, rhodopsin-like superfamily (1);	0.218873	0.32218	N	0.006411	T	0.27594	0.0678	H	0.97390	3.995	0.09310	N	1	D	0.56968	0.978	P	0.58266	0.836	T	0.15206	-1.0445	10	0.87932	D	0	.	6.3694	0.21473	0.0:0.0:0.2532:0.7467	.	97	Q8NGV6	OR5H6_HUMAN	R	97	ENSP00000373196:M97R	ENSP00000373196:M97R	M	+	2	0	OR5H6	99466108	0.008000	0.16893	0.002000	0.10522	0.007000	0.05969	1.769000	0.38522	0.092000	0.17331	0.163000	0.16589	ATG	.	.		0.408	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2		
NR1I2	8856	hgsc.bcm.edu	37	3	119530549	119530549	+	Silent	SNP	C	C	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:119530549C>G	ENST00000337940.4	+	4	660	c.612C>G	c.(610-612)acC>acG	p.T204T	NR1I2_ENST00000466380.1_Silent_p.T165T|NR1I2_ENST00000393716.2_Silent_p.T165T	NM_022002.2	NP_071285.1	O75469	NR1I2_HUMAN	nuclear receptor subfamily 1, group I, member 2	165	Hinge.				drug export (GO:0046618)|exogenous drug catabolic process (GO:0042738)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|steroid metabolic process (GO:0008202)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)|xenobiotic transport (GO:0042908)	nucleoplasm (GO:0005654)	drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.175)	Docetaxel(DB01248)|Erlotinib(DB00530)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Paclitaxel(DB01229)|Rifampicin(DB01045)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Vitamin E(DB00163)	TTGACACTACCTTCTCCCATT	0.532																																					p.T204T		Atlas-SNP	.											.	NR1I2	44	.	0			c.C612G						.						107.0	93.0	98.0					3																	119530549		2203	4300	6503	SO:0001819	synonymous_variant	8856	exon4			CACTACCTTCTCC	AF061056	CCDS2995.1, CCDS43136.1, CCDS54627.1	3q12-q13.3	2013-03-25			ENSG00000144852	ENSG00000144852		"""Nuclear hormone receptors"""	7968	protein-coding gene	gene with protein product	"""pregnane X receptor"", ""orphan nuclear receptor PXR"""	603065				9727070, 9770465	Standard	NM_003889		Approved	ONR1, PXR, BXR, SXR, PAR2	uc003edk.3	O75469	OTTHUMG00000159400	ENST00000337940.4:c.612C>G	chr3.hg19:g.119530549C>G		50.0	0.0		58.0	28.0	NM_022002	Q006P5|Q008C8|Q96AC7|Q9UJ22|Q9UJ23|Q9UJ24|Q9UJ25|Q9UJ26|Q9UJ27|Q9UNW4	Silent	SNP	ENST00000337940.4	hg19	CCDS2995.1																																																																																			.	.		0.532	NR1I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355126.1		
ILDR1	286676	hgsc.bcm.edu	37	3	121712452	121712452	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:121712452C>A	ENST00000344209.5	-	7	1270	c.1144G>T	c.(1144-1146)Gac>Tac	p.D382Y	ILDR1_ENST00000462014.1_Missense_Mutation_p.D350Y|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000393631.1_Missense_Mutation_p.D293Y|ILDR1_ENST00000273691.3_Missense_Mutation_p.D338Y	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	382					positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		GGCCCCCGGTCCTGGAGCTCC	0.597																																					p.D382Y		Atlas-SNP	.											.	ILDR1	120	.	0			c.G1144T						.						66.0	65.0	65.0					3																	121712452		2203	4300	6503	SO:0001583	missense	286676	exon7			CCCGGTCCTGGAG	BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"""deafness, autosomal recessive 42"""	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.1144G>T	chr3.hg19:g.121712452C>A	ENSP00000345667:p.Asp382Tyr	102.0	0.0		111.0	58.0	NM_001199799	Q6ZP61|Q7Z578	Missense_Mutation	SNP	ENST00000344209.5	hg19	CCDS56271.1	.	.	.	.	.	.	.	.	.	.	C	11.26	1.585387	0.28268	.	.	ENSG00000145103	ENST00000273691;ENST00000344209;ENST00000393631;ENST00000462014	T;T;T;T	0.80480	-0.86;-0.64;-1.38;-0.46	5.59	1.45	0.22620	.	0.643972	0.15526	N	0.257764	T	0.80358	0.4608	L	0.54323	1.7	0.09310	N	0.999996	P;B;P;P	0.52692	0.946;0.0;0.892;0.955	P;B;P;P	0.55161	0.77;0.0;0.643;0.643	T	0.67945	-0.5539	10	0.44086	T	0.13	-7.8368	5.2014	0.15267	0.1369:0.5202:0.266:0.0769	.	293;382;338;350	Q86SU0-5;Q86SU0;Q86SU0-2;Q86SU0-6	.;ILDR1_HUMAN;.;.	Y	338;382;293;350	ENSP00000273691:D338Y;ENSP00000345667:D382Y;ENSP00000377251:D293Y;ENSP00000419414:D350Y	ENSP00000273691:D338Y	D	-	1	0	ILDR1	123195142	0.401000	0.25303	0.124000	0.21820	0.181000	0.23173	0.985000	0.29578	0.272000	0.22027	-0.143000	0.13931	GAC	.	.		0.597	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924	
CCDC37	348807	hgsc.bcm.edu	37	3	126135180	126135180	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:126135180A>T	ENST00000352312.1	+	5	346	c.247A>T	c.(247-249)Atg>Ttg	p.M83L	CCDC37_ENST00000505024.1_Missense_Mutation_p.M83L|CCDC37_ENST00000393425.1_Missense_Mutation_p.M83L	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	83										NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		GCAGAAGACGATGCGGGTGCA	0.682																																					p.M83L		Atlas-SNP	.											.	CCDC37	69	.	0			c.A247T						.						37.0	33.0	34.0					3																	126135180		2202	4298	6500	SO:0001583	missense	348807	exon5			AAGACGATGCGGG	AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.247A>T	chr3.hg19:g.126135180A>T	ENSP00000344749:p.Met83Leu	89.0	0.0		76.0	22.0	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Missense_Mutation	SNP	ENST00000352312.1	hg19	CCDS3037.1	.	.	.	.	.	.	.	.	.	.	A	0.006	-2.093653	0.00364	.	.	ENSG00000163885	ENST00000352312;ENST00000393425;ENST00000505024	T;T;T	0.25579	1.79;1.79;1.79	4.59	0.872	0.19113	.	0.303339	0.32386	N	0.006161	T	0.04952	0.0133	N	0.00742	-1.23	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.39663	-0.9603	10	0.02654	T	1	-17.6983	5.3001	0.15773	0.404:0.4415:0.0:0.1545	.	83;83	Q494V2-2;Q494V2	.;CCD37_HUMAN	L	83	ENSP00000344749:M83L;ENSP00000377076:M83L;ENSP00000423046:M83L	ENSP00000344749:M83L	M	+	1	0	CCDC37	127617870	0.000000	0.05858	0.013000	0.15412	0.034000	0.12701	-0.597000	0.05713	-0.090000	0.12462	-0.680000	0.03767	ATG	.	.		0.682	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628	
STAG1	10274	hgsc.bcm.edu	37	3	136196226	136196226	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:136196226A>T	ENST00000383202.2	-	10	1187	c.931T>A	c.(931-933)Tgt>Agt	p.C311S	STAG1_ENST00000236698.5_Missense_Mutation_p.C311S|STAG1_ENST00000434713.2_Missense_Mutation_p.C85S	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	311	SCD. {ECO:0000255|PROSITE- ProRule:PRU00750}.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						TCTTCAATACAAATGGCTCTA	0.348																																					p.C311S		Atlas-SNP	.											.	STAG1	135	.	0			c.T931A						.						120.0	114.0	116.0					3																	136196226		2203	4299	6502	SO:0001583	missense	10274	exon10			CAATACAAATGGC	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.931T>A	chr3.hg19:g.136196226A>T	ENSP00000372689:p.Cys311Ser	43.0	0.0		54.0	26.0	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	hg19	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.766467	0.90020	.	.	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713	T;T;T	0.31510	1.49;1.49;1.49	5.09	5.09	0.68999	Stromalin conservative domain (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.57740	0.2074	M	0.82823	2.61	0.80722	D	1	D;P;D	0.76494	0.999;0.948;0.999	D;P;D	0.70935	0.971;0.63;0.971	T	0.62253	-0.6893	10	0.46703	T	0.11	.	15.1528	0.72713	1.0:0.0:0.0:0.0	.	328;311;311	Q4LE48;Q6P275;Q8WVM7	.;.;STAG1_HUMAN	S	311;311;85	ENSP00000372689:C311S;ENSP00000236698:C311S;ENSP00000404396:C85S	ENSP00000236698:C311S	C	-	1	0	STAG1	137678916	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.031000	0.59945	0.533000	0.62120	TGT	.	.		0.348	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862	
P2RY1	5028	hgsc.bcm.edu	37	3	152553693	152553693	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:152553693A>T	ENST00000305097.3	+	1	958	c.122A>T	c.(121-123)aAa>aTa	p.K41I		NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	41					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			TCGTCGTTCAAATGCGCCTTG	0.622																																					p.K41I		Atlas-SNP	.											.	P2RY1	49	.	0			c.A122T						.						83.0	73.0	76.0					3																	152553693		2203	4300	6503	SO:0001583	missense	5028	exon1			CGTTCAAATGCGC	U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.122A>T	chr3.hg19:g.152553693A>T	ENSP00000304767:p.Lys41Ile	112.0	0.0		112.0	59.0	NM_002563		Missense_Mutation	SNP	ENST00000305097.3	hg19	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	A	10.24	1.294501	0.23564	.	.	ENSG00000169860	ENST00000305097	T	0.36520	1.25	5.37	-7.62	0.01294	.	0.758261	0.12413	N	0.471082	T	0.15696	0.0378	N	0.08118	0	0.09310	N	1	B	0.16603	0.018	B	0.18871	0.023	T	0.17048	-1.0382	10	0.46703	T	0.11	.	11.3924	0.49822	0.7134:0.1016:0.1849:0.0	.	41	P47900	P2RY1_HUMAN	I	41	ENSP00000304767:K41I	ENSP00000304767:K41I	K	+	2	0	P2RY1	154036383	0.001000	0.12720	0.000000	0.03702	0.281000	0.26958	-0.174000	0.09839	-1.876000	0.01131	-0.256000	0.11100	AAA	.	.		0.622	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563	
MECOM	2122	hgsc.bcm.edu	37	3	168840403	168840403	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:168840403T>A	ENST00000464456.1	-	5	1579	c.379A>T	c.(379-381)Agt>Tgt	p.S127C	MECOM_ENST00000472280.1_Missense_Mutation_p.S127C|MECOM_ENST00000433243.2_Missense_Mutation_p.S127C|MECOM_ENST00000264674.3_Missense_Mutation_p.S191C|MECOM_ENST00000468789.1_Missense_Mutation_p.S127C|MECOM_ENST00000460814.1_Missense_Mutation_p.S127C|MECOM_ENST00000392736.3_Missense_Mutation_p.S127C|MECOM_ENST00000494292.1_Missense_Mutation_p.S315C	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						TGCTTTCCACTGTCATGTGAC	0.433																																					p.S315C		Atlas-SNP	.											.	MECOM	216	.	0			c.A943T						.						222.0	185.0	198.0					3																	168840403		2203	4300	6503	SO:0001583	missense	2122	exon6			TTCCACTGTCATG	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.379A>T	chr3.hg19:g.168840403T>A	ENSP00000419770:p.Ser127Cys	121.0	0.0		95.0	45.0	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000464456.1	hg19	CCDS54669.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.282114	0.80692	.	.	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243;ENST00000492586	T;T;T;T;T;T;T;T;T	0.15952	2.38;2.38;2.38;2.38;2.38;2.38;2.38;2.38;2.38	5.68	4.52	0.55395	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.263556	0.29892	N	0.010924	T	0.33118	0.0852	L	0.51422	1.61	0.58432	D	0.999995	D;D;D;D;D	0.76494	0.999;0.996;0.998;0.998;0.997	D;P;P;P;P	0.66847	0.947;0.794;0.862;0.891;0.817	T	0.03008	-1.1083	10	0.87932	D	0	-11.5787	11.6019	0.51008	0.0:0.0695:0.0:0.9305	.	315;127;315;191;127	Q03112-3;Q03112-6;E7EQ57;Q03112-4;Q03112	.;.;.;.;EVI1_HUMAN	C	191;127;127;127;315;127;127;127;102	ENSP00000264674:S191C;ENSP00000376493:S127C;ENSP00000419770:S127C;ENSP00000420048:S127C;ENSP00000417899:S315C;ENSP00000419995:S127C;ENSP00000420466:S127C;ENSP00000394302:S127C;ENSP00000417506:S102C	ENSP00000264674:S191C	S	-	1	0	MECOM	170323097	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	0.989000	0.38761	0.533000	0.62120	AGT	.	.		0.433	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991	
GPR160	26996	hgsc.bcm.edu	37	3	169802417	169802417	+	Missense_Mutation	SNP	A	A	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:169802417A>C	ENST00000355897.5	+	4	1265	c.657A>C	c.(655-657)gaA>gaC	p.E219D		NM_014373.2	NP_055188.1	Q9UJ42	GP160_HUMAN	G protein-coupled receptor 160	219						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2)	8	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			ATATGAATGAAACTATCTTAT	0.333																																					p.E219D		Atlas-SNP	.											.	GPR160	26	.	0			c.A657C						.						82.0	82.0	82.0					3																	169802417		2203	4300	6503	SO:0001583	missense	26996	exon4			GAATGAAACTATC	AB083583	CCDS3211.1	3q26.2-q27	2012-08-21			ENSG00000173890	ENSG00000173890		"""GPCR / Class A : Orphans"""	23693	protein-coding gene	gene with protein product						12044878	Standard	NM_014373		Approved	GPCR150, GPCR1	uc003fgi.3	Q9UJ42	OTTHUMG00000158776	ENST00000355897.5:c.657A>C	chr3.hg19:g.169802417A>C	ENSP00000348161:p.Glu219Asp	65.0	0.0		70.0	35.0	NM_014373	D3DNQ2	Missense_Mutation	SNP	ENST00000355897.5	hg19	CCDS3211.1	.	.	.	.	.	.	.	.	.	.	A	10.88	1.474890	0.26511	.	.	ENSG00000173890	ENST00000355897	.	.	.	5.7	1.62	0.23740	GPCR, rhodopsin-like superfamily (1);	0.289956	0.29587	N	0.011725	T	0.45135	0.1327	L	0.43152	1.355	0.23036	N	0.998391	D	0.61697	0.99	P	0.55749	0.783	T	0.34403	-0.9830	9	0.51188	T	0.08	.	9.8917	0.41294	0.2784:0.0:0.7216:0.0	.	219	Q9UJ42	GP160_HUMAN	D	219	.	ENSP00000348161:E219D	E	+	3	2	GPR160	171285111	1.000000	0.71417	0.117000	0.21633	0.110000	0.19582	3.045000	0.49838	0.004000	0.14682	-0.408000	0.06270	GAA	.	.		0.333	GPR160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352167.1	NM_014373	
KLHL24	54800	hgsc.bcm.edu	37	3	183381339	183381339	+	Silent	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:183381339A>T	ENST00000454652.2	+	5	1400	c.1014A>T	c.(1012-1014)gtA>gtT	p.V338V	KLHL24_ENST00000242810.6_Silent_p.V338V|KLHL24_ENST00000476808.1_Silent_p.V338V	NM_017644.3	NP_060114.2	Q6TFL4	KLH24_HUMAN	kelch-like family member 24	338						cell projection (GO:0042995)|cytoplasm (GO:0005737)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)			ACGATCCTGTAACAGGAGAAT	0.413																																					p.V338V		Atlas-SNP	.											.	KLHL24	56	.	0			c.A1014T						.						149.0	137.0	141.0					3																	183381339		2203	4300	6503	SO:0001819	synonymous_variant	54800	exon4			TCCTGTAACAGGA		CCDS3246.1	3q27.1	2013-02-22	2013-02-22		ENSG00000114796	ENSG00000114796		"""Kelch-like"", ""BTB/POZ domain containing"""	25947	protein-coding gene	gene with protein product		611295	"""kelch-like 24 (Drosophila)"""				Standard	XM_005247552		Approved	DRE1, FLJ20059	uc003flv.3	Q6TFL4	OTTHUMG00000156911	ENST00000454652.2:c.1014A>T	chr3.hg19:g.183381339A>T		75.0	0.0		70.0	40.0	NM_017644	A5PLN8|Q9H620|Q9NXT9	Silent	SNP	ENST00000454652.2	hg19	CCDS3246.1																																																																																			.	.		0.413	KLHL24-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346586.2	NM_017644	
MUC4	4585	hgsc.bcm.edu	37	3	195511179	195511179	+	Silent	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr3:195511179T>A	ENST00000463781.3	-	2	7731	c.7272A>T	c.(7270-7272)tcA>tcT	p.S2424S	MUC4_ENST00000475231.1_Silent_p.S2424S|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGTGGAAGCTGAGGAAAGGC	0.587																																					p.S2424S		Atlas-SNP	.											.	MUC4	1505	.	0			c.A7272T						.						48.0	48.0	48.0					3																	195511179		645	1580	2225	SO:0001819	synonymous_variant	4585	exon2			GGAAGCTGAGGAA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7272A>T	chr3.hg19:g.195511179T>A		357.0	0.0		370.0	31.0	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	hg19	CCDS54700.1																																																																																			.	.		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLIT2	9353	hgsc.bcm.edu	37	4	20487848	20487848	+	Nonsense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr4:20487848A>T	ENST00000504154.1	+	7	817	c.565A>T	c.(565-567)Aga>Tga	p.R189*	SLIT2_ENST00000503837.1_Nonsense_Mutation_p.R189*|SLIT2_ENST00000503823.1_Nonsense_Mutation_p.R189*|SLIT2_ENST00000273739.5_Nonsense_Mutation_p.R189*	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	189					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						CAACATTACTAGACTTTCTGT	0.274																																					p.R189X		Atlas-SNP	.											.	SLIT2	290	.	0			c.A565T						.						73.0	74.0	74.0					4																	20487848		2202	4299	6501	SO:0001587	stop_gained	9353	exon7			ATTACTAGACTTT	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.565A>T	chr4.hg19:g.20487848A>T	ENSP00000422591:p.Arg189*	311.0	0.0		330.0	251.0	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Nonsense_Mutation	SNP	ENST00000504154.1	hg19	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	A	35	5.496967	0.96355	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	.	.	.	5.3	4.03	0.46877	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	.	10.8909	0.46994	0.6576:0.3424:0.0:0.0	.	.	.	.	X	189	.	ENSP00000273739:R189X	R	+	1	2	SLIT2	20096946	1.000000	0.71417	0.939000	0.37840	0.992000	0.81027	3.618000	0.54188	2.120000	0.65058	0.459000	0.35465	AGA	.	.		0.274	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
TMEM156	80008	hgsc.bcm.edu	37	4	38995620	38995620	+	Splice_Site	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr4:38995620T>A	ENST00000381938.3	-	3	466		c.e3-2			NM_024943.1	NP_079219.1	Q8N614	TM156_HUMAN	transmembrane protein 156							integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						TGATAAGAACTAGAAAGTGAT	0.328																																					.		Atlas-SNP	.											.	TMEM156	31	.	0			c.359-2A>T						.						63.0	64.0	64.0					4																	38995620		2202	4300	6502	SO:0001630	splice_region_variant	80008	exon4			AAGAACTAGAAAG	AK026888	CCDS3448.1	4p14	2008-02-05			ENSG00000121895	ENSG00000121895			26260	protein-coding gene	gene with protein product						12477932	Standard	NM_024943		Approved	FLJ23235	uc003gto.3	Q8N614	OTTHUMG00000128582	ENST00000381938.3:c.359-2A>T	chr4.hg19:g.38995620T>A		131.0	0.0		111.0	85.0	NM_024943	Q9H5N9	Splice_Site	SNP	ENST00000381938.3	hg19	CCDS3448.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.246822	0.59103	.	.	ENSG00000121895	ENST00000381938;ENST00000344606	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.3895	0.49806	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMEM156	38672015	0.996000	0.38824	0.950000	0.38849	0.794000	0.44872	4.025000	0.57225	2.174000	0.68829	0.533000	0.62120	.	.	.		0.328	TMEM156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250435.3	NM_024943	Intron
GRXCR1	389207	hgsc.bcm.edu	37	4	43032535	43032535	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr4:43032535G>A	ENST00000399770.2	+	4	851	c.851G>A	c.(850-852)cGt>cAt	p.R284H		NM_001080476.2	NP_001073945.1	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	284					auditory receptor cell differentiation (GO:0042491)|cell redox homeostasis (GO:0045454)|inner ear receptor cell development (GO:0060119)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of phosphatase activity (GO:0010923)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of sound (GO:0007605)|vestibular receptor cell development (GO:0060118)	kinocilium (GO:0060091)|stereocilium (GO:0032420)	electron carrier activity (GO:0009055)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(22)|ovary(1)|prostate(2)|skin(1)	32						GGTCTTCAGCGTTGTAAGAAC	0.393																																					p.R284H		Atlas-SNP	.											.	GRXCR1	78	.	0			c.G851A						.						143.0	134.0	136.0					4																	43032535		1891	4118	6009	SO:0001583	missense	389207	exon4			TTCAGCGTTGTAA		CCDS43225.1	4p14	2014-06-12			ENSG00000215203	ENSG00000215203			31673	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 88"""	613283	"""deafness, autosomal recessive 25"""	DFNB25		20137778	Standard	NM_001080476		Approved	PPP1R88	uc003gwt.3	A8MXD5	OTTHUMG00000160434	ENST00000399770.2:c.851G>A	chr4.hg19:g.43032535G>A	ENSP00000382670:p.Arg284His	75.0	0.0		93.0	17.0	NM_001080476		Missense_Mutation	SNP	ENST00000399770.2	hg19	CCDS43225.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.405470	0.83230	.	.	ENSG00000215203	ENST00000399770	T	0.21932	1.98	5.64	5.64	0.86602	.	0.173392	0.39909	U	0.001231	T	0.39937	0.1097	M	0.81682	2.555	0.53688	D	0.999975	D	0.67145	0.996	P	0.49502	0.613	T	0.42275	-0.9461	10	0.72032	D	0.01	-11.3334	18.6692	0.91504	0.0:0.0:1.0:0.0	.	284	A8MXD5	GRCR1_HUMAN	H	284	ENSP00000382670:R284H	ENSP00000382670:R284H	R	+	2	0	GRXCR1	42727292	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	6.834000	0.75339	2.649000	0.89929	0.579000	0.79373	CGT	.	.		0.393	GRXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360576.1	NM_001080476	
GK2	2712	hgsc.bcm.edu	37	4	80327914	80327914	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr4:80327914C>T	ENST00000358842.3	-	1	1458	c.1441G>A	c.(1441-1443)Gtt>Att	p.V481I		NM_033214.2	NP_149991.2	Q01415	GALK2_HUMAN	glycerol kinase 2	0					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)			autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	39						ATCCTGAGAACTGACAAAGCC	0.498																																					p.V481I		Atlas-SNP	.											.	GK2	102	.	0			c.G1441A						.						129.0	123.0	125.0					4																	80327914		2203	4300	6503	SO:0001583	missense	2712	exon1			TGAGAACTGACAA	BC029820	CCDS3585.1	4q13	2008-02-05	2002-10-03	2002-10-04	ENSG00000196475	ENSG00000196475		"""Glycerol kinases"""	4291	protein-coding gene	gene with protein product		600148	"""glycerol kinase pseudogene 2"""	GKP2		7987308	Standard	NM_033214		Approved	GKTA	uc003hlu.3	Q14410	OTTHUMG00000130199	ENST00000358842.3:c.1441G>A	chr4.hg19:g.80327914C>T	ENSP00000351706:p.Val481Ile	154.0	0.0		130.0	27.0	NM_033214	Q7Z4Q4	Missense_Mutation	SNP	ENST00000358842.3	hg19	CCDS3585.1	.	.	.	.	.	.	.	.	.	.	C	0.179	-1.064393	0.01934	.	.	ENSG00000196475	ENST00000358842	T	0.14516	2.5	4.11	-4.57	0.03421	.	0.711220	0.13539	N	0.380325	T	0.06371	0.0164	N	0.19112	0.55	0.09310	N	1	B	0.11235	0.004	B	0.17098	0.017	T	0.24512	-1.0158	10	0.54805	T	0.06	-16.3104	2.8385	0.05522	0.1143:0.3204:0.1124:0.4529	.	481	Q14410	GLPK2_HUMAN	I	481	ENSP00000351706:V481I	ENSP00000351706:V481I	V	-	1	0	GK2	80546938	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.214000	0.09292	-1.253000	0.02488	0.585000	0.79938	GTT	.	.		0.498	GK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252517.2	NM_033214	
ADAMTS12	81792	hgsc.bcm.edu	37	5	33576426	33576426	+	Silent	SNP	T	T	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:33576426T>C	ENST00000504830.1	-	19	4040	c.3705A>G	c.(3703-3705)agA>agG	p.R1235R	ADAMTS12_ENST00000352040.3_Silent_p.R1150R|ADAMTS12_ENST00000504582.1_5'Flank	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1235	Spacer 2.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						TCCCCTCAACTCTGGGTGTCC	0.577										HNSCC(64;0.19)																											p.R1235R		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.A3705G						.						129.0	127.0	128.0					5																	33576426		2203	4300	6503	SO:0001819	synonymous_variant	81792	exon19			CTCAACTCTGGGT	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.3705A>G	chr5.hg19:g.33576426T>C		129.0	0.0		196.0	98.0	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	hg19	CCDS34140.1																																																																																			.	.		0.577	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
HCN1	348980	hgsc.bcm.edu	37	5	45353293	45353293	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:45353293T>A	ENST00000303230.4	-	5	1343	c.1286A>T	c.(1285-1287)cAg>cTg	p.Q429L		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	429					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						ATGTATCTTCTGACGCATATC	0.333																																					p.Q429L		Atlas-SNP	.											.	HCN1	298	.	0			c.A1286T						.						160.0	147.0	151.0					5																	45353293		2203	4299	6502	SO:0001583	missense	348980	exon5			ATCTTCTGACGCA	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.1286A>T	chr5.hg19:g.45353293T>A	ENSP00000307342:p.Gln429Leu	50.0	0.0		82.0	30.0	NM_021072		Missense_Mutation	SNP	ENST00000303230.4	hg19	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	T	19.04	3.750570	0.69533	.	.	ENSG00000164588	ENST00000303230	D	0.96459	-4.02	5.97	5.97	0.96955	Cyclic nucleotide-binding-like (1);	0.000000	0.64402	D	0.000005	D	0.94857	0.8338	L	0.60845	1.875	0.80722	D	1	B	0.22909	0.077	B	0.13407	0.009	D	0.92407	0.5934	10	0.59425	D	0.04	.	16.4473	0.83942	0.0:0.0:0.0:1.0	.	429	O60741	HCN1_HUMAN	L	429	ENSP00000307342:Q429L	ENSP00000307342:Q429L	Q	-	2	0	HCN1	45389050	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.033000	0.88852	2.281000	0.76405	0.533000	0.62120	CAG	.	.		0.333	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072	
POC5	134359	hgsc.bcm.edu	37	5	74981226	74981226	+	Missense_Mutation	SNP	C	C	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:74981226C>G	ENST00000428202.2	-	10	1402	c.1213G>C	c.(1213-1215)Gct>Cct	p.A405P	POC5_ENST00000510798.1_Missense_Mutation_p.A288P|POC5_ENST00000514838.2_Missense_Mutation_p.A377P|POC5_ENST00000380475.2_Missense_Mutation_p.A288P|POC5_ENST00000446329.2_Missense_Mutation_p.A380P	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	405					cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						ATCGGAGGAGCTGAAGGATCC	0.498																																					p.A405P		Atlas-SNP	.											.	POC5	82	.	0			c.G1213C						.						177.0	193.0	188.0					5																	74981226		2018	4198	6216	SO:0001583	missense	134359	exon10			GAGGAGCTGAAGG	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 37"", ""POC5 centriolar protein homolog (Chlamydomonas)"""	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.1213G>C	chr5.hg19:g.74981226C>G	ENSP00000410216:p.Ala405Pro	105.0	0.0		97.0	32.0	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Missense_Mutation	SNP	ENST00000428202.2	hg19	CCDS47236.1	.	.	.	.	.	.	.	.	.	.	C	12.91	2.079968	0.36662	.	.	ENSG00000152359	ENST00000428202;ENST00000514838;ENST00000380475;ENST00000510798;ENST00000446329	T;T;T;T;T	0.46063	1.83;1.42;0.88;0.88;1.82	4.14	2.27	0.28462	.	0.838861	0.10828	N	0.629672	T	0.52208	0.1720	L	0.54323	1.7	0.09310	N	1	D;D;B	0.55385	0.971;0.971;0.026	P;P;B	0.58454	0.779;0.839;0.009	T	0.35773	-0.9775	10	0.54805	T	0.06	-3.6516	9.0897	0.36603	0.4146:0.5854:0.0:0.0	.	288;405;380	Q8NA72-2;Q8NA72;Q8NA72-3	.;POC5_HUMAN;.	P	405;377;288;288;380	ENSP00000410216:A405P;ENSP00000420971:A377P;ENSP00000369842:A288P;ENSP00000426796:A288P;ENSP00000399481:A380P	ENSP00000369842:A288P	A	-	1	0	POC5	75016982	0.004000	0.15560	0.003000	0.11579	0.035000	0.12851	1.879000	0.39618	0.634000	0.30469	0.561000	0.74099	GCT	.	.		0.498	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408	
PPIP5K2	23262	hgsc.bcm.edu	37	5	102515845	102515845	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:102515845A>T	ENST00000358359.3	+	24	3387	c.2878A>T	c.(2878-2880)Agg>Tgg	p.R960W	PPIP5K2_ENST00000513500.1_3'UTR|PPIP5K2_ENST00000414217.1_Missense_Mutation_p.R960W|PPIP5K2_ENST00000321521.9_Missense_Mutation_p.R960W	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	960					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						TCATATACACAGGAAGTCTCC	0.323																																					p.R960W		Atlas-SNP	.											.	PPIP5K2	98	.	0			c.A2878T						.						90.0	88.0	89.0					5																	102515845		2203	4300	6503	SO:0001583	missense	23262	exon23			ATACACAGGAAGT	AB007893	CCDS34207.1, CCDS64212.1, CCDS75283.1	5q21.1	2014-05-06	2010-01-26	2010-01-26	ENSG00000145725	ENSG00000145725	2.7.4.24		29035	protein-coding gene	gene with protein product		611648	"""histidine acid phosphatase domain containing 1"""	HISPPD1		9455477, 17690096, 18981179	Standard	NM_001276277		Approved	KIAA0433, VIP2	uc003koe.4	O43314	OTTHUMG00000181461	ENST00000358359.3:c.2878A>T	chr5.hg19:g.102515845A>T	ENSP00000351126:p.Arg960Trp	73.0	0.0		113.0	26.0	NM_015216	A1NI53|A6NGS8|Q8TB50	Missense_Mutation	SNP	ENST00000358359.3	hg19		.	.	.	.	.	.	.	.	.	.	A	23.4	4.406314	0.83230	.	.	ENSG00000145725	ENST00000321521;ENST00000358359;ENST00000451606;ENST00000414217;ENST00000509597	T;T;T;T	0.26373	2.31;2.3;2.31;1.74	5.98	5.98	0.97165	.	0.062501	0.64402	D	0.000004	T	0.47801	0.1465	M	0.69358	2.11	0.45129	D	0.99814	D;D;D	0.60160	0.987;0.957;0.984	P;P;P	0.62885	0.877;0.908;0.901	T	0.47911	-0.9080	10	0.87932	D	0	.	15.0407	0.71788	1.0:0.0:0.0:0.0	.	975;960;960	E9PGM8;O43314-2;O43314	.;.;VIP2_HUMAN	W	960;960;975;960;234	ENSP00000313070:R960W;ENSP00000351126:R960W;ENSP00000416016:R960W;ENSP00000424948:R234W	ENSP00000313070:R960W	R	+	1	2	PPIP5K2	102543744	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.839000	0.55835	2.289000	0.77006	0.482000	0.46254	AGG	.	.		0.323	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216	
DMXL1	1657	hgsc.bcm.edu	37	5	118407346	118407346	+	Missense_Mutation	SNP	T	T	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:118407346T>G	ENST00000311085.8	+	1	162	c.82T>G	c.(82-84)Ttc>Gtc	p.F28V	CTB-161M19.4_ENST00000510128.1_RNA|CTB-161M19.4_ENST00000504820.1_RNA|DMXL1_ENST00000539542.1_Missense_Mutation_p.F28V|snoU13_ENST00000458753.1_RNA	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	28										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		CGACCAGCGCTTCACGGTGAG	0.687																																					p.F28V		Atlas-SNP	.											.	DMXL1	268	.	0			c.T82G						.						44.0	35.0	38.0					5																	118407346		2193	4293	6486	SO:0001583	missense	1657	exon1			CAGCGCTTCACGG	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.82T>G	chr5.hg19:g.118407346T>G	ENSP00000309690:p.Phe28Val	62.0	0.0		94.0	18.0	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	hg19	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	T	17.59	3.428424	0.62844	.	.	ENSG00000172869	ENST00000503802;ENST00000311085;ENST00000539542	T;T;T	0.12879	2.82;2.64;2.82	4.46	4.46	0.54185	WD40 repeat-like-containing domain (1);	0.054402	0.64402	D	0.000001	T	0.21103	0.0508	M	0.79693	2.465	0.44227	D	0.997069	B;B	0.09022	0.002;0.001	B;B	0.18263	0.021;0.005	T	0.03630	-1.1018	10	0.52906	T	0.07	-9.652	13.0056	0.58703	0.0:0.0:0.0:1.0	.	28;28	F5H269;Q9Y485	.;DMXL1_HUMAN	V	28	ENSP00000427692:F28V;ENSP00000309690:F28V;ENSP00000439479:F28V	ENSP00000309690:F28V	F	+	1	0	DMXL1	118435245	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.351000	0.44071	1.768000	0.52137	0.459000	0.35465	TTC	.	.		0.687	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
TGFBI	7045	hgsc.bcm.edu	37	5	135388630	135388630	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:135388630G>C	ENST00000442011.2	+	8	1109	c.948G>C	c.(946-948)atG>atC	p.M316I	TGFBI_ENST00000305126.8_Missense_Mutation_p.M316I	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	316	FAS1 2. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGTCAGCTATGTGTGCTGAAG	0.572																																					p.M316I		Atlas-SNP	.											.	TGFBI	76	.	0			c.G948C						.						69.0	77.0	74.0					5																	135388630		2147	4245	6392	SO:0001583	missense	7045	exon8			AGCTATGTGTGCT	M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"""transforming growth factor, beta-induced, 68kD"""	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.948G>C	chr5.hg19:g.135388630G>C	ENSP00000416330:p.Met316Ile	100.0	0.0		148.0	48.0	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Missense_Mutation	SNP	ENST00000442011.2	hg19	CCDS47266.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.07|16.07	3.017612|3.017612	0.54576|0.54576	.|.	.|.	ENSG00000120708|ENSG00000120708	ENST00000442011;ENST00000398813;ENST00000305126|ENST00000514554	D;D|.	0.90788|.	-2.73;-2.73|.	5.65|5.65	5.65|5.65	0.86999|0.86999	FAS1 domain (5);|.	0.218491|.	0.56097|.	D|.	0.000027|.	T|T	0.45256|0.45256	0.1333|0.1333	N|N	0.04655|0.04655	-0.195|-0.195	0.44985|0.44985	D|D	0.998|0.998	P;P|.	0.45212|.	0.853;0.807|.	P;P|.	0.47376|.	0.545;0.475|.	T|T	0.40776|0.40776	-0.9545|-0.9545	10|5	0.20519|.	T|.	0.43|.	-12.9086|-12.9086	20.073|20.073	0.97731|0.97731	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	49;316|.	B9ZVW9;Q15582|.	.;BGH3_HUMAN|.	I|L	316;49;316|34	ENSP00000416330:M316I;ENSP00000306306:M316I|.	ENSP00000306306:M316I|.	M|V	+|+	3|1	0|0	TGFBI|TGFBI	135416529|135416529	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.862000|0.862000	0.49288|0.49288	4.670000|4.670000	0.61583|0.61583	2.811000|2.811000	0.96726|0.96726	0.655000|0.655000	0.94253|0.94253	ATG|GTG	.	.		0.572	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1		
ANKHD1	54882	hgsc.bcm.edu	37	5	139838859	139838859	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:139838859A>G	ENST00000360839.2	+	9	1745	c.1591A>G	c.(1591-1593)Ata>Gta	p.I531V	ANKHD1_ENST00000394722.3_Missense_Mutation_p.I520V|ANKHD1_ENST00000394723.3_Missense_Mutation_p.I531V|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.I531V|ANKHD1_ENST00000297183.6_Missense_Mutation_p.I531V	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	531						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGGGCTGATATAGAACTTGG	0.453																																					p.I531V		Atlas-SNP	.											.	ANKHD1	233	.	0			c.A1591G						.						91.0	94.0	93.0					5																	139838859		2203	4300	6503	SO:0001583	missense	54882	exon9			GCTGATATAGAAC	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"""Ankyrin repeat domain containing"""	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.1591A>G	chr5.hg19:g.139838859A>G	ENSP00000354085:p.Ile531Val	100.0	0.0		138.0	42.0	NM_024668	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	hg19	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.80|14.80	2.643079|2.643079	0.47153|0.47153	.|.	.|.	ENSG00000131503|ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000246149|ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000310356;ENST00000421134;ENST00000394723;ENST00000394722;ENST00000532219	.|T;T;T;T;T;T	.|0.62788	.|0.02;0.02;0.0;0.0;0.0;0.02	5.51|5.51	5.51|5.51	0.81932|0.81932	.|Ankyrin repeat-containing domain (4);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.54967|0.54967	0.1891|0.1891	N|N	0.13299|0.13299	0.325|0.325	0.58432|0.58432	D|D	0.999994|0.999994	.|B;P;P;B;B	.|0.47677	.|0.296;0.899;0.777;0.35;0.424	.|B;P;P;B;B	.|0.51101	.|0.101;0.659;0.566;0.101;0.263	T|T	0.53070|0.53070	-0.8490|-0.8490	6|10	.|0.21014	.|T	.|0.42	.|.	15.6258|15.6258	0.76855|0.76855	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|531;531;531;520;531	.|Q8IWZ3-5;Q8IWZ2;Q8IWZ3;Q8IWZ3-3;Q8IWZ3-2	.|.;.;ANKH1_HUMAN;.;.	M|V	6|531;545;531;531;46;531;531;520;531	.|ENSP00000354085:I531V;ENSP00000297183:I531V;ENSP00000394489:I531V;ENSP00000378212:I531V;ENSP00000378211:I520V;ENSP00000432016:I531V	.|ENSP00000432016:I531V	I|I	+|+	3|1	3|0	ANKHD1|ANKHD1-EIF4EBP3;ANKHD1	139819043|139819043	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	5.890000|5.890000	0.69774|0.69774	2.105000|2.105000	0.64084|0.64084	0.454000|0.454000	0.30748|0.30748	ATA|ATA	.	.		0.453	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747	
AFAP1L1	134265	hgsc.bcm.edu	37	5	148682070	148682070	+	Silent	SNP	T	T	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:148682070T>C	ENST00000296721.4	+	5	515	c.417T>C	c.(415-417)ccT>ccC	p.P139P	AFAP1L1_ENST00000515000.1_Silent_p.P139P|AFAP1L1_ENST00000522492.1_3'UTR	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	139						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAAGTCGCCTGAGTACATCA	0.597																																					p.P139P		Atlas-SNP	.											.	AFAP1L1	86	.	0			c.T417C						.						27.0	24.0	25.0					5																	148682070		2202	4294	6496	SO:0001819	synonymous_variant	134265	exon5			GTCGCCTGAGTAC	AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"""Pleckstrin homology (PH) domain containing"""	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.417T>C	chr5.hg19:g.148682070T>C		51.0	0.0		59.0	17.0	NM_001146337	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Silent	SNP	ENST00000296721.4	hg19	CCDS34274.1																																																																																			.	.		0.597	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406	
FAT2	2196	hgsc.bcm.edu	37	5	150946663	150946663	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:150946663A>T	ENST00000261800.5	-	1	1842	c.1830T>A	c.(1828-1830)ttT>ttA	p.F610L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	610	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GATTTAGATCAAAATACTCTA	0.418																																					p.F610L		Atlas-SNP	.											.	FAT2	465	.	0			c.T1830A						.						104.0	106.0	106.0					5																	150946663		2203	4300	6503	SO:0001583	missense	2196	exon1			TAGATCAAAATAC	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.1830T>A	chr5.hg19:g.150946663A>T	ENSP00000261800:p.Phe610Leu	88.0	0.0		126.0	42.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	A	14.23	2.474515	0.43942	.	.	ENSG00000086570	ENST00000261800	T	0.70749	-0.51	5.75	-1.01	0.10169	Cadherin (4);Cadherin-like (1);	0.087556	0.49916	D	0.000121	D	0.82962	0.5151	M	0.88704	2.975	0.47341	D	0.999396	D	0.76494	0.999	D	0.83275	0.996	T	0.81549	-0.0882	10	0.72032	D	0.01	.	10.008	0.41968	0.6136:0.0:0.3864:0.0	.	610	Q9NYQ8	FAT2_HUMAN	L	610	ENSP00000261800:F610L	ENSP00000261800:F610L	F	-	3	2	FAT2	150926856	0.932000	0.31603	0.035000	0.18076	0.475000	0.33008	1.745000	0.38278	-0.408000	0.07565	-0.250000	0.11733	TTT	.	.		0.418	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
CYFIP2	26999	hgsc.bcm.edu	37	5	156816275	156816275	+	Silent	SNP	C	C	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr5:156816275C>T	ENST00000521420.1	+	28	3299	c.3208C>T	c.(3208-3210)Ctg>Ttg	p.L1070L	CYFIP2_ENST00000442283.2_3'UTR|CYFIP2_ENST00000347377.6_Silent_p.L1096L|CYFIP2_ENST00000318218.6_Silent_p.L1121L|CYFIP2_ENST00000541131.1_Silent_p.L1021L|CYFIP2_ENST00000377576.3_Silent_p.L1096L|CYFIP2_ENST00000522463.1_Silent_p.L900L|CYFIP2_ENST00000435847.2_Silent_p.L795L					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CGAGGTCATCCTGACCCGCAT	0.617																																					p.L1096L		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C3286T						.						69.0	78.0	75.0					5																	156816275		2190	4289	6479	SO:0001819	synonymous_variant	26999	exon29			GTCATCCTGACCC	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"""p53 inducible protein"""	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.3208C>T	chr5.hg19:g.156816275C>T		61.0	0.0		96.0	57.0	NM_001037332		Silent	SNP	ENST00000521420.1	hg19																																																																																				.	.		0.617	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332	
KIF13A	63971	hgsc.bcm.edu	37	6	17794911	17794911	+	Silent	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr6:17794911T>A	ENST00000259711.6	-	24	3072	c.2967A>T	c.(2965-2967)atA>atT	p.I989I	KIF13A_ENST00000378843.2_Silent_p.I989I|KIF13A_ENST00000378814.5_Silent_p.I989I|KIF13A_ENST00000378816.5_Silent_p.I989I|KIF13A_ENST00000378826.2_Silent_p.I989I	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	989					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			TCCACATTTCTATTCTTCGCG	0.418																																					p.I989I		Atlas-SNP	.											.	KIF13A	276	.	0			c.A2967T						.						102.0	99.0	100.0					6																	17794911		1960	4150	6110	SO:0001819	synonymous_variant	63971	exon24			CATTTCTATTCTT	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"""Kinesins"""	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.2967A>T	chr6.hg19:g.17794911T>A		43.0	0.0		83.0	31.0	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	hg19	CCDS47381.1	.	.	.	.	.	.	.	.	.	.	T	12.17	1.858692	0.32791	.	.	ENSG00000137177	ENST00000358380	.	.	.	5.45	-2.51	0.06365	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.7765	0.29041	0.2149:0.0:0.3669:0.4183	.	.	.	.	L	383	.	.	X	-	2	0	KIF13A	17902890	1.000000	0.71417	0.950000	0.38849	0.992000	0.81027	0.553000	0.23391	-0.183000	0.10585	0.533000	0.62120	TAG	.	.		0.418	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
ITPR3	3710	hgsc.bcm.edu	37	6	33643557	33643557	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr6:33643557C>T	ENST00000374316.5	+	26	4266	c.3206C>T	c.(3205-3207)cCg>cTg	p.P1069L	ITPR3_ENST00000605930.1_Missense_Mutation_p.P1069L			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1069					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	GACTATGCGCCGCTGGTCTCG	0.642																																					p.P1069L		Atlas-SNP	.											.	ITPR3	409	.	0			c.C3206T						.						40.0	31.0	34.0					6																	33643557		2203	4300	6503	SO:0001583	missense	3710	exon25			ATGCGCCGCTGGT	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.3206C>T	chr6.hg19:g.33643557C>T	ENSP00000363435:p.Pro1069Leu	93.0	0.0		111.0	34.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.706114	0.48412	.	.	ENSG00000096433	ENST00000374316	D	0.92647	-3.08	5.67	4.79	0.61399	.	0.249581	0.41194	N	0.000936	D	0.90000	0.6878	M	0.83774	2.66	0.80722	D	1	B	0.21071	0.051	B	0.19391	0.025	D	0.89456	0.3733	10	0.87932	D	0	-39.1943	14.9016	0.70684	0.0:0.9304:0.0:0.0696	.	1069	Q14573	ITPR3_HUMAN	L	1069	ENSP00000363435:P1069L	ENSP00000363435:P1069L	P	+	2	0	ITPR3	33751535	1.000000	0.71417	0.374000	0.26016	0.183000	0.23260	6.082000	0.71318	2.697000	0.92050	0.655000	0.94253	CCG	.	.		0.642	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
KLHDC3	116138	hgsc.bcm.edu	37	6	42986094	42986094	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr6:42986094G>A	ENST00000326974.4	+	6	728	c.533G>A	c.(532-534)cGc>cAc	p.R178H	KLHDC3_ENST00000244670.8_Missense_Mutation_p.R44H|KLHDC3_ENST00000332245.8_Missense_Mutation_p.R119H	NM_057161.3	NP_476502.1	Q9BQ90	KLDC3_HUMAN	kelch domain containing 3	178					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|reciprocal meiotic recombination (GO:0007131)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)	chromatin binding (GO:0003682)			cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			AGCCCTGCACGCTGGAGGGAC	0.552																																					p.R178H		Atlas-SNP	.											.	KLHDC3	23	.	0			c.G533A						.						40.0	35.0	37.0					6																	42986094		2203	4300	6503	SO:0001583	missense	116138	exon6			CTGCACGCTGGAG	AB055925	CCDS4880.1	6p21.1	2003-06-12			ENSG00000124702	ENSG00000124702			20704	protein-coding gene	gene with protein product		611248				12444059, 12606021	Standard	NM_057161		Approved	PEAS, hPeas, dJ20C7.3	uc003otl.3	Q9BQ90	OTTHUMG00000014714	ENST00000326974.4:c.533G>A	chr6.hg19:g.42986094G>A	ENSP00000313995:p.Arg178His	47.0	0.0		60.0	32.0	NM_057161	A8K2W9	Missense_Mutation	SNP	ENST00000326974.4	hg19	CCDS4880.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.146365	0.57044	.	.	ENSG00000124702	ENST00000326974;ENST00000432243;ENST00000244670;ENST00000394096;ENST00000426116;ENST00000332245	T;T;T	0.67171	-0.25;-0.25;-0.25	5.64	4.77	0.60923	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.56232	0.1971	L	0.49640	1.575	0.80722	D	1	P;P;P;D	0.64830	0.603;0.593;0.765;0.994	B;B;B;P	0.52856	0.063;0.045;0.147;0.711	T	0.56774	-0.7923	10	0.13853	T	0.58	.	14.4033	0.67065	0.0709:0.0:0.9291:0.0	.	178;119;44;178	E7ENU0;E7ERR0;F8W6A4;Q9BQ90	.;.;.;KLDC3_HUMAN	H	178;178;44;178;151;119	ENSP00000313995:R178H;ENSP00000244670:R44H;ENSP00000331562:R119H	ENSP00000244670:R44H	R	+	2	0	KLHDC3	43094072	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	9.102000	0.94226	1.394000	0.46624	0.561000	0.74099	CGC	.	.		0.552	KLHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040570.1	NM_057161	
GRM1	2911	hgsc.bcm.edu	37	6	146720714	146720714	+	Missense_Mutation	SNP	C	C	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr6:146720714C>G	ENST00000282753.1	+	7	2774	c.2539C>G	c.(2539-2541)Cgc>Ggc	p.R847G	GRM1_ENST00000492807.2_Missense_Mutation_p.R847G|GRM1_ENST00000355289.4_Missense_Mutation_p.R847G|GRM1_ENST00000507907.1_Missense_Mutation_p.R847G|GRM1_ENST00000392299.2_Missense_Mutation_p.R847G|GRM1_ENST00000361719.2_Missense_Mutation_p.R847G			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	847					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		GAGGAATGTCCGCAGTGCCTT	0.512																																					p.R847G		Atlas-SNP	.											.	GRM1	419	.	0			c.C2539G						.						106.0	87.0	93.0					6																	146720714		2203	4300	6503	SO:0001583	missense	2911	exon8			AATGTCCGCAGTG	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.2539C>G	chr6.hg19:g.146720714C>G	ENSP00000282753:p.Arg847Gly	94.0	0.0		49.0	37.0	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	hg19	CCDS5209.1	.	.	.	.	.	.	.	.	.	.	C	19.78	3.891888	0.72524	.	.	ENSG00000152822	ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907	D;D;D;D;D;D	0.89415	-2.48;-2.51;-2.51;-2.48;-2.51;-2.51	5.68	5.68	0.88126	GPCR, family 3, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94453	0.8215	M	0.81341	2.54	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.997;1.0	D	0.94259	0.7500	10	0.66056	D	0.02	.	19.7753	0.96389	0.0:1.0:0.0:0.0	.	847;847;847	F8W805;Q13255;Q13255-2	.;GRM1_HUMAN;.	G	847	ENSP00000354896:R847G;ENSP00000376119:R847G;ENSP00000424095:R847G;ENSP00000282753:R847G;ENSP00000347437:R847G;ENSP00000425599:R847G	ENSP00000282753:R847G	R	+	1	0	GRM1	146762407	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.686000	0.91538	0.585000	0.79938	CGC	.	.		0.512	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838	
ZNF479	90827	hgsc.bcm.edu	37	7	57194367	57194367	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:57194367A>T	ENST00000331162.4	-	3	368	c.98T>A	c.(97-99)cTg>cAg	p.L33Q		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	33	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(53)|ovary(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	84			GBM - Glioblastoma multiforme(1;9.18e-12)			AGCACAATCCAGGCATTGCCA	0.408																																					p.L33Q		Atlas-SNP	.											.	ZNF479	193	.	0			c.T98A						.						59.0	60.0	60.0					7																	57194367		2181	4288	6469	SO:0001583	missense	90827	exon3			CAATCCAGGCATT	AF277624	CCDS43590.1	7p11.2	2013-01-08			ENSG00000185177	ENSG00000185177		"""Zinc fingers, C2H2-type"", ""-"""	23258	protein-coding gene	gene with protein product						11410164	Standard	NM_033273		Approved	KR19	uc010kzo.3	Q96JC4	OTTHUMG00000156682	ENST00000331162.4:c.98T>A	chr7.hg19:g.57194367A>T	ENSP00000333776:p.Leu33Gln	326.0	0.0		467.0	122.0	NM_033273		Missense_Mutation	SNP	ENST00000331162.4	hg19	CCDS43590.1	.	.	.	.	.	.	.	.	.	.	a	11.64	1.698177	0.30142	.	.	ENSG00000185177	ENST00000331162	T	0.19250	2.16	1.25	1.25	0.21368	Krueppel-associated box (4);	.	.	.	.	T	0.56906	0.2017	H	0.98068	4.14	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.44757	-0.9307	9	0.87932	D	0	.	6.2934	0.21073	1.0:0.0:0.0:0.0	.	33	Q96JC4	ZN479_HUMAN	Q	33	ENSP00000333776:L33Q	ENSP00000333776:L33Q	L	-	2	0	ZNF479	57198309	0.694000	0.27738	0.096000	0.21009	0.021000	0.10359	3.306000	0.51881	0.558000	0.29135	0.324000	0.21423	CTG	.	.		0.408	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202	
RABGEF1	27342	hgsc.bcm.edu	37	7	66270375	66270375	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:66270375A>T	ENST00000284957.5	+	8	1146	c.1069A>T	c.(1069-1071)Acc>Tcc	p.T357S	RABGEF1_ENST00000439720.2_Missense_Mutation_p.T370S|KCTD7_ENST00000510829.2_Missense_Mutation_p.T357S|KCTD7_ENST00000451741.2_Missense_Mutation_p.T357S|RABGEF1_ENST00000484547.2_3'UTR|RABGEF1_ENST00000450873.2_Missense_Mutation_p.T357S|KCTD7_ENST00000380828.2_Missense_Mutation_p.T397S|RABGEF1_ENST00000437078.2_Missense_Mutation_p.T371S			Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1	574					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein targeting to membrane (GO:0006612)	early endosome (GO:0005769)	DNA binding (GO:0003677)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|stomach(1)	27						CTACTATTTCACCAATCTGGT	0.502																																					p.T357S		Atlas-SNP	.											.	RABGEF1	56	.	0			c.A1069T						.						85.0	75.0	78.0					7																	66270375		2203	4300	6503	SO:0001583	missense	27342	exon8			TATTTCACCAATC	AJ250042	CCDS5535.1, CCDS69308.1, CCDS75610.1	7q11.21	2010-07-09			ENSG00000154710	ENSG00000154710			17676	protein-coding gene	gene with protein product		609700				12505986, 11098082	Standard	NM_014504		Approved	rabex-5, RABEX5	uc003tvh.3	Q9UJ41	OTTHUMG00000129547	ENST00000284957.5:c.1069A>T	chr7.hg19:g.66270375A>T	ENSP00000284957:p.Thr357Ser	50.0	0.0		82.0	20.0	NM_014504	B4DZM7|Q3HKR2|Q3HKR3|Q53FG0	Missense_Mutation	SNP	ENST00000284957.5	hg19	CCDS5535.1	.	.	.	.	.	.	.	.	.	.	A	32	5.149651	0.94645	.	.	ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000154710;ENSG00000154710;ENSG00000154710;ENSG00000154710	ENST00000380827;ENST00000380828;ENST00000510829;ENST00000451741;ENST00000539561;ENST00000284957;ENST00000450873;ENST00000439720;ENST00000437078	T;T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.6	5.6	0.85130	Vacuolar sorting protein 9, subgroup (1);Vacuolar sorting protein 9 (2);	0.000000	0.85682	D	0.000000	T	0.61464	0.2349	M	0.72624	2.21	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.58233	-0.7672	10	0.17832	T	0.49	-20.5411	14.9658	0.71193	1.0:0.0:0.0:0.0	.	371;191;574	B4DZM7;B3KMF1;Q9UJ41	.;.;RABX5_HUMAN	S	441;397;357;357;273;357;357;370;371	ENSP00000370208:T397S;ENSP00000421124:T357S;ENSP00000398177:T357S;ENSP00000284957:T357S;ENSP00000415815:T357S;ENSP00000403429:T370S;ENSP00000390480:T371S	ENSP00000370207:T441S	T	+	1	0	RABGEF1;KCTD7	65907810	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.802000	0.91910	2.135000	0.66039	0.533000	0.62120	ACC	.	.		0.502	RABGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251737.3	NM_014504	
WBSCR17	64409	hgsc.bcm.edu	37	7	71142287	71142287	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:71142287C>A	ENST00000333538.5	+	9	2130	c.1496C>A	c.(1495-1497)cCa>cAa	p.P499Q	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	499	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				GGCTGGGGACCACAGGTAGGA	0.532																																					p.P499Q		Atlas-SNP	.											.	WBSCR17	208	.	0			c.C1496A						.						151.0	149.0	150.0					7																	71142287		2203	4300	6503	SO:0001583	missense	64409	exon9			GGGGACCACAGGT	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"""Glycosyltransferase family 2 domain containing"""	16347	protein-coding gene	gene with protein product	"""polypeptide N-acetylgalactosaminyltransferase-like 3"", ""polypeptide GalNAc transferase 3"""	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1496C>A	chr7.hg19:g.71142287C>A	ENSP00000329654:p.Pro499Gln	64.0	0.0		103.0	56.0	NM_022479	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	hg19	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.566464	0.86439	.	.	ENSG00000185274	ENST00000333538	T	0.25085	1.82	5.35	5.35	0.76521	Ricin B-related lectin (1);Ricin B lectin (3);	0.283398	0.27876	N	0.017499	T	0.48926	0.1527	L	0.58428	1.81	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.34004	-0.9846	10	0.49607	T	0.09	.	18.2305	0.89934	0.0:1.0:0.0:0.0	.	499	Q6IS24	GLTL3_HUMAN	Q	499	ENSP00000329654:P499Q	ENSP00000329654:P499Q	P	+	2	0	WBSCR17	70780223	1.000000	0.71417	0.973000	0.42090	0.897000	0.52465	7.203000	0.77864	2.779000	0.95612	0.650000	0.86243	CCA	.	.		0.532	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479	
COL1A2	1278	hgsc.bcm.edu	37	7	94029552	94029552	+	Silent	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:94029552A>T	ENST00000297268.6	+	5	648	c.177A>T	c.(175-177)acA>acT	p.T59T		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	59			T -> P (in dbSNP:rs1800221). {ECO:0000269|PubMed:4011429}.		blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	ATGGTCCCACAGGCCCTCCTG	0.532										HNSCC(75;0.22)																											p.T59T		Atlas-SNP	.											.	COL1A2	240	.	0			c.A177T						.						94.0	92.0	92.0					7																	94029552		2203	4300	6503	SO:0001819	synonymous_variant	1278	exon5			TCCCACAGGCCCT	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.177A>T	chr7.hg19:g.94029552A>T		81.0	0.0		123.0	67.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Silent	SNP	ENST00000297268.6	hg19	CCDS34682.1																																																																																			.	.		0.532	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
LRRC61	65999	hgsc.bcm.edu	37	7	150034126	150034126	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:150034126A>G	ENST00000359623.4	+	3	764	c.176A>G	c.(175-177)gAc>gGc	p.D59G	LRRC61_ENST00000493307.1_Missense_Mutation_p.D59G|LRRC61_ENST00000323078.7_Missense_Mutation_p.D59G	NM_001142928.1	NP_001136400.1	Q9BV99	LRC61_HUMAN	leucine rich repeat containing 61	59										endometrium(2)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(82;0.011)			GAGTGGCTGGACCTATCAGGC	0.652																																					p.D59G		Atlas-SNP	.											.	LRRC61	17	.	0			c.A176G						.						67.0	57.0	60.0					7																	150034126		2201	4298	6499	SO:0001583	missense	65999	exon2			GGCTGGACCTATC	BC001354	CCDS5901.1	7q31-q35	2006-02-07			ENSG00000127399	ENSG00000127399			21704	protein-coding gene	gene with protein product							Standard	NM_023942		Approved	MGC3036, FLJ31392, HSPC295	uc003wgv.4	Q9BV99	OTTHUMG00000158326	ENST00000359623.4:c.176A>G	chr7.hg19:g.150034126A>G	ENSP00000352642:p.Asp59Gly	26.0	0.0		38.0	17.0	NM_023942	B3KUW0|D3DWY8	Missense_Mutation	SNP	ENST00000359623.4	hg19	CCDS5901.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.036052	0.75617	.	.	ENSG00000127399	ENST00000323078;ENST00000359623;ENST00000493307	T;T;T	0.11821	2.74;2.74;2.74	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.34250	0.0891	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.04103	-1.0977	10	0.33141	T	0.24	-34.5686	12.6413	0.56711	1.0:0.0:0.0:0.0	.	59	Q9BV99	LRC61_HUMAN	G	59	ENSP00000339047:D59G;ENSP00000352642:D59G;ENSP00000420560:D59G	ENSP00000339047:D59G	D	+	2	0	LRRC61	149665059	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	6.318000	0.72866	1.878000	0.54408	0.454000	0.30748	GAC	.	.		0.652	LRRC61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350696.1	NM_023942	
KCNB2	9312	hgsc.bcm.edu	37	8	73480433	73480433	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr8:73480433A>T	ENST00000523207.1	+	2	1052	c.464A>T	c.(463-465)gAg>gTg	p.E155V		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	155					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.E155V(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	CTGAGGCGAGAGGCAGAGACT	0.453																																					p.E155V		Atlas-SNP	.											KCNB2,acral,malignant_melanoma,+1,1	KCNB2	228	.	1	Substitution - Missense(1)	prostate(1)	c.A464T						.						134.0	141.0	138.0					8																	73480433		2203	4300	6503	SO:0001583	missense	9312	exon2			GGCGAGAGGCAGA	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.464A>T	chr8.hg19:g.73480433A>T	ENSP00000430846:p.Glu155Val	72.0	0.0		103.0	39.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.419981	0.83559	.	.	ENSG00000182674	ENST00000523207	D	0.97752	-4.52	6.07	6.07	0.98685	.	0.000000	0.33813	U	0.004527	D	0.96716	0.8928	L	0.58101	1.795	0.80722	D	1	P	0.34462	0.454	B	0.37601	0.254	D	0.96476	0.9352	10	0.66056	D	0.02	.	16.3141	0.82909	1.0:0.0:0.0:0.0	.	155	Q92953	KCNB2_HUMAN	V	155	ENSP00000430846:E155V	ENSP00000430846:E155V	E	+	2	0	KCNB2	73642987	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	9.339000	0.96797	2.326000	0.78906	0.533000	0.62120	GAG	.	.		0.453	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
TRMT12	55039	hgsc.bcm.edu	37	8	125464081	125464081	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr8:125464081A>T	ENST00000328599.3	+	1	1034	c.913A>T	c.(913-915)Agg>Tgg	p.R305W	TRMT12_ENST00000521443.1_Intron	NM_017956.3	NP_060426.2	Q53H54	TYW2_HUMAN	tRNA methyltransferase 12 homolog (S. cerevisiae)	305					tRNA processing (GO:0008033)		transferase activity (GO:0016740)			breast(2)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			TATTGCAGATAGGGTGATCCT	0.463																																					p.R305W		Atlas-SNP	.											.	TRMT12	28	.	0			c.A913T						.						80.0	80.0	80.0					8																	125464081		2203	4300	6503	SO:0001583	missense	55039	exon1			GCAGATAGGGTGA	AF313041	CCDS6349.1	8q24.13	2011-05-09	2006-11-16		ENSG00000183665	ENSG00000183665			26091	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 2"""	611244	"""tRNA methyltranferase 12 homolog (S. cerevisiae)"""			16005430, 17150819	Standard	NM_017956		Approved	FLJ20772, Trm12, TYW2	uc003yra.4	Q53H54	OTTHUMG00000165022	ENST00000328599.3:c.913A>T	chr8.hg19:g.125464081A>T	ENSP00000329858:p.Arg305Trp	45.0	0.0		60.0	24.0	NM_017956	Q6PKB9|Q96F21|Q9NWK6	Missense_Mutation	SNP	ENST00000328599.3	hg19	CCDS6349.1	.	.	.	.	.	.	.	.	.	.	A	19.64	3.866351	0.71949	.	.	ENSG00000183665	ENST00000328599	T	0.30981	1.51	5.41	1.5	0.22942	.	0.000000	0.85682	D	0.000000	T	0.64962	0.2646	H	0.95917	3.74	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	T	0.72462	-0.4286	10	0.87932	D	0	-18.3481	11.9586	0.52995	0.5774:0.4226:0.0:0.0	.	305	Q53H54	TYW2_HUMAN	W	305	ENSP00000329858:R305W	ENSP00000329858:R305W	R	+	1	2	TRMT12	125533262	1.000000	0.71417	0.982000	0.44146	0.969000	0.65631	1.868000	0.39509	0.077000	0.16863	0.459000	0.35465	AGG	.	.		0.463	TRMT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381465.1	NM_017956	
ASPN	54829	hgsc.bcm.edu	37	9	95232978	95232978	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr9:95232978A>T	ENST00000375544.3	-	3	603	c.360T>A	c.(358-360)aaT>aaA	p.N120K	ASPN_ENST00000375543.1_Missense_Mutation_p.N120K|ASPN_ENST00000395538.3_Missense_Mutation_p.N120K|CENPP_ENST00000375587.3_Intron	NM_017680.4	NP_060150	Q9BXN1	ASPN_HUMAN	asporin	120					bone mineralization (GO:0030282)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9						CTTTAAAATCATTTTCTTTGA	0.289																																					p.N120K		Atlas-SNP	.											.	ASPN	52	.	0			c.T360A						.						79.0	82.0	81.0					9																	95232978		2201	4289	6490	SO:0001583	missense	54829	exon3			AAAATCATTTTCT	AF316824		9q22.31	2008-05-14	2007-02-15		ENSG00000106819	ENSG00000106819		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	14872	protein-coding gene	gene with protein product	"""asporin proteoglycan"""	608135	"""asporin (LRR class 1)"""				Standard	NM_017680		Approved	FLJ20129, SLRR1C, PLAP1	uc004ase.2	Q9BXN1	OTTHUMG00000020227	ENST00000375544.3:c.360T>A	chr9.hg19:g.95232978A>T	ENSP00000364694:p.Asn120Lys	93.0	0.0		72.0	42.0	NM_001193335	Q5TBF3|Q96K79|Q96LD0|Q9NXP3	Missense_Mutation	SNP	ENST00000375544.3	hg19		.	.	.	.	.	.	.	.	.	.	A	14.50	2.553652	0.45487	.	.	ENSG00000106819	ENST00000375544;ENST00000375543;ENST00000395538	T;T;T	0.56941	0.43;0.43;0.43	5.7	-4.31	0.03698	.	0.134360	0.64402	D	0.000002	T	0.29423	0.0733	N	0.25825	0.765	0.32875	D	0.509751	B;B	0.17465	0.02;0.022	B;B	0.23852	0.049;0.049	T	0.02167	-1.1202	10	0.49607	T	0.09	.	3.383	0.07261	0.3018:0.2095:0.3862:0.1025	.	120;120	Q5TBF2;Q9BXN1	.;ASPN_HUMAN	K	120	ENSP00000364694:N120K;ENSP00000364693:N120K;ENSP00000378909:N120K	ENSP00000364693:N120K	N	-	3	2	ASPN	94272799	0.509000	0.26163	0.988000	0.46212	0.995000	0.86356	-0.147000	0.10234	-0.333000	0.08476	-0.256000	0.11100	AAT	.	.		0.289	ASPN-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053094.1	NM_017680	
WNK2	65268	hgsc.bcm.edu	37	9	96079849	96079849	+	Silent	SNP	G	G	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr9:96079849G>A	ENST00000297954.4	+	29	6675	c.6675G>A	c.(6673-6675)gcG>gcA	p.A2225A	WNK2_ENST00000395477.2_Silent_p.A2188A|WNK2_ENST00000471076.1_3'UTR|WNK2_ENST00000427277.2_Silent_p.A1800A|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000349097.3_Silent_p.A1837A|WNK2_ENST00000356055.3_3'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	2225					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						TGCCCCCAGCGCCCGGCCCTC	0.647																																					p.A2188A		Atlas-SNP	.											.	WNK2	277	.	0			c.G6564A						.						71.0	64.0	67.0					9																	96079849		2203	4300	6503	SO:0001819	synonymous_variant	65268	exon28			CCCAGCGCCCGGC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.6675G>A	chr9.hg19:g.96079849G>A		45.0	0.0		24.0	15.0	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	1.105|1.105	-0.659938|-0.659938	0.03454|0.03454	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730;ENST00000448251	T|.	0.61859|.	0.07|.	5.8|5.8	-7.3|-7.3	0.01446|0.01446	.|.	0.891771|.	0.09390|.	N|.	0.808668|.	T|T	0.28167|0.28167	0.0695|0.0695	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.31447|0.31447	-0.9943|-0.9943	7|4	0.23891|.	T|.	0.37|.	.|.	9.7361|9.7361	0.40388|0.40388	0.5466:0.0949:0.3585:0.0|0.5466:0.0949:0.3585:0.0	.|.	.|.	.|.	.|.	T|H	1680|2184;985	ENSP00000414622:A1680T|.	ENSP00000414622:A1680T|.	A|R	+|+	1|2	0|0	WNK2|WNK2	95119670|95119670	0.061000|0.061000	0.20836|0.20836	0.000000|0.000000	0.03702|0.03702	0.030000|0.030000	0.12068|0.12068	0.288000|0.288000	0.18939|0.18939	-2.221000|-2.221000	0.00728|0.00728	-0.753000|-0.753000	0.03488|0.03488	GCC|CGC	.	.		0.647	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
COL15A1	1306	hgsc.bcm.edu	37	9	101777823	101777823	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr9:101777823T>C	ENST00000375001.3	+	10	1901	c.1478T>C	c.(1477-1479)aTg>aCg	p.M493T		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	493	4 X tandem repeats.|Nonhelical region 1 (NC1).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				ACAGCCACCATGGCCCCTGAG	0.572																																					p.M493T		Atlas-SNP	.											.	COL15A1	211	.	0			c.T1478C						.						54.0	48.0	50.0					9																	101777823		2203	4300	6503	SO:0001583	missense	1306	exon10			CCACCATGGCCCC	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.1478T>C	chr9.hg19:g.101777823T>C	ENSP00000364140:p.Met493Thr	46.0	0.0		30.0	25.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	hg19	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	T	1.194	-0.634417	0.03584	.	.	ENSG00000204291	ENST00000375001;ENST00000536083	D	0.89196	-2.48	3.76	-7.51	0.01346	.	.	.	.	.	T	0.73705	0.3621	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.60357	-0.7279	9	0.13108	T	0.6	2.6614	10.3435	0.43893	0.0:0.1623:0.116:0.7216	.	493	P39059	COFA1_HUMAN	T	493;463	ENSP00000364140:M493T	ENSP00000364140:M493T	M	+	2	0	COL15A1	100817644	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.946000	0.00167	-2.145000	0.00801	-0.911000	0.02809	ATG	.	.		0.572	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
USP20	10868	hgsc.bcm.edu	37	9	132636872	132636872	+	Silent	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr9:132636872A>T	ENST00000315480.4	+	18	1916	c.1758A>T	c.(1756-1758)ctA>ctT	p.L586L	USP20_ENST00000358355.1_Silent_p.L586L|USP20_ENST00000372429.3_Silent_p.L586L			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	586	USP.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				GCATTCACCTAAAGCGCTTTC	0.607																																					p.L586L		Atlas-SNP	.											.	USP20	186	.	0			c.A1758T						.						61.0	66.0	65.0					9																	132636872		2118	4237	6355	SO:0001819	synonymous_variant	10868	exon18			TCACCTAAAGCGC	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"""Ubiquitin-specific peptidases"""	12619	protein-coding gene	gene with protein product		615143	"""ubiquitin specific protease 20"""			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.1758A>T	chr9.hg19:g.132636872A>T		93.0	0.0		62.0	44.0	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Silent	SNP	ENST00000315480.4	hg19	CCDS43892.1																																																																																			.	.		0.607	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2		
KIAA1217	56243	hgsc.bcm.edu	37	10	24813464	24813464	+	Missense_Mutation	SNP	C	C	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:24813464C>G	ENST00000376454.3	+	13	2699	c.2669C>G	c.(2668-2670)tCc>tGc	p.S890C	KIAA1217_ENST00000396446.1_Missense_Mutation_p.S573C|KIAA1217_ENST00000307544.6_Missense_Mutation_p.S573C|KIAA1217_ENST00000376462.1_Missense_Mutation_p.S810C|KIAA1217_ENST00000376451.2_Missense_Mutation_p.S573C|KIAA1217_ENST00000376452.3_Missense_Mutation_p.S855C|KIAA1217_ENST00000430453.2_Intron|KIAA1217_ENST00000458595.1_Missense_Mutation_p.S855C|KIAA1217_ENST00000396445.1_Missense_Mutation_p.S573C	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	890					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						GCGCAGAGCTCCCCTGTGGTC	0.662																																					p.S890C		Atlas-SNP	.											.	KIAA1217	235	.	0			c.C2669G						.						66.0	54.0	58.0					10																	24813464		2203	4300	6503	SO:0001583	missense	56243	exon13			AGAGCTCCCCTGT	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.2669C>G	chr10.hg19:g.24813464C>G	ENSP00000365637:p.Ser890Cys	47.0	0.0		46.0	21.0	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	hg19	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.548084	0.65311	.	.	ENSG00000120549	ENST00000376462;ENST00000376456;ENST00000458595;ENST00000442879;ENST00000376454;ENST00000376452;ENST00000438429;ENST00000307544;ENST00000450158;ENST00000396445;ENST00000376451;ENST00000396446	T;T;T;T;T;T;T;T;T;T	0.55052	0.54;0.54;0.54;0.54;0.54;0.54;0.54;0.54;0.54;0.54	5.42	5.42	0.78866	.	0.120213	0.64402	D	0.000020	T	0.71143	0.3305	M	0.66939	2.045	0.58432	D	0.999999	D;D;D;D;D;D;D;D	0.76494	0.999;0.998;0.992;0.994;0.998;0.992;0.983;0.99	D;P;P;P;D;P;P;P	0.65773	0.913;0.838;0.867;0.889;0.938;0.877;0.839;0.81	T	0.73341	-0.4013	10	0.66056	D	0.02	.	19.2009	0.93711	0.0:1.0:0.0:0.0	.	855;855;573;573;573;573;890;890	Q5T5P2-7;A6NLF3;Q5T5P2-4;Q5T5P2-8;Q5T5P2-3;Q5T5P2-6;Q5T5P2;Q5T5P2-2	.;.;.;.;.;.;SKT_HUMAN;.	C	810;855;855;573;890;855;705;573;573;573;573;573	ENSP00000365645:S810C;ENSP00000365639:S855C;ENSP00000392625:S855C;ENSP00000365637:S890C;ENSP00000365635:S855C;ENSP00000404798:S705C;ENSP00000302343:S573C;ENSP00000379722:S573C;ENSP00000365634:S573C;ENSP00000379723:S573C	ENSP00000302343:S573C	S	+	2	0	KIAA1217	24853470	1.000000	0.71417	0.800000	0.32199	0.059000	0.15707	7.287000	0.78681	2.549000	0.85964	0.491000	0.48974	TCC	.	.		0.662	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
FAM21C	253725	hgsc.bcm.edu	37	10	46272808	46272808	+	Nonsense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:46272808A>T	ENST00000336378.4	+	22	2342	c.2224A>T	c.(2224-2226)Aag>Tag	p.K742*	FAM21C_ENST00000374362.2_Nonsense_Mutation_p.K744*|FAM21C_ENST00000540872.1_Nonsense_Mutation_p.K744*|FAM21C_ENST00000359860.4_Nonsense_Mutation_p.K686*|FAM21C_ENST00000537517.1_Intron	NM_015262.2	NP_056077.2	Q9Y4E1	FA21C_HUMAN	family with sequence similarity 21, member C	742					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome (GO:0005768)|plasma membrane (GO:0005886)|WASH complex (GO:0071203)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						GTCTGTGGATAAGAAGGTTGA	0.423																																					p.K744X		Atlas-SNP	.											.	FAM21C	68	.	0			c.A2230T						.						134.0	133.0	133.0					10																	46272808		1816	4048	5864	SO:0001587	stop_gained	253725	exon22			GTGGATAAGAAGG		CCDS44374.1, CCDS44374.2, CCDS53528.1, CCDS53529.1	10q11.22	2014-05-09			ENSG00000172661	ENSG00000172661			23414	protein-coding gene	gene with protein product		613631				20498093	Standard	NM_015262		Approved	Em:AC012044.3, KIAA0592	uc001jcu.3	Q9Y4E1	OTTHUMG00000018089	ENST00000336378.4:c.2224A>T	chr10.hg19:g.46272808A>T	ENSP00000337541:p.Lys742*	384.0	0.0		389.0	157.0	NM_015262	B4DZQ6|B9EK53|F5H0J6|F5H871|Q5SQU4|Q5SQU5|Q7L521|Q9UG79	Nonsense_Mutation	SNP	ENST00000336378.4	hg19		.	.	.	.	.	.	.	.	.	.	A	26.4	4.732498	0.89482	.	.	ENSG00000172661	ENST00000336378;ENST00000540872;ENST00000374362;ENST00000399588;ENST00000359860;ENST00000436993	.	.	.	3.01	-1.42	0.08913	.	1.772090	0.02631	N	0.104260	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.2029	5.1852	0.15180	0.3039:0.5442:0.1519:0.0	.	.	.	.	X	742;744;744;744;686;656	.	ENSP00000337541:K742X	K	+	1	0	FAM21C	45592814	0.005000	0.15991	0.002000	0.10522	0.371000	0.29859	-0.267000	0.08619	-0.368000	0.08040	0.241000	0.17934	AAG	.	.		0.423	FAM21C-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
PCDH15	65217	hgsc.bcm.edu	37	10	55912909	55912909	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:55912909A>T	ENST00000320301.6	-	14	2129	c.1735T>A	c.(1735-1737)Tac>Aac	p.Y579N	PCDH15_ENST00000373965.2_Missense_Mutation_p.Y586N|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000373955.1_Missense_Mutation_p.Y579N|PCDH15_ENST00000409834.1_Missense_Mutation_p.Y190N|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000361849.3_Missense_Mutation_p.Y579N|PCDH15_ENST00000373957.3_Missense_Mutation_p.Y557N|PCDH15_ENST00000395438.1_Missense_Mutation_p.Y579N|PCDH15_ENST00000437009.1_Missense_Mutation_p.Y579N|PCDH15_ENST00000395445.1_Missense_Mutation_p.Y586N|PCDH15_ENST00000395433.1_Missense_Mutation_p.Y557N|PCDH15_ENST00000414778.1_Missense_Mutation_p.Y584N|PCDH15_ENST00000395430.1_Missense_Mutation_p.Y579N|PCDH15_ENST00000395446.1_Missense_Mutation_p.Y579N|PCDH15_ENST00000395432.2_Missense_Mutation_p.Y542N	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	579	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GTGAGTGCGTAAGTCCGCCCG	0.483										HNSCC(58;0.16)																											p.Y584N		Atlas-SNP	.											.	PCDH15	1715	.	0			c.T1750A						.						137.0	119.0	125.0					10																	55912909		2203	4300	6503	SO:0001583	missense	65217	exon15			GTGCGTAAGTCCG	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1735T>A	chr10.hg19:g.55912909A>T	ENSP00000322604:p.Tyr579Asn	88.0	0.0		88.0	18.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	A	16.44	3.123189	0.56613	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46	5.83	5.83	0.93111	Cadherin (5);Cadherin-like (1);	.	.	.	.	D	0.88051	0.6333	H	0.97131	3.945	0.58432	D	0.999997	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.999;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.995;0.998;0.997;0.999;0.997;0.998;0.995;0.995;0.997;0.998;0.99;0.995;0.986;0.982;0.998	D	0.91955	0.5574	9	0.87932	D	0	.	15.8727	0.79132	1.0:0.0:0.0:0.0	.	557;579;579;584;579;542;579;579;586;586;579;584;579;557;579	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	N	586;584;579;579;190;586;579;542;579;557;557;579;579;584;579;579	ENSP00000363076:Y586N;ENSP00000410304:Y584N;ENSP00000378826:Y579N;ENSP00000386693:Y190N;ENSP00000378832:Y586N;ENSP00000378833:Y579N;ENSP00000378820:Y542N;ENSP00000354950:Y579N;ENSP00000378821:Y557N;ENSP00000363068:Y557N;ENSP00000322604:Y579N;ENSP00000378818:Y579N;ENSP00000412628:Y579N;ENSP00000363066:Y579N	ENSP00000322604:Y579N	Y	-	1	0	PCDH15	55582915	1.000000	0.71417	0.192000	0.23308	0.112000	0.19704	8.740000	0.91579	2.231000	0.72958	0.528000	0.53228	TAC	.	.		0.483	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
RHOBTB1	9886	hgsc.bcm.edu	37	10	62647978	62647978	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:62647978G>A	ENST00000337910.5	-	6	1785	c.1448C>T	c.(1447-1449)aCg>aTg	p.T483M	RHOBTB1_ENST00000357917.4_Missense_Mutation_p.T483M	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	483					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					ACCCGAGAACGTTCCCTTGCT	0.468																																					p.T483M		Atlas-SNP	.											.	RHOBTB1	61	.	0			c.C1448T						.						81.0	78.0	79.0					10																	62647978		2203	4300	6503	SO:0001583	missense	9886	exon6			GAGAACGTTCCCT	AB018283	CCDS7261.1	10q22.1	2013-01-08			ENSG00000072422	ENSG00000072422		"""BTB/POZ domain containing"""	18738	protein-coding gene	gene with protein product		607351				11222756	Standard	NM_014836		Approved	KIAA0740	uc001jlh.3	O94844	OTTHUMG00000018292	ENST00000337910.5:c.1448C>T	chr10.hg19:g.62647978G>A	ENSP00000338671:p.Thr483Met	77.0	0.0		70.0	35.0	NM_014836		Missense_Mutation	SNP	ENST00000337910.5	hg19	CCDS7261.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.475541	0.63737	.	.	ENSG00000072422	ENST00000357917;ENST00000337910	T;T	0.68025	-0.3;-0.3	5.75	5.75	0.90469	BTB/POZ (1);BTB/POZ fold (2);	0.066716	0.64402	D	0.000008	D	0.83055	0.5171	M	0.80746	2.51	0.58432	D	0.999999	D	0.89917	1.0	D	0.79108	0.992	T	0.80854	-0.1196	10	0.34782	T	0.22	.	19.9525	0.97208	0.0:0.0:1.0:0.0	.	483	O94844	RHBT1_HUMAN	M	483	ENSP00000350595:T483M;ENSP00000338671:T483M	ENSP00000338671:T483M	T	-	2	0	RHOBTB1	62317984	1.000000	0.71417	0.955000	0.39395	0.687000	0.40016	7.631000	0.83237	2.719000	0.93026	0.655000	0.94253	ACG	.	.		0.468	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1		
DDX21	9188	hgsc.bcm.edu	37	10	70730090	70730090	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:70730090A>T	ENST00000354185.4	+	8	1468	c.1370A>T	c.(1369-1371)aAt>aTt	p.N457I		NM_001256910.1|NM_004728.3	NP_001243839.1|NP_004719.2	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 21	457	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|osteoblast differentiation (GO:0001649)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	20						CTGTCCCAGAATTCAGCTATA	0.453																																					p.N457I		Atlas-SNP	.											.	DDX21	57	.	0			c.A1370T						.						68.0	66.0	67.0					10																	70730090		2203	4300	6503	SO:0001583	missense	9188	exon8			CCCAGAATTCAGC	U41387	CCDS31211.1, CCDS73144.1	10q21	2013-05-13	2012-02-23		ENSG00000165732	ENSG00000165732		"""DEAD-boxes"""	2744	protein-coding gene	gene with protein product		606357	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 21"""			8614622, 18180292	Standard	NM_004728		Approved	RH-II/GU, GURDB	uc001jov.2	Q9NR30	OTTHUMG00000018366	ENST00000354185.4:c.1370A>T	chr10.hg19:g.70730090A>T	ENSP00000346120:p.Asn457Ile	73.0	0.0		91.0	14.0	NM_004728	B2RDL0|Q13436|Q5VX41|Q68D35	Missense_Mutation	SNP	ENST00000354185.4	hg19	CCDS31211.1	.	.	.	.	.	.	.	.	.	.	A	17.88	3.496376	0.64186	.	.	ENSG00000165732	ENST00000354185	T	0.04406	3.63	5.73	-0.928	0.10448	Helicase, C-terminal (2);	0.172541	0.64402	D	0.000009	T	0.05456	0.0144	N	0.16478	0.41	0.44966	D	0.997984	P	0.52692	0.955	P	0.55871	0.786	T	0.44436	-0.9328	10	0.52906	T	0.07	-27.1742	6.759	0.23530	0.4783:0.1307:0.391:0.0	.	457	Q9NR30	DDX21_HUMAN	I	457	ENSP00000346120:N457I	ENSP00000346120:N457I	N	+	2	0	DDX21	70400096	0.987000	0.35691	0.091000	0.20842	0.625000	0.37756	2.869000	0.48444	-0.105000	0.12132	0.533000	0.62120	AAT	.	.		0.453	DDX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048374.1	NM_004728	
TDRD1	56165	hgsc.bcm.edu	37	10	115959029	115959029	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:115959029T>C	ENST00000369280.1	+	4	942	c.482T>C	c.(481-483)tTa>tCa	p.L161S	TDRD1_ENST00000422662.1_5'UTR|TDRD1_ENST00000369282.1_Missense_Mutation_p.L161S|TDRD1_ENST00000251864.2_Missense_Mutation_p.L161S|TDRD1_ENST00000369281.2_Missense_Mutation_p.L161S			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	161					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		TTCACCTCCTTAGGACCTCCT	0.418																																					p.L161S		Atlas-SNP	.											.	TDRD1	126	.	0			c.T482C						.						149.0	137.0	141.0					10																	115959029		2203	4300	6503	SO:0001583	missense	56165	exon4			CCTCCTTAGGACC	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"""Tudor domain containing"""	11712	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.1"""	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.482T>C	chr10.hg19:g.115959029T>C	ENSP00000358286:p.Leu161Ser	150.0	0.0		161.0	86.0	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Missense_Mutation	SNP	ENST00000369280.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.12	3.307334	0.60305	.	.	ENSG00000095627	ENST00000369282;ENST00000251864;ENST00000369281;ENST00000369280	T;T;T;T	0.20881	2.93;2.9;2.04;2.93	6.05	6.05	0.98169	.	0.252959	0.34046	N	0.004315	T	0.37046	0.0989	L	0.36672	1.1	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;1.0	D;D;D;D	0.91635	0.997;0.997;0.999;0.992	T	0.08006	-1.0743	10	0.59425	D	0.04	-12.3224	14.1164	0.65156	0.0:0.0:0.0:1.0	.	161;161;161;161	Q9BXT4;B7WPM2;Q9BXT4-3;Q9BXT4-2	TDRD1_HUMAN;.;.;.	S	161	ENSP00000358288:L161S;ENSP00000251864:L161S;ENSP00000358287:L161S;ENSP00000358286:L161S	ENSP00000251864:L161S	L	+	2	0	TDRD1	115949019	0.982000	0.34865	0.994000	0.49952	0.396000	0.30629	4.890000	0.63178	2.320000	0.78422	0.528000	0.53228	TTA	.	.		0.418	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2		
VWA2	340706	hgsc.bcm.edu	37	10	116048949	116048949	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:116048949G>T	ENST00000392982.3	+	12	2073	c.1823G>T	c.(1822-1824)gGc>gTc	p.G608V	VWA2_ENST00000603594.1_Missense_Mutation_p.G608V			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	608	VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		GGTGGGGTGGGCTCAGCCGGC	0.657																																					p.G608V		Atlas-SNP	.											.	VWA2	64	.	0			c.G1823T						.						32.0	30.0	31.0					10																	116048949		2201	4300	6501	SO:0001583	missense	340706	exon12			GGGTGGGCTCAGC	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.1823G>T	chr10.hg19:g.116048949G>T	ENSP00000376708:p.Gly608Val	45.0	0.0		30.0	15.0	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	hg19		.	.	.	.	.	.	.	.	.	.	G	15.76	2.929055	0.52759	.	.	ENSG00000165816	ENST00000392982;ENST00000298715	T	0.77877	-1.13	5.29	5.29	0.74685	von Willebrand factor, type A (3);	0.061486	0.64402	D	0.000005	D	0.84973	0.5591	M	0.66939	2.045	0.58432	D	0.999998	P;D;D	0.71674	0.876;0.998;0.998	P;D;P	0.65323	0.734;0.934;0.892	D	0.86107	0.1560	10	0.66056	D	0.02	.	12.7097	0.57082	0.0:0.2158:0.7842:0.0	.	304;608;608	Q5GFL6-3;Q5GFL6;Q5GFL6-2	.;VWA2_HUMAN;.	V	608	ENSP00000376708:G608V	ENSP00000298715:G608V	G	+	2	0	VWA2	116038939	1.000000	0.71417	0.901000	0.35422	0.454000	0.32378	3.872000	0.56085	2.460000	0.83146	0.655000	0.94253	GGC	.	.		0.657	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
OR56B1	387748	hgsc.bcm.edu	37	11	5758461	5758461	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:5758461T>A	ENST00000317121.3	+	1	781	c.715T>A	c.(715-717)Tca>Aca	p.S239T	TRIM5_ENST00000380027.1_Intron	NM_001005180.2	NP_001005180.1	Q8NGI3	O56B1_HUMAN	olfactory receptor, family 56, subfamily B, member 1	239						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	13		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.086)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.184)		TAGACTGAACTCAGCTGAAGC	0.418																																					p.S239T		Atlas-SNP	.											.	OR56B1	38	.	0			c.T715A						.						128.0	122.0	124.0					11																	5758461		2201	4297	6498	SO:0001583	missense	387748	exon1			CTGAACTCAGCTG	BK004386	CCDS31395.1	11p15.4	2012-08-09		2004-03-10	ENSG00000181023	ENSG00000181023		"""GPCR / Class A : Olfactory receptors"""	15245	protein-coding gene	gene with protein product				OR56B1P			Standard	NM_001005180		Approved		uc001mbt.2	Q8NGI3	OTTHUMG00000066891	ENST00000317121.3:c.715T>A	chr11.hg19:g.5758461T>A	ENSP00000322939:p.Ser239Thr	56.0	0.0		53.0	24.0	NM_001005180	B2RNY6|B3KV42|Q6IF76	Missense_Mutation	SNP	ENST00000317121.3	hg19	CCDS31395.1	.	.	.	.	.	.	.	.	.	.	T	16.14	3.039125	0.55003	.	.	ENSG00000181023	ENST00000317121	T	0.00325	8.1	5.87	5.87	0.94306	GPCR, rhodopsin-like superfamily (1);	0.215458	0.23303	U	0.049649	T	0.00637	0.0021	M	0.83692	2.655	0.09310	N	1	D	0.59357	0.985	D	0.66847	0.947	T	0.46484	-0.9188	10	0.59425	D	0.04	.	9.5113	0.39078	0.1572:0.0:0.0:0.8428	.	239	Q8NGI3	O56B1_HUMAN	T	239	ENSP00000322939:S239T	ENSP00000322939:S239T	S	+	1	0	OR56B1	5715037	0.460000	0.25776	0.054000	0.19295	0.923000	0.55619	2.027000	0.41078	2.253000	0.74438	0.533000	0.62120	TCA	.	.		0.418	OR56B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143354.1	NM_001005180	
MICAL2	9645	hgsc.bcm.edu	37	11	12265545	12265545	+	Silent	SNP	C	C	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:12265545C>T	ENST00000256194.4	+	21	2958	c.2670C>T	c.(2668-2670)ctC>ctT	p.L890L	MICAL2_ENST00000342902.5_Silent_p.L890L|MICAL2_ENST00000379612.3_Intron|MICAL2_ENST00000527546.1_Intron|MICAL2_ENST00000537344.1_Intron	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	890					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		ATAAACTACTCTCTAAAGGCC	0.478																																					p.L890L		Atlas-SNP	.											.	MICAL2	114	.	0			c.C2670T						.						327.0	283.0	298.0					11																	12265545		2201	4294	6495	SO:0001819	synonymous_variant	9645	exon21			ACTACTCTCTAAA	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.2670C>T	chr11.hg19:g.12265545C>T		112.0	0.0		133.0	10.0	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	hg19	CCDS7809.1																																																																																			.	.		0.478	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
SAA4	6291	hgsc.bcm.edu	37	11	18253952	18253952	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:18253952T>C	ENST00000278222.4	-	3	400	c.220A>G	c.(220-222)Aaa>Gaa	p.K74E	SAA2-SAA4_ENST00000524555.1_RNA	NM_006512.3	NP_006503.2	P35542	SAA4_HUMAN	serum amyloid A4, constitutive	74					acute-phase response (GO:0006953)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(1)|stomach(1)	13						CTGATGAGTTTAGCAGCCCAG	0.507																																					p.K152E		Atlas-SNP	.											.	.	.	.	0			c.A454G						.						164.0	164.0	164.0					11																	18253952		2199	4293	6492	SO:0001583	missense	100528017	exon5			TGAGTTTAGCAGC	M81349	CCDS7832.1	11p15.1-p14	2008-07-21			ENSG00000148965	ENSG00000148965			10516	protein-coding gene	gene with protein product		104752				8325654	Standard	NM_006512		Approved	C-SAA, CSAA		P35542	OTTHUMG00000166483	ENST00000278222.4:c.220A>G	chr11.hg19:g.18253952T>C	ENSP00000278222:p.Lys74Glu	113.0	0.0		120.0	37.0	NM_001199744	Q6FHJ4	Missense_Mutation	SNP	ENST00000278222.4	hg19	CCDS7832.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.456689	0.26161	.	.	ENSG00000148965	ENST00000278222	T	0.10099	2.91	3.58	0.437	0.16555	.	.	.	.	.	T	0.04407	0.0121	N	0.11284	0.12	0.24179	N	0.995592	B	0.31256	0.316	B	0.28991	0.097	T	0.44832	-0.9302	9	0.13470	T	0.59	9.7551	5.3805	0.16189	0.0:0.3737:0.0:0.6263	.	74	P35542	SAA4_HUMAN	E	74	ENSP00000278222:K74E	ENSP00000278222:K74E	K	-	1	0	SAA4	18210528	0.000000	0.05858	0.340000	0.25575	0.732000	0.41865	-0.462000	0.06704	0.292000	0.22492	0.383000	0.25322	AAA	.	.		0.507	SAA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389988.1	NM_006512	
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077115	19077115	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:19077115A>T	ENST00000329773.2	-	2	922	c.835T>A	c.(835-837)Tac>Aac	p.Y279N		NM_054030.2	NP_473371.1	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	279					positive regulation of cytokinesis (GO:0032467)|sensory perception of pain (GO:0019233)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide binding (GO:0042923)			NS(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	15						ACGAAGAAGTAAATGATGGGG	0.478																																					p.Y279N	GBM(198;1966 2199 4849 37227 49954)	Atlas-SNP	.											.	MRGPRX2	42	.	0			c.T835A						.						70.0	75.0	73.0					11																	19077115		2199	4293	6492	SO:0001583	missense	117194	exon2			AGAAGTAAATGAT		CCDS7847.1	11p15.1	2013-10-10			ENSG00000183695	ENSG00000183695		"""GPCR / Class A : Orphans"""	17983	protein-coding gene	gene with protein product		607228				11551509	Standard	NM_054030		Approved	MRGX2	uc001mph.3	Q96LB1	OTTHUMG00000166098	ENST00000329773.2:c.835T>A	chr11.hg19:g.19077115A>T	ENSP00000333800:p.Tyr279Asn	77.0	0.0		81.0	28.0	NM_054030	B5B0C7|Q4QXW4|Q4QXW7|Q4QXX0|Q4QXX2|Q4QXX3|Q4QXX4|Q4QXX6|Q4QXX7	Missense_Mutation	SNP	ENST00000329773.2	hg19	CCDS7847.1	.	.	.	.	.	.	.	.	.	.	.	23.9	4.472045	0.84533	.	.	ENSG00000183695	ENST00000329773	D	0.93307	-3.2	5.26	5.26	0.73747	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000026	D	0.97573	0.9205	H	0.95679	3.705	0.39544	D	0.968865	D	0.89917	1.0	D	0.91635	0.999	D	0.99387	1.0924	10	0.87932	D	0	.	13.4552	0.61195	1.0:0.0:0.0:0.0	.	279	Q96LB1	MRGX2_HUMAN	N	279	ENSP00000333800:Y279N	ENSP00000333800:Y279N	Y	-	1	0	MRGPRX2	19033691	1.000000	0.71417	0.999000	0.59377	0.942000	0.58702	7.385000	0.79763	2.343000	0.79666	0.533000	0.62120	TAC	.	.		0.478	MRGPRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387819.1	NM_054030	
OR4X1	390113	hgsc.bcm.edu	37	11	48285788	48285788	+	Nonsense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:48285788A>T	ENST00000320048.1	+	1	376	c.376A>T	c.(376-378)Aag>Tag	p.K126*		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	28						GGCCATCTGCAAGCCCTTGCA	0.552																																					p.K126X		Atlas-SNP	.											.	OR4X1	75	.	0			c.A376T						.						87.0	79.0	82.0					11																	48285788		2201	4298	6499	SO:0001587	stop_gained	390113	exon1			ATCTGCAAGCCCT	AB065544	CCDS31487.1	11p11.2	2013-10-10	2013-10-10		ENSG00000176567	ENSG00000176567		"""GPCR / Class A : Olfactory receptors"""	14854	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily X, member 1"""				Standard	NM_001004726		Approved		uc010rht.2	Q8NH49	OTTHUMG00000165301	ENST00000320048.1:c.376A>T	chr11.hg19:g.48285788A>T	ENSP00000321506:p.Lys126*	70.0	0.0		94.0	33.0	NM_001004726	Q6IF74	Nonsense_Mutation	SNP	ENST00000320048.1	hg19	CCDS31487.1	.	.	.	.	.	.	.	.	.	.	A	12.52	1.963728	0.34659	.	.	ENSG00000176567	ENST00000320048	.	.	.	4.26	4.26	0.50523	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.0635	0.30646	0.794:0.206:0.0:0.0	.	.	.	.	X	126	.	ENSP00000321506:K126X	K	+	1	0	OR4X1	48242364	0.118000	0.22208	1.000000	0.80357	0.229000	0.25112	1.709000	0.37909	1.911000	0.55334	0.456000	0.33151	AAG	.	.		0.552	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726	
OR4C11	219429	hgsc.bcm.edu	37	11	55371245	55371245	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:55371245C>T	ENST00000302231.4	-	1	629	c.605G>A	c.(604-606)gGg>gAg	p.G202E		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						GCAAATTGCCCCACTGTTAGA	0.403																																					p.G202E		Atlas-SNP	.											.	OR4C11	73	.	0			c.G605A						.						88.0	73.0	78.0					11																	55371245		2179	4012	6191	SO:0001583	missense	219429	exon1			ATTGCCCCACTGT	AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"""GPCR / Class A : Olfactory receptors"""	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.605G>A	chr11.hg19:g.55371245C>T	ENSP00000306651:p.Gly202Glu	115.0	0.0		161.0	25.0	NM_001004700	B9EIL4|Q8NGL8	Missense_Mutation	SNP	ENST00000302231.4	hg19	CCDS31503.1	.	.	.	.	.	.	.	.	.	.	C	12.43	1.935284	0.34189	.	.	ENSG00000172188	ENST00000302231	T	0.38401	1.14	4.34	4.34	0.51931	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	U	0.000143	T	0.64940	0.2644	M	0.89095	3.005	0.27902	N	0.938934	D	0.89917	1.0	D	0.83275	0.996	T	0.63377	-0.6651	10	0.87932	D	0	.	14.0633	0.64812	0.0:1.0:0.0:0.0	.	202	Q6IEV9	OR4CB_HUMAN	E	202	ENSP00000306651:G202E	ENSP00000306651:G202E	G	-	2	0	OR4C11	55127821	0.000000	0.05858	0.917000	0.36280	0.049000	0.14656	-0.188000	0.09642	2.425000	0.82216	0.478000	0.44815	GGG	.	.		0.403	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700	
OR4C6	219432	hgsc.bcm.edu	37	11	55433436	55433436	+	Missense_Mutation	SNP	T	T	C	rs367617569		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:55433436T>C	ENST00000314259.3	+	1	823	c.794T>C	c.(793-795)aTa>aCa	p.I265T		NM_001004704.1	NP_001004704.1	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C, member 6	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|lung(49)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	71						ACTCACCCCATAGACAAGGCA	0.473																																					p.I265T		Atlas-SNP	.											.	OR4C6	114	.	0			c.T794C						.	T	THR/ILE	0,4400		0,0,2200	105.0	102.0	103.0		794	2.9	0.9	11		103	1,8591	1.2+/-3.3	0,1,4295	no	missense	OR4C6	NM_001004704.1	89	0,1,6495	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging	265/310	55433436	1,12991	2200	4296	6496	SO:0001583	missense	219432	exon1			ACCCCATAGACAA	CR593785	CCDS31506.1	11q11	2012-08-09			ENSG00000181903	ENSG00000181903		"""GPCR / Class A : Olfactory receptors"""	14743	protein-coding gene	gene with protein product							Standard	NM_001004704		Approved		uc010rik.2	Q8NH72	OTTHUMG00000166800	ENST00000314259.3:c.794T>C	chr11.hg19:g.55433436T>C	ENSP00000324769:p.Ile265Thr	76.0	0.0		74.0	27.0	NM_001004704	B2RP11|Q6IFD2	Missense_Mutation	SNP	ENST00000314259.3	hg19	CCDS31506.1	.	.	.	.	.	.	.	.	.	.	T	12.40	1.927195	0.34002	0.0	1.16E-4	ENSG00000181903	ENST00000314259	T	0.00115	8.71	4.07	2.86	0.33363	GPCR, rhodopsin-like superfamily (1);	0.167338	0.27927	N	0.017287	T	0.00144	0.0004	N	0.16368	0.405	0.09310	N	1	P	0.42296	0.775	P	0.48873	0.593	T	0.42682	-0.9437	10	0.51188	T	0.08	.	4.637	0.12530	0.1705:0.0995:0.0:0.7299	.	265	Q8NH72	OR4C6_HUMAN	T	265	ENSP00000324769:I265T	ENSP00000324769:I265T	I	+	2	0	OR4C6	55190012	0.000000	0.05858	0.937000	0.37676	0.540000	0.34992	-5.249000	0.00137	1.484000	0.48361	0.444000	0.29173	ATA	.	.		0.473	OR4C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391504.1	NM_001004704	
OR5AS1	219447	hgsc.bcm.edu	37	11	55798176	55798176	+	Silent	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:55798176T>A	ENST00000313555.1	+	1	282	c.282T>A	c.(280-282)ccT>ccA	p.P94P		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	94						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					GCATCTCTCCTTATGGGTGTG	0.433																																					p.P94P		Atlas-SNP	.											.	OR5AS1	121	.	0			c.T282A						.						87.0	77.0	80.0					11																	55798176		2201	4296	6497	SO:0001819	synonymous_variant	219447	exon1			CTCTCCTTATGGG	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"""GPCR / Class A : Olfactory receptors"""	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.282T>A	chr11.hg19:g.55798176T>A		46.0	0.0		75.0	35.0	NM_001001921	Q6IFB8	Silent	SNP	ENST00000313555.1	hg19	CCDS31516.1																																																																																			.	.		0.433	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921	
OR8J3	81168	hgsc.bcm.edu	37	11	55905001	55905001	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:55905001T>A	ENST00000301529.1	-	1	193	c.194A>T	c.(193-195)cAt>cTt	p.H65L		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	65						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					GATAGCTAGATGTCTCAGGAA	0.438																																					p.H65L		Atlas-SNP	.											.	OR8J3	112	.	0			c.A194T						.						144.0	140.0	141.0					11																	55905001		2201	4296	6497	SO:0001583	missense	81168	exon1			GCTAGATGTCTCA		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"""GPCR / Class A : Olfactory receptors"""	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.194A>T	chr11.hg19:g.55905001T>A	ENSP00000301529:p.His65Leu	94.0	0.0		133.0	57.0	NM_001004064	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	hg19	CCDS31520.1	.	.	.	.	.	.	.	.	.	.	T	10.12	1.262808	0.23051	.	.	ENSG00000167822	ENST00000301529	T	0.02944	4.1	3.26	1.81	0.25067	GPCR, rhodopsin-like superfamily (1);	0.185693	0.38058	N	0.001835	T	0.07503	0.0189	M	0.81802	2.56	0.09310	N	1	P	0.51653	0.947	P	0.49451	0.611	T	0.07829	-1.0752	10	0.87932	D	0	.	8.367	0.32393	0.2358:0.0:0.0:0.7642	.	65	Q8NGG0	OR8J3_HUMAN	L	65	ENSP00000301529:H65L	ENSP00000301529:H65L	H	-	2	0	OR8J3	55661577	0.000000	0.05858	0.002000	0.10522	0.070000	0.16714	0.882000	0.28186	1.268000	0.44264	0.240000	0.17902	CAT	.	.		0.438	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064	
OR5M10	390167	hgsc.bcm.edu	37	11	56344760	56344760	+	Silent	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:56344760A>T	ENST00000526812.2	-	1	503	c.438T>A	c.(436-438)acT>acA	p.T146T		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	146						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(2)	25						TGTAAGGCACAGTGACCAGAG	0.453																																					p.T146T		Atlas-SNP	.											.	OR5M10	56	.	0			c.T438A						.						182.0	172.0	175.0					11																	56344760		2017	4203	6220	SO:0001819	synonymous_variant	390167	exon1			AGGCACAGTGACC	BK004515	CCDS53630.1	11q11	2012-08-09				ENSG00000254834		"""GPCR / Class A : Olfactory receptors"""	15290	protein-coding gene	gene with protein product							Standard	NM_001004741		Approved		uc001niz.1	Q6IEU7		ENST00000526812.2:c.438T>A	chr11.hg19:g.56344760A>T		117.0	0.0		157.0	60.0	NM_001004741	B9EIL9	Silent	SNP	ENST00000526812.2	hg19	CCDS53630.1																																																																																			.	.		0.453	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741	
PRG3	10394	hgsc.bcm.edu	37	11	57147137	57147137	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:57147137A>T	ENST00000287143.2	-	3	314	c.205T>A	c.(205-207)Tgt>Agt	p.C69S		NM_006093.3	NP_006084.2	Q8TBJ4	LPPR1_HUMAN	proteoglycan 3	0					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			large_intestine(3)|lung(5)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	13						TTGTCTTGACAGGCAGAAGCC	0.542																																					p.C69S	Melanoma(154;1456 2519 19358 45229)	Atlas-SNP	.											.	PRG3	35	.	0			c.T205A						.						118.0	99.0	105.0					11																	57147137		2201	4296	6497	SO:0001583	missense	10394	exon3			CTTGACAGGCAGA	AF132209	CCDS7954.1	11q12.1	2008-02-05			ENSG00000156575	ENSG00000156575			9363	protein-coding gene	gene with protein product		606814				10318872, 11170744	Standard	NM_006093		Approved	MBPH	uc001njv.2	Q9Y2Y8	OTTHUMG00000167026	ENST00000287143.2:c.205T>A	chr11.hg19:g.57147137A>T	ENSP00000287143:p.Cys69Ser	81.0	0.0		114.0	33.0	NM_006093	Q5VX23|Q9NXE2	Missense_Mutation	SNP	ENST00000287143.2	hg19	CCDS7954.1	.	.	.	.	.	.	.	.	.	.	A	6.244	0.413080	0.11812	.	.	ENSG00000156575	ENST00000287143	T	0.38240	1.15	4.61	-9.23	0.00672	.	2.082990	0.02179	N	0.060318	T	0.10809	0.0264	N	0.02916	-0.46	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.13926	-1.0491	10	0.20046	T	0.44	4.6396	0.8412	0.01150	0.154:0.2949:0.2088:0.3423	.	69	Q9Y2Y8	PRG3_HUMAN	S	69	ENSP00000287143:C69S	ENSP00000287143:C69S	C	-	1	0	PRG3	56903713	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.816000	0.04477	-1.358000	0.02177	-1.476000	0.00998	TGT	.	.		0.542	PRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392467.1	NM_006093	
PCNXL3	399909	hgsc.bcm.edu	37	11	65391690	65391690	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:65391690A>T	ENST00000355703.3	+	14	3108	c.2569A>T	c.(2569-2571)Agc>Tgc	p.S857C		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	857						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						GATCGCGTACAGCCGTCCTGT	0.632																																					p.S857C		Atlas-SNP	.											.	PCNXL3	140	.	0			c.A2569T						.						55.0	61.0	59.0					11																	65391690		2182	4273	6455	SO:0001583	missense	399909	exon14			GCGTACAGCCGTC	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.2569A>T	chr11.hg19:g.65391690A>T	ENSP00000347931:p.Ser857Cys	26.0	0.0		42.0	14.0	NM_032223	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	hg19	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.756911	0.89843	.	.	ENSG00000197136	ENST00000355703	T	0.60424	0.19	4.75	4.75	0.60458	.	.	.	.	.	T	0.74906	0.3778	M	0.81341	2.54	0.49051	D	0.999749	D	0.69078	0.997	D	0.70935	0.971	T	0.78912	-0.2017	9	0.87932	D	0	.	12.1857	0.54236	1.0:0.0:0.0:0.0	.	857	Q9H6A9	PCX3_HUMAN	C	857	ENSP00000347931:S857C	ENSP00000347931:S857C	S	+	1	0	PCNXL3	65148266	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.497000	0.90488	1.783000	0.52377	0.379000	0.24179	AGC	.	.		0.632	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
GRIA4	2893	hgsc.bcm.edu	37	11	105769114	105769114	+	Silent	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:105769114A>T	ENST00000530497.1	+	6	846	c.846A>T	c.(844-846)ctA>ctT	p.L282L	GRIA4_ENST00000393125.2_Silent_p.L282L|GRIA4_ENST00000428631.2_Silent_p.L282L|GRIA4_ENST00000393127.2_Silent_p.L282L|GRIA4_ENST00000282499.5_Silent_p.L282L|GRIA4_ENST00000525187.1_Silent_p.L282L			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	282					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		GGAAGAAACTAGATCAGAGAG	0.348																																					p.L282L		Atlas-SNP	.											.	GRIA4	380	.	0			c.A846T						.						60.0	62.0	61.0					11																	105769114		2202	4299	6501	SO:0001819	synonymous_variant	2893	exon7			GAAACTAGATCAG	U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4574	protein-coding gene	gene with protein product		138246	"""glutamate receptor, ionotrophic, AMPA 4"""	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.846A>T	chr11.hg19:g.105769114A>T		151.0	0.0		173.0	72.0	NM_001077244	Q86XE8	Silent	SNP	ENST00000530497.1	hg19	CCDS8333.1																																																																																			.	.		0.348	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1		
SCN3B	55800	hgsc.bcm.edu	37	11	123524465	123524465	+	Silent	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:123524465A>T	ENST00000392770.2	-	1	847	c.45T>A	c.(43-45)ctT>ctA	p.L15L	SCN3B_ENST00000299333.3_Silent_p.L15L|SCN3B_ENST00000530277.1_Silent_p.L15L	NM_018400.3	NP_060870.1	Q9NY72	SCN3B_HUMAN	sodium channel, voltage-gated, type III, beta subunit	15					atrial cardiac muscle cell action potential (GO:0086014)|axon guidance (GO:0007411)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|positive regulation of heart rate (GO:0010460)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|ventricular cardiac muscle cell action potential (GO:0086005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|skin(2)	26		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)	Valproic Acid(DB00313)|Zonisamide(DB00909)	CCCAGTAGATAAGCACGAGAG	0.493																																					p.L15L		Atlas-SNP	.											.	SCN3B	53	.	0			c.T45A						.						202.0	203.0	203.0					11																	123524465		2202	4299	6501	SO:0001819	synonymous_variant	55800	exon1			GTAGATAAGCACG	AJ243396	CCDS8442.1	11q24.1	2014-09-17	2012-02-28		ENSG00000166257	ENSG00000166257		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"", ""Immunoglobulin superfamily / V-set domain containing"""	20665	protein-coding gene	gene with protein product		608214	"""sodium channel, voltage-gated, type III, beta"""			10688874	Standard	XR_428980		Approved	HSA243396	uc001pzb.1	Q9NY72	OTTHUMG00000166006	ENST00000392770.2:c.45T>A	chr11.hg19:g.123524465A>T		77.0	0.0		70.0	36.0	NM_018400	A5H1I5|Q17RL3|Q9ULR2	Silent	SNP	ENST00000392770.2	hg19	CCDS8442.1																																																																																			.	.		0.493	SCN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387412.1	NM_018400	
PDE3A	5139	hgsc.bcm.edu	37	12	20523005	20523005	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:20523005G>T	ENST00000359062.3	+	1	827	c.787G>T	c.(787-789)Gcg>Tcg	p.A263S	RP11-284H19.1_ENST00000535755.1_RNA	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	263					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	GCCGCAGTCCGCGGAGGCGGC	0.612																																					p.A263S		Atlas-SNP	.											.	PDE3A	184	.	0			c.G787T						.						31.0	36.0	34.0					12																	20523005		2198	4299	6497	SO:0001583	missense	5139	exon1			CAGTCCGCGGAGG		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"""Phosphodiesterases"""	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.787G>T	chr12.hg19:g.20523005G>T	ENSP00000351957:p.Ala263Ser	29.0	0.0		37.0	22.0	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	hg19	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.741618	0.30865	.	.	ENSG00000172572	ENST00000359062	T	0.61742	0.08	4.06	-1.52	0.08637	.	3.626890	0.00465	N	0.000107	T	0.26810	0.0656	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.10132	-1.0643	10	0.20519	T	0.43	.	2.1787	0.03868	0.1553:0.1102:0.3239:0.4106	.	263	Q14432	PDE3A_HUMAN	S	263	ENSP00000351957:A263S	ENSP00000351957:A263S	A	+	1	0	PDE3A	20414272	0.000000	0.05858	0.665000	0.29768	0.995000	0.86356	-0.540000	0.06106	-0.182000	0.10602	0.650000	0.86243	GCG	.	.		0.612	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2		
NR4A1	3164	hgsc.bcm.edu	37	12	52452600	52452600	+	Missense_Mutation	SNP	G	G	C	rs577412593		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:52452600G>C	ENST00000243050.1	+	8	1983	c.1669G>C	c.(1669-1671)Ggc>Cgc	p.G557R	NR4A1_ENST00000360284.3_Missense_Mutation_p.G570R|NR4A1_ENST00000394824.2_Missense_Mutation_p.G557R|NR4A1_ENST00000394825.1_Missense_Mutation_p.G557R|NR4A1_ENST00000550082.1_Missense_Mutation_p.G570R|RP11-1100L3.8_ENST00000564363.1_lincRNA|NR4A1_ENST00000545748.1_Missense_Mutation_p.G611R	NM_002135.4	NP_002126.2	P22736	NR4A1_HUMAN	nuclear receptor subfamily 4, group A, member 1	557					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell chemotaxis (GO:0035767)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)	16				BRCA - Breast invasive adenocarcinoma(357;0.0967)		ACGTCTGTTGGGCAAACTGCC	0.652																																					p.G570R		Atlas-SNP	.											.	NR4A1	77	.	0			c.G1708C						.						46.0	42.0	44.0					12																	52452600		2203	4300	6503	SO:0001583	missense	3164	exon8			CTGTTGGGCAAAC	L13740	CCDS8818.1, CCDS55828.1, CCDS73471.1	12q13	2013-01-16			ENSG00000123358	ENSG00000123358		"""Nuclear hormone receptors"""	7980	protein-coding gene	gene with protein product		139139		HMR, GFRP1		2626032	Standard	NM_002135		Approved	TR3, N10, NAK-1, NGFIB, NUR77	uc001rzt.3	P22736	OTTHUMG00000150393	ENST00000243050.1:c.1669G>C	chr12.hg19:g.52452600G>C	ENSP00000243050:p.Gly557Arg	44.0	0.0		41.0	23.0	NM_001202233	B4DML7|Q15627|Q53Y00|Q6IBU8	Missense_Mutation	SNP	ENST00000243050.1	hg19	CCDS8818.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.849188	0.51270	.	.	ENSG00000123358	ENST00000360284;ENST00000545748;ENST00000550082;ENST00000243050;ENST00000394825;ENST00000394824	D;D;D;D;D;D	0.96587	-4.06;-4.06;-4.06;-4.06;-4.06;-4.06	5.06	5.06	0.68205	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.052982	0.85682	D	0.000000	D	0.97424	0.9157	M	0.81802	2.56	0.54753	D	0.999986	D;B	0.76494	0.999;0.307	P;B	0.62435	0.902;0.095	D	0.96736	0.9543	10	0.51188	T	0.08	.	11.7688	0.51945	0.0846:0.0:0.9154:0.0	.	570;557	B4DML7;P22736	.;NR4A1_HUMAN	R	570;611;570;557;557;557	ENSP00000353427:G570R;ENSP00000440864:G611R;ENSP00000449539:G570R;ENSP00000243050:G557R;ENSP00000378302:G557R;ENSP00000378301:G557R	ENSP00000243050:G557R	G	+	1	0	NR4A1	50738867	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.564000	0.67359	2.813000	0.96785	0.655000	0.94253	GGC	.	.		0.652	NR4A1-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317922.2		
LGR5	8549	hgsc.bcm.edu	37	12	71977559	71977560	+	Nonsense_Mutation	DNP	CC	CC	AA			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:71977559_71977560CC>AA	ENST00000266674.5	+	18	2080_2081	c.1769_1770CC>AA	c.(1768-1770)tCC>tAA	p.S590*	RP11-186F10.2_ENST00000546601.1_RNA|LGR5_ENST00000540815.2_Nonsense_Mutation_p.S566*|LGR5_ENST00000536515.1_Nonsense_Mutation_p.S518*			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	590					G-protein coupled receptor signaling pathway (GO:0007186)|inner ear development (GO:0048839)|positive regulation of canonical Wnt signaling pathway (GO:0090263)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)		NUP107/LGR5(2)	endometrium(2)|kidney(3)|large_intestine(2)|lung(24)|ovary(1)|pancreas(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	48						CTGTACATTTCCCCCATTAAAC	0.5																																					p.S590Y|p.S590S		Atlas-SNP	.											.	LGR5	103	.	0			c.C1769A|c.C1770A						.																																			SO:0001587	stop_gained	8549	exon18			ACATTTCCCCCAT|CATTTCCCCCATT	AF062006	CCDS9000.1, CCDS61194.1, CCDS61195.1	12q22-q23	2012-08-21	2011-01-25	2004-11-12				"""GPCR / Class A : Orphans"""	4504	protein-coding gene	gene with protein product		606667	"""G protein-coupled receptor 49"", ""leucine-rich repeat-containing G protein-coupled receptor 5"""	GPR67, GPR49		9642114	Standard	NM_003667		Approved	HG38, FEX	uc001swl.4	O75473	OTTHUMG00000169543	Exception_encountered	chr12.hg19:g.71977559_71977560delinsAA	ENSP00000266674:p.Ser590*	148.0|146.0	0.0		161.0|160.0	67.0|66.0	NM_003667	D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Missense_Mutation|Silent	SNP	ENST00000266674.5	hg19	CCDS9000.1																																																																																			.	.		0.500	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667	
LRRIQ1	84125	hgsc.bcm.edu	37	12	85554467	85554467	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:85554467G>T	ENST00000393217.2	+	24	4858	c.4797G>T	c.(4795-4797)caG>caT	p.Q1599H	LRRIQ1_ENST00000528777.3_3'UTR	NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1599										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		AGATGGTACAGCCCAGAAGAG	0.308																																					p.Q1599H		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.G4797T						.						120.0	108.0	112.0					12																	85554467		1823	4079	5902	SO:0001583	missense	84125	exon24			GGTACAGCCCAGA	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.4797G>T	chr12.hg19:g.85554467G>T	ENSP00000376910:p.Gln1599His	68.0	0.0		105.0	44.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	hg19	CCDS41816.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.853|1.853	-0.464480|-0.464480	0.04476|0.04476	.|.	.|.	ENSG00000133640|ENSG00000133640	ENST00000393217|ENST00000526363	T|.	0.53640|.	0.61|.	4.77|4.77	-1.33|-1.33	0.09172|0.09172	.|.	.|.	.|.	.|.	.|.	T|T	0.19604|0.19604	0.0471|0.0471	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	B|.	0.14805|.	0.011|.	B|.	0.14023|.	0.01|.	T|T	0.25398|0.25398	-1.0133|-1.0133	9|5	0.41790|.	T|.	0.15|.	.|.	2.7392|2.7392	0.05249|0.05249	0.234:0.12:0.5228:0.1232|0.234:0.12:0.5228:0.1232	.|.	1599|.	Q96JM4|.	LRIQ1_HUMAN|.	H|I	1599|20	ENSP00000376910:Q1599H|.	ENSP00000376910:Q1599H|.	Q|S	+|+	3|2	2|0	LRRIQ1|LRRIQ1	84078598|84078598	0.001000|0.001000	0.12720|0.12720	0.015000|0.015000	0.15790|0.15790	0.347000|0.347000	0.29111|0.29111	0.366000|0.366000	0.20365|0.20365	-0.136000|-0.136000	0.11475|0.11475	0.557000|0.557000	0.71058|0.71058	CAG|AGC	.	.		0.308	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
AMDHD1	144193	hgsc.bcm.edu	37	12	96360279	96360279	+	Missense_Mutation	SNP	T	T	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:96360279T>G	ENST00000266736.2	+	8	1292	c.1186T>G	c.(1186-1188)Tca>Gca	p.S396A		NM_152435.2	NP_689648.2	Q96NU7	HUTI_HUMAN	amidohydrolase domain containing 1	396					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	imidazolonepropionase activity (GO:0050480)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|skin(1)	22						TATCATCAATTCATCCCGGTG	0.448																																					p.S396A		Atlas-SNP	.											.	AMDHD1	56	.	0			c.T1186G						.						220.0	206.0	211.0					12																	96360279		2203	4300	6503	SO:0001583	missense	144193	exon8			ATCAATTCATCCC	AB075878	CCDS9057.1	12q23.1	2006-02-02				ENSG00000139344			28577	protein-coding gene	gene with protein product							Standard	NM_152435		Approved	MGC35366	uc001tel.2	Q96NU7	OTTHUMG00000170353	ENST00000266736.2:c.1186T>G	chr12.hg19:g.96360279T>G	ENSP00000266736:p.Ser396Ala	37.0	0.0		75.0	18.0	NM_152435	A8K463|Q68CI8	Missense_Mutation	SNP	ENST00000266736.2	hg19	CCDS9057.1	.	.	.	.	.	.	.	.	.	.	T	0.369	-0.934822	0.02340	.	.	ENSG00000139344	ENST00000266736	T	0.71103	-0.54	5.82	-1.44	0.08856	Metal-dependent hydrolase, composite domain (1);	0.784314	0.12321	N	0.479276	T	0.46308	0.1386	N	0.02802	-0.49	0.24577	N	0.99389	B	0.02656	0.0	B	0.01281	0.0	T	0.13683	-1.0500	10	0.12430	T	0.62	-7.277	20.0123	0.97464	0.0:0.0:0.7636:0.2364	.	396	Q96NU7	HUTI_HUMAN	A	396	ENSP00000266736:S396A	ENSP00000266736:S396A	S	+	1	0	AMDHD1	94884410	0.173000	0.23056	0.975000	0.42487	0.390000	0.30446	-0.267000	0.08619	-0.496000	0.06650	-0.396000	0.06452	TCA	.	.		0.448	AMDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408640.1	NM_152435	
RASAL1	8437	hgsc.bcm.edu	37	12	113553065	113553065	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:113553065G>T	ENST00000261729.5	-	12	1323	c.1008C>A	c.(1006-1008)gaC>gaA	p.D336E	RASAL1_ENST00000548055.1_Missense_Mutation_p.D336E|RASAL1_ENST00000446861.3_Missense_Mutation_p.D336E|RASAL1_ENST00000546530.1_Missense_Mutation_p.D336E|RASAL1_ENST00000418411.2_5'UTR			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	336	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						GGGTGTTGGGGTCCACTGGGA	0.567																																					p.D336E		Atlas-SNP	.											.	RASAL1	89	.	0			c.C1008A						.						176.0	182.0	180.0					12																	113553065		2203	4300	6503	SO:0001583	missense	8437	exon12			GTTGGGGTCCACT	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"""Pleckstrin homology (PH) domain containing"""	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.1008C>A	chr12.hg19:g.113553065G>T	ENSP00000261729:p.Asp336Glu	93.0	0.0		153.0	40.0	NM_004658	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Missense_Mutation	SNP	ENST00000261729.5	hg19	CCDS9165.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.671794	0.29693	.	.	ENSG00000111344	ENST00000546530;ENST00000261729;ENST00000446861;ENST00000548055	T;T;T;T	0.17054	2.3;2.3;2.3;2.3	4.78	1.42	0.22433	Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.000000	0.85682	D	0.000000	T	0.25457	0.0619	L	0.42632	1.34	0.42957	D	0.994399	D;D;D;D;P;P;D	0.89917	1.0;1.0;1.0;1.0;0.46;0.655;1.0	D;D;D;D;B;P;D	0.97110	0.998;1.0;0.996;1.0;0.327;0.557;0.999	T	0.06862	-1.0803	10	0.19147	T	0.46	.	7.3437	0.26652	0.4556:0.0:0.5444:0.0	.	336;336;336;348;336;336;336	B7ZKM4;B4DG06;F8VRH9;Q59H24;F8VQX1;O95294;O95294-2	.;.;.;.;.;RASL1_HUMAN;.	E	336	ENSP00000450244:D336E;ENSP00000261729:D336E;ENSP00000395920:D336E;ENSP00000448510:D336E	ENSP00000261729:D336E	D	-	3	2	RASAL1	112037448	1.000000	0.71417	0.999000	0.59377	0.428000	0.31595	0.807000	0.27140	0.449000	0.26747	-0.424000	0.05967	GAC	.	.		0.567	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658	
SETD1B	23067	hgsc.bcm.edu	37	12	122261330	122261330	+	Silent	SNP	C	C	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:122261330C>T	ENST00000604567.1	+	12	4913	c.4845C>T	c.(4843-4845)tcC>tcT	p.S1615S	SETD1B_ENST00000542440.1_Silent_p.S1572S|SETD1B_ENST00000267197.5_Silent_p.S1572S			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	1615	Pro-rich.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						AGTGGCCCTCCGAGGCCATTC	0.677																																					p.S1572S		Atlas-SNP	.											.	SETD1B	105	.	0			c.C4716T						.						6.0	9.0	8.0					12																	122261330		682	1573	2255	SO:0001819	synonymous_variant	23067	exon12			GCCCTCCGAGGCC	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.4845C>T	chr12.hg19:g.122261330C>T		31.0	0.0		49.0	19.0	NM_015048	F6MFW1	Silent	SNP	ENST00000604567.1	hg19																																																																																				.	.		0.677	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
VPS33A	65082	hgsc.bcm.edu	37	12	122717409	122717409	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr12:122717409C>A	ENST00000267199.4	-	12	1659	c.1547G>T	c.(1546-1548)cGc>cTc	p.R516L	RP11-512M8.5_ENST00000535844.1_Missense_Mutation_p.R477L	NM_022916.4	NP_075067.2	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33 homolog A (S. cerevisiae)	516					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of developmental pigmentation (GO:0048070)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	28	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)		TGGGAGGATGCGGAGGACCTC	0.592																																					p.R516L		Atlas-SNP	.											.	VPS33A	61	.	0			c.G1547T						.						45.0	42.0	43.0					12																	122717409		2203	4300	6503	SO:0001583	missense	65082	exon12			AGGATGCGGAGGA	AK026048	CCDS9231.1	12q24.31	2008-06-23	2006-04-04		ENSG00000139719	ENSG00000139719			18179	protein-coding gene	gene with protein product		610034	"""vacuolar protein sorting 33A (yeast)"""			11250079	Standard	NM_022916		Approved		uc001ucd.3	Q96AX1	OTTHUMG00000168920	ENST00000267199.4:c.1547G>T	chr12.hg19:g.122717409C>A	ENSP00000267199:p.Arg516Leu	83.0	0.0		118.0	41.0	NM_022916	Q547V4|Q9H5Q0	Missense_Mutation	SNP	ENST00000267199.4	hg19	CCDS9231.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168288	0.78339	.	.	ENSG00000139719	ENST00000267199	T	0.29142	1.58	5.54	4.54	0.55810	.	0.052923	0.64402	D	0.000001	T	0.27832	0.0685	M	0.65498	2.005	0.80722	D	1	P	0.34587	0.458	B	0.34824	0.19	T	0.23547	-1.0185	10	0.51188	T	0.08	-24.5461	3.6122	0.08065	0.0:0.6492:0.0:0.3508	.	516	Q96AX1	VP33A_HUMAN	L	516	ENSP00000267199:R516L	ENSP00000446319:R477L	R	-	2	0	VPS33A	121283362	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.182000	0.71995	2.596000	0.87737	0.655000	0.94253	CGC	.	.		0.592	VPS33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401607.2		
SACS	26278	hgsc.bcm.edu	37	13	23910455	23910455	+	Silent	SNP	T	T	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr13:23910455T>G	ENST00000382292.3	-	9	7833	c.7560A>C	c.(7558-7560)acA>acC	p.T2520T	SACS_ENST00000382298.3_Silent_p.T2520T|SACS_ENST00000402364.1_Silent_p.T1770T			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2520					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GCCCAAATTCTGTGCCAAGTG	0.398																																					p.T2520T		Atlas-SNP	.											.	SACS	871	.	0			c.A7560C						.						118.0	114.0	115.0					13																	23910455		2203	4299	6502	SO:0001819	synonymous_variant	26278	exon10			AAATTCTGTGCCA	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.7560A>C	chr13.hg19:g.23910455T>G		98.0	0.0		77.0	26.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	hg19	CCDS9300.2																																																																																			.	.		0.398	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
PARP4	143	hgsc.bcm.edu	37	13	25043232	25043232	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr13:25043232T>A	ENST00000381989.3	-	17	2168	c.2063A>T	c.(2062-2064)gAa>gTa	p.E688V		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	688	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TTGCTGGGCTTCTTCCTTCTC	0.443																																					p.E688V		Atlas-SNP	.											.	PARP4	142	.	0			c.A2063T						.						110.0	102.0	105.0					13																	25043232		2203	4300	6503	SO:0001583	missense	143	exon17			TGGGCTTCTTCCT	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.2063A>T	chr13.hg19:g.25043232T>A	ENSP00000371419:p.Glu688Val	53.0	0.0		44.0	9.0	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	hg19	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	T	6.476	0.456029	0.12283	.	.	ENSG00000102699	ENST00000381989	T	0.23754	1.89	4.08	-1.28	0.09318	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.824151	0.11071	N	0.602925	T	0.17831	0.0428	L	0.42744	1.35	0.27802	N	0.942462	B	0.14012	0.009	B	0.15052	0.012	T	0.27365	-1.0076	10	0.66056	D	0.02	-0.5016	3.071	0.06230	0.125:0.0921:0.1621:0.6207	.	688	Q9UKK3	PARP4_HUMAN	V	688	ENSP00000371419:E688V	ENSP00000371419:E688V	E	-	2	0	PARP4	23941232	0.984000	0.35163	0.789000	0.31954	0.152000	0.21847	0.917000	0.28665	-0.389000	0.07786	0.369000	0.22263	GAA	.	.		0.443	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
FREM2	341640	hgsc.bcm.edu	37	13	39454462	39454462	+	Silent	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr13:39454462A>T	ENST00000280481.7	+	24	9264	c.9048A>T	c.(9046-9048)acA>acT	p.T3016T		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	3016					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CGATCTATACAGTGAGATCGA	0.433																																					p.T3016T		Atlas-SNP	.											.	FREM2	385	.	0			c.A9048T						.						94.0	90.0	91.0					13																	39454462		2203	4300	6503	SO:0001819	synonymous_variant	341640	exon24			CTATACAGTGAGA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.9048A>T	chr13.hg19:g.39454462A>T		85.0	0.0		46.0	18.0	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	hg19	CCDS31960.1																																																																																			.	.		0.433	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
TTC5	91875	hgsc.bcm.edu	37	14	20760207	20760207	+	Missense_Mutation	SNP	T	T	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr14:20760207T>G	ENST00000258821.3	-	9	1194	c.1138A>C	c.(1138-1140)Att>Ctt	p.I380L		NM_138376.2	NP_612385.2	Q8N0Z6	TTC5_HUMAN	tetratricopeptide repeat domain 5	380					DNA repair (GO:0006281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_cancers(95;0.00092)		Epithelial(56;1.1e-06)|all cancers(55;8.07e-06)	GBM - Glioblastoma multiforme(265;0.0106)		GAGTCTCCAATGAGCACTCCC	0.473																																					p.I380L		Atlas-SNP	.											.	TTC5	34	.	0			c.A1138C						.						106.0	89.0	95.0					14																	20760207		2203	4300	6503	SO:0001583	missense	91875	exon9			CTCCAATGAGCAC	BC008647	CCDS9546.1	14q11.2	2013-01-11			ENSG00000136319	ENSG00000136319		"""Tetratricopeptide (TTC) repeat domain containing"""	19274	protein-coding gene	gene with protein product						11511361	Standard	NM_138376		Approved	Strap	uc001vwt.3	Q8N0Z6	OTTHUMG00000029506	ENST00000258821.3:c.1138A>C	chr14.hg19:g.20760207T>G	ENSP00000258821:p.Ile380Leu	52.0	0.0		66.0	29.0	NM_138376	A8MQ18|Q96HF9	Missense_Mutation	SNP	ENST00000258821.3	hg19	CCDS9546.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.3|25.3	4.626093|4.626093	0.87560|0.87560	.|.	.|.	ENSG00000136319|ENSG00000136319	ENST00000423949|ENST00000258821	.|T	.|0.35605	.|1.3	4.71|4.71	4.71|4.71	0.59529|0.59529	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.46833|0.46833	0.1413|0.1413	M|M	0.71036|0.71036	2.16|2.16	0.58432|0.58432	D|D	0.999999|0.999999	.|B	.|0.31548	.|0.328	.|B	.|0.41619	.|0.361	T|T	0.52990|0.52990	-0.8501|-0.8501	5|10	.|0.72032	.|D	.|0.01	.|.	13.6327|13.6327	0.62204|0.62204	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|380	.|Q8N0Z6	.|TTC5_HUMAN	P|L	324|380	.|ENSP00000258821:I380L	.|ENSP00000258821:I380L	H|I	-|-	2|1	0|0	TTC5|TTC5	19830047|19830047	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.895000|0.895000	0.52256|0.52256	6.239000|6.239000	0.72356|0.72356	2.123000|2.123000	0.65237|0.65237	0.456000|0.456000	0.33151|0.33151	CAT|ATT	.	.		0.473	TTC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073529.4	NM_138376	
ADAM20	8748	hgsc.bcm.edu	37	14	70990228	70990228	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr14:70990228T>A	ENST00000256389.3	-	2	1641	c.1397A>T	c.(1396-1398)gAa>gTa	p.E466V	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	416	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		CTCCCCTTCTTCAACCACTAG	0.438																																					p.E466V		Atlas-SNP	.											.	ADAM20	59	.	0			c.A1397T						.						141.0	123.0	129.0					14																	70990228		2203	4300	6503	SO:0001583	missense	8748	exon2			CCTTCTTCAACCA	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"""ADAM metallopeptidase domain containing"""	199	protein-coding gene	gene with protein product		603712	"""a disintegrin and metalloproteinase domain 20"""			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.1397A>T	chr14.hg19:g.70990228T>A	ENSP00000256389:p.Glu466Val	127.0	0.0		130.0	47.0	NM_003814	Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	hg19	CCDS32111.1	.	.	.	.	.	.	.	.	.	.	T	15.27	2.784097	0.49997	.	.	ENSG00000134007	ENST00000256389	T	0.22743	1.94	4.54	4.54	0.55810	Blood coagulation inhibitor, Disintegrin (4);	0.000000	0.37809	U	0.001923	T	0.65069	0.2656	H	0.99273	4.495	0.35140	D	0.768745	D	0.89917	1.0	D	0.91635	0.999	D	0.85266	0.1053	10	0.87932	D	0	.	14.1752	0.65537	0.0:0.0:0.0:1.0	.	416	O43506	ADA20_HUMAN	V	466	ENSP00000256389:E466V	ENSP00000256389:E466V	E	-	2	0	ADAM20	70059981	1.000000	0.71417	0.974000	0.42286	0.121000	0.20230	5.619000	0.67729	1.803000	0.52742	0.455000	0.32223	GAA	.	.		0.438	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2		
CLMN	79789	hgsc.bcm.edu	37	14	95677202	95677202	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr14:95677202A>T	ENST00000298912.4	-	7	736	c.623T>A	c.(622-624)gTg>gAg	p.V208E		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	208	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		AAAGTCCTGCACCGCCACGCC	0.582																																					p.V208E		Atlas-SNP	.											.	CLMN	103	.	0			c.T623A						.						85.0	91.0	89.0					14																	95677202		2203	4300	6503	SO:0001583	missense	79789	exon7			TCCTGCACCGCCA	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.623T>A	chr14.hg19:g.95677202A>T	ENSP00000298912:p.Val208Glu	68.0	0.0		85.0	37.0	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	hg19	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.872604	0.91587	.	.	ENSG00000165959	ENST00000298912	T	0.64438	-0.1	5.93	5.93	0.95920	Calponin homology domain (5);	0.000000	0.35838	N	0.002959	D	0.84142	0.5407	M	0.92649	3.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88028	0.2773	10	0.87932	D	0	.	16.3721	0.83368	1.0:0.0:0.0:0.0	.	208	Q96JQ2	CLMN_HUMAN	E	208	ENSP00000298912:V208E	ENSP00000298912:V208E	V	-	2	0	CLMN	94746955	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.962000	0.93254	2.257000	0.74773	0.533000	0.62120	GTG	.	.		0.582	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2		
AK7	122481	hgsc.bcm.edu	37	14	96875253	96875253	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr14:96875253G>A	ENST00000267584.4	+	4	517	c.473G>A	c.(472-474)tGg>tAg	p.W158*	AK7_ENST00000554313.1_3'UTR	NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	158					axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		GTGATGACTTGGGCGCGCTCC	0.468																																					p.W158X		Atlas-SNP	.											.	AK7	69	.	0			c.G473A						.						90.0	87.0	88.0					14																	96875253		2203	4300	6503	SO:0001587	stop_gained	122481	exon4			TGACTTGGGCGCG	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"""Adenylate kinases"""	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.473G>A	chr14.hg19:g.96875253G>A	ENSP00000267584:p.Trp158*	105.0	0.0		147.0	53.0	NM_152327	Q8IYP6	Nonsense_Mutation	SNP	ENST00000267584.4	hg19	CCDS9945.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.404954	0.62288	.	.	ENSG00000140057	ENST00000267584	.	.	.	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.7302	15.7785	0.78242	0.0:0.0:1.0:0.0	.	.	.	.	X	158	.	ENSP00000267584:W158X	W	+	2	0	AK7	95945006	1.000000	0.71417	0.996000	0.52242	0.037000	0.13140	6.236000	0.72339	2.535000	0.85469	0.655000	0.94253	TGG	.	.		0.468	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1		
ZNF106	64397	hgsc.bcm.edu	37	15	42729475	42729475	+	Silent	SNP	T	T	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:42729475T>C	ENST00000263805.4	-	10	4958	c.4632A>G	c.(4630-4632)ctA>ctG	p.L1544L	ZNF106_ENST00000565380.1_Silent_p.L772L|ZNF106_ENST00000565611.1_Silent_p.L729L	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	1544					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										AACAGGTATATAGCAAGTTCC	0.398																																					p.L1544L		Atlas-SNP	.											.	ZFP106	117	.	0			c.A4632G						.						145.0	138.0	140.0					15																	42729475		2203	4299	6502	SO:0001819	synonymous_variant	64397	exon10			GGTATATAGCAAG	AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"""Zinc fingers, C2H2-type"""	12886	protein-coding gene	gene with protein product	"""SH3-domain binding protein 3"""		"""zinc finger protein 106 homolog (mouse)"""	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.4632A>G	chr15.hg19:g.42729475T>C		81.0	0.0		91.0	23.0	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Silent	SNP	ENST00000263805.4	hg19	CCDS32208.1																																																																																			.	.		0.398	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
SEMA6D	80031	hgsc.bcm.edu	37	15	48058329	48058329	+	Nonsense_Mutation	SNP	T	T	A	rs113249348		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:48058329T>A	ENST00000316364.5	+	15	2035	c.1596T>A	c.(1594-1596)taT>taA	p.Y532*	SEMA6D_ENST00000389433.2_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000558816.1_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000536845.2_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000537942.1_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000355997.3_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000354744.4_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000358066.4_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000389428.3_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000558014.1_Nonsense_Mutation_p.Y532*|SEMA6D_ENST00000389432.2_Nonsense_Mutation_p.Y532*	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	532	PSI.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		GTGACCCGTATTGTGGCTGGT	0.463																																					p.Y532X		Atlas-SNP	.											.	SEMA6D	322	.	0			c.T1596A						.						103.0	91.0	95.0					15																	48058329		2198	4297	6495	SO:0001587	stop_gained	80031	exon15			CCCGTATTGTGGC	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.1596T>A	chr15.hg19:g.48058329T>A	ENSP00000324857:p.Tyr532*	98.0	0.0		125.0	13.0	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Nonsense_Mutation	SNP	ENST00000316364.5	hg19	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	T	41	8.907301	0.98998	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997	.	.	.	5.89	-0.111	0.13576	.	0.055415	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4731	0.44648	0.0:0.5971:0.0:0.4029	.	.	.	.	X	532	.	ENSP00000324857:Y532X	Y	+	3	2	SEMA6D	45845621	1.000000	0.71417	0.952000	0.39060	0.996000	0.88848	0.886000	0.28241	-0.276000	0.09206	-0.290000	0.09829	TAT	.	T|0.500;C|0.500		0.463	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
SLC12A1	6557	hgsc.bcm.edu	37	15	48513119	48513119	+	Splice_Site	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:48513119T>A	ENST00000558405.1	+	3	568	c.554T>A	c.(553-555)gTa>gAa	p.V185E	SLC12A1_ENST00000561031.1_Splice_Site_p.V185E|SLC12A1_ENST00000396577.3_Splice_Site_p.V185E|SLC12A1_ENST00000380993.3_Splice_Site_p.V185E|SLC12A1_ENST00000330289.6_Splice_Site_p.V185E			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	185					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	TATCCACAGGTAAGATGCATG	0.473																																					p.V185E		Atlas-SNP	.											.	SLC12A1	243	.	0			c.T554A						.						120.0	113.0	115.0					15																	48513119		2198	4297	6495	SO:0001630	splice_region_variant	6557	exon4			CACAGGTAAGATG		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"""Solute carriers"""	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.553-1T>A	chr15.hg19:g.48513119T>A		104.0	0.0		135.0	58.0	NM_001184832	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	hg19	CCDS10129.2	.	.	.	.	.	.	.	.	.	.	T	28.2	4.898311	0.91962	.	.	ENSG00000074803	ENST00000380993;ENST00000396577;ENST00000330289	D;D;D	0.99023	-5.34;-5.34;-5.34	5.96	5.96	0.96718	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.99450	0.9805	M	0.92970	3.365	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.81914	0.986;0.995	D	0.98519	1.0622	10	0.87932	D	0	.	16.4484	0.83959	0.0:0.0:0.0:1.0	.	185;185	Q8IUN5;Q13621	.;S12A1_HUMAN	E	185	ENSP00000370381:V185E;ENSP00000379822:V185E;ENSP00000331550:V185E	ENSP00000331550:V185E	V	+	2	0	SLC12A1	46300411	1.000000	0.71417	0.994000	0.49952	0.845000	0.48019	7.698000	0.84413	2.285000	0.76669	0.533000	0.62120	GTA	.	.		0.473	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1		Missense_Mutation
IGDCC3	9543	hgsc.bcm.edu	37	15	65621468	65621468	+	Missense_Mutation	SNP	C	C	T	rs149849455		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:65621468C>T	ENST00000327987.4	-	14	2475	c.2224G>A	c.(2224-2226)Gct>Act	p.A742T	IGDCC3_ENST00000559231.1_5'Flank	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	742					neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TCACACGGAGCGGGGGCTGCA	0.672																																					p.A742T		Atlas-SNP	.											.	IGDCC3	82	.	0			c.G2224A						.	C	THR/ALA	0,4402		0,0,2201	15.0	18.0	17.0		2224	-2.6	0.0	15	dbSNP_134	17	1,8595		0,1,4297	no	missense	IGDCC3	NM_004884.3	58	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	benign	742/815	65621468	1,12997	2201	4298	6499	SO:0001583	missense	9543	exon14			ACGGAGCGGGGGC	AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9700	protein-coding gene	gene with protein product		604184	"""putative neuronal cell adhesion molecule"""	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.2224G>A	chr15.hg19:g.65621468C>T	ENSP00000332773:p.Ala742Thr	62.0	0.0		67.0	37.0	NM_004884	O95215	Missense_Mutation	SNP	ENST00000327987.4	hg19	CCDS10205.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077256	0.36662	0.0	1.16E-4	ENSG00000174498	ENST00000327987;ENST00000443278	T	0.65364	-0.15	5.3	-2.6	0.06190	.	2.424390	0.01794	N	0.032480	T	0.47820	0.1466	N	0.19112	0.55	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.35151	-0.9800	10	0.36615	T	0.2	-0.1839	10.404	0.44246	0.0:0.4979:0.0:0.5021	.	742	Q8IVU1	IGDC3_HUMAN	T	742;565	ENSP00000332773:A742T	ENSP00000332773:A742T	A	-	1	0	IGDCC3	63408521	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.706000	0.01895	-0.793000	0.04475	-0.145000	0.13849	GCT	.	C|1.000;T|0.000		0.672	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884	
EDC3	80153	hgsc.bcm.edu	37	15	74925259	74925259	+	Silent	SNP	G	G	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:74925259G>A	ENST00000315127.4	-	7	1402	c.1221C>T	c.(1219-1221)gtC>gtT	p.V407V	EDC3_ENST00000568176.1_Silent_p.V407V|EDC3_ENST00000426797.3_Silent_p.V407V	NM_001142444.1|NM_025083.3	NP_001135916.1|NP_079359.2	Q96F86	EDC3_HUMAN	enhancer of mRNA decapping 3	407	YjeF N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00719}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|membrane (GO:0016020)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GGCAGTTGATGACCAGGTCCA	0.597											OREG0023286	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V407V		Atlas-SNP	.											.	EDC3	32	.	0			c.C1221T						.						68.0	48.0	55.0					15																	74925259		2197	4296	6493	SO:0001819	synonymous_variant	80153	exon8			GTTGATGACCAGG	BC011534	CCDS10267.1	15q24.1	2013-05-02	2013-05-02	2006-07-07	ENSG00000179151	ENSG00000179151			26114	protein-coding gene	gene with protein product		609842	"""yjeF domain containing (E.coli)"", ""LSM16 homolog (EDC3, S. cerevisiae)"", ""enhancer of mRNA decapping 3 homolog (S. cerevisiae)"""	YJDC, LSM16		15225602, 17533573, 22483619	Standard	NM_025083		Approved	FLJ21128, hYjeF_N2-15q23, YJEFN2	uc002aym.3	Q96F86	OTTHUMG00000142815	ENST00000315127.4:c.1221C>T	chr15.hg19:g.74925259G>A		67.0	0.0	1156	85.0	23.0	NM_001142444	B3KPH0|D3DW61|Q9H797	Silent	SNP	ENST00000315127.4	hg19	CCDS10267.1																																																																																			.	.		0.597	EDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286399.1	NM_025083	
ACAN	176	hgsc.bcm.edu	37	15	89402447	89402447	+	Missense_Mutation	SNP	G	G	A	rs533925391		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:89402447G>A	ENST00000561243.1	+	11	6631	c.6631G>A	c.(6631-6633)Gtt>Att	p.V2211I	ACAN_ENST00000559004.1_Missense_Mutation_p.V2211I|ACAN_ENST00000439576.2_Missense_Mutation_p.V2211I|ACAN_ENST00000352105.7_Missense_Mutation_p.V2211I			P16112	PGCA_HUMAN	aggrecan	2096	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.|G3.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GCAGCTGGGCGTTGTCATCAG	0.597													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18793	0.0		0.0	False		,,,				2504	0.0				p.V2211I		Atlas-SNP	.											.	ACAN	220	.	0			c.G6631A						.						44.0	50.0	48.0					15																	89402447		2134	4239	6373	SO:0001583	missense	176	exon12			CTGGGCGTTGTCA	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.6631G>A	chr15.hg19:g.89402447G>A	ENSP00000453342:p.Val2211Ile	111.0	0.0		130.0	53.0	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	hg19	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	G	0.119	-1.128582	0.01756	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.02606	4.36;4.23	5.12	-1.75	0.08031	.	0.642182	0.11888	N	0.519845	T	0.01765	0.0056	N	0.21583	0.68	0.09310	N	1	P;B	0.39311	0.667;0.304	B;B	0.37780	0.258;0.06	T	0.45963	-0.9225	10	0.21540	T	0.41	-2.0E-4	3.0641	0.06209	0.2863:0.11:0.4916:0.1121	.	2211;2211	E7ENV9;E7EX88	.;.	I	2211;2211;2097	ENSP00000387356:V2211I;ENSP00000341615:V2211I	ENSP00000268134:V2097I	V	+	1	0	ACAN	87203451	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.782000	0.04643	-0.274000	0.09232	-1.342000	0.01247	GTT	.	.		0.597	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
FURIN	5045	hgsc.bcm.edu	37	15	91424605	91424605	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:91424605A>G	ENST00000268171.3	+	16	2161	c.1882A>G	c.(1882-1884)Agc>Ggc	p.S628G		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	628					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			TACGCACTATAGCACCGAGAA	0.657																																					p.S628G		Atlas-SNP	.											.	FURIN	85	.	0			c.A1882G						.						74.0	69.0	71.0					15																	91424605		2197	4297	6494	SO:0001583	missense	5045	exon16			CACTATAGCACCG	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"""paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"""	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.1882A>G	chr15.hg19:g.91424605A>G	ENSP00000268171:p.Ser628Gly	68.0	0.0		73.0	16.0	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Missense_Mutation	SNP	ENST00000268171.3	hg19	CCDS10364.1	.	.	.	.	.	.	.	.	.	.	A	10.10	1.258843	0.23051	.	.	ENSG00000140564	ENST00000268171	D	0.85861	-2.04	5.02	3.88	0.44766	Growth factor, receptor (1);	0.199858	0.52532	D	0.000062	T	0.70298	0.3208	N	0.15975	0.35	0.25058	N	0.991089	B	0.06786	0.001	B	0.06405	0.002	T	0.55186	-0.8180	10	0.21014	T	0.42	-26.9162	9.8671	0.41150	0.8561:0.0:0.1439:0.0	.	628	P09958	FURIN_HUMAN	G	628	ENSP00000268171:S628G	ENSP00000268171:S628G	S	+	1	0	FURIN	89225609	.	.	1.000000	0.80357	0.572000	0.35998	.	.	1.893000	0.54813	0.454000	0.30748	AGC	.	.		0.657	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569	
SEPT12	124404	hgsc.bcm.edu	37	16	4827877	4827877	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr16:4827877G>C	ENST00000268231.8	-	10	1261	c.998C>G	c.(997-999)gCc>gGc	p.A333G	SEPT12_ENST00000396693.5_Missense_Mutation_p.A287G	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN	septin 12	333					cell cycle (GO:0007049)|cell division (GO:0051301)	cleavage furrow (GO:0032154)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|sperm annulus (GO:0097227)|spindle (GO:0005819)|stress fiber (GO:0001725)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						TCCTGGGGAGGCCGGGGCCAG	0.632																																					p.A333G		Atlas-SNP	.											.	SEPT12	40	.	0			c.C998G						.						28.0	29.0	29.0					16																	4827877		2175	4272	6447	SO:0001583	missense	124404	exon10			GGGGAGGCCGGGG	AK058139	CCDS10522.1, CCDS53987.1	16p13.3	2013-01-21			ENSG00000140623	ENSG00000140623		"""Septins"""	26348	protein-coding gene	gene with protein product		611562				14611653, 15915442	Standard	NM_001154458		Approved	FLJ25410	uc002cxq.3	Q8IYM1	OTTHUMG00000129481	ENST00000268231.8:c.998C>G	chr16.hg19:g.4827877G>C	ENSP00000268231:p.Ala333Gly	127.0	0.0		112.0	56.0	NM_144605	Q0P6B0|Q1PBH0|Q96LL0	Missense_Mutation	SNP	ENST00000268231.8	hg19	CCDS10522.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.320559	0.41096	.	.	ENSG00000140623	ENST00000396693;ENST00000268231	T;T	0.55413	0.52;0.55	4.59	2.57	0.30868	.	0.824903	0.10352	N	0.684976	T	0.29684	0.0741	N	0.08118	0	0.09310	N	1	B;B	0.31769	0.288;0.339	B;B	0.30572	0.117;0.076	T	0.17992	-1.0351	10	0.49607	T	0.09	.	5.4604	0.16614	0.184:0.1627:0.6533:0.0	.	287;333	Q8IYM1-2;Q8IYM1	.;SEP12_HUMAN	G	287;333	ENSP00000379922:A287G;ENSP00000268231:A333G	ENSP00000268231:A333G	A	-	2	0	SEPT12	4767878	0.011000	0.17503	0.091000	0.20842	0.418000	0.31294	1.466000	0.35310	0.636000	0.30508	0.462000	0.41574	GCC	.	.		0.632	SEPT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251645.2	NM_144605	
MKL2	57496	hgsc.bcm.edu	37	16	14304134	14304134	+	Silent	SNP	A	A	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr16:14304134A>G	ENST00000341243.5	+	2	156	c.156A>G	c.(154-156)agA>agG	p.R52R	MKL2_ENST00000571589.1_Silent_p.R63R|MKL2_ENST00000572567.1_Silent_p.R52R|MKL2_ENST00000573051.1_Silent_p.R12R|MKL2_ENST00000318282.5_Silent_p.R63R|MKL2_ENST00000574045.1_Silent_p.R63R			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	52					blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GGAGGACGAGAGAACAACTAG	0.488																																					p.R63R		Atlas-SNP	.											.	MKL2	103	.	0			c.A189G						.						178.0	137.0	151.0					16																	14304134		2197	4300	6497	SO:0001819	synonymous_variant	57496	exon4			GACGAGAGAACAA	AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.156A>G	chr16.hg19:g.14304134A>G		91.0	0.0		86.0	39.0	NM_014048	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Silent	SNP	ENST00000341243.5	hg19																																																																																				.	.		0.488	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048	
DNAH3	55567	hgsc.bcm.edu	37	16	21071601	21071601	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr16:21071601A>T	ENST00000261383.3	-	26	3796	c.3797T>A	c.(3796-3798)aTt>aAt	p.I1266N	DNAH3_ENST00000415178.1_Missense_Mutation_p.I1266N	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1266	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		ATATGCTTCAATCCCAAGTCC	0.498																																					p.I1266N		Atlas-SNP	.											.	DNAH3	1142	.	0			c.T3797A						.						212.0	199.0	203.0					16																	21071601		2201	4300	6501	SO:0001583	missense	55567	exon26			GCTTCAATCCCAA	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.3797T>A	chr16.hg19:g.21071601A>T	ENSP00000261383:p.Ile1266Asn	127.0	0.0		64.0	11.0	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	A	13.74	2.327509	0.41197	.	.	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.61742	0.08;0.08	5.47	5.47	0.80525	Dynein heavy chain, domain-2 (1);	0.223435	0.39687	N	0.001289	T	0.72078	0.3416	M	0.71296	2.17	0.52099	D	0.999941	D	0.69078	0.997	P	0.60541	0.876	T	0.74185	-0.3747	10	0.49607	T	0.09	.	15.5585	0.76219	1.0:0.0:0.0:0.0	.	1266	Q8TD57	DYH3_HUMAN	N	1266	ENSP00000261383:I1266N;ENSP00000394245:I1266N	ENSP00000261383:I1266N	I	-	2	0	DNAH3	20979102	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.473000	0.90410	2.088000	0.63022	0.519000	0.50382	ATT	.	.		0.498	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
HS3ST4	9951	hgsc.bcm.edu	37	16	26147301	26147301	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr16:26147301T>A	ENST00000331351.5	+	2	1495	c.1103T>A	c.(1102-1104)aTg>aAg	p.M368K	HS3ST4_ENST00000475436.1_3'UTR	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	368					heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		GCCGGGGAAATGGCCAAAGTA	0.493																																					p.M368K		Atlas-SNP	.											.	HS3ST4	120	.	0			c.T1103A						.						84.0	82.0	82.0					16																	26147301		1568	3582	5150	SO:0001583	missense	9951	exon2			GGGAAATGGCCAA	AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.1103T>A	chr16.hg19:g.26147301T>A	ENSP00000330606:p.Met368Lys	121.0	0.0		135.0	70.0	NM_006040	Q5QI42|Q8NDC2	Missense_Mutation	SNP	ENST00000331351.5	hg19	CCDS53995.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.786606	0.90367	.	.	ENSG00000182601	ENST00000331351	D	0.82893	-1.66	5.56	5.56	0.83823	Sulfotransferase domain (1);	0.058199	0.64402	U	0.000005	D	0.92149	0.7511	M	0.91663	3.23	0.80722	D	1	D	0.62365	0.991	D	0.63957	0.92	D	0.93807	0.7106	10	0.87932	D	0	.	14.8801	0.70525	0.0:0.0:0.0:1.0	.	368	Q9Y661	HS3S4_HUMAN	K	368	ENSP00000330606:M368K	ENSP00000330606:M368K	M	+	2	0	HS3ST4	26054802	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.004000	0.88535	2.102000	0.63906	0.533000	0.62120	ATG	.	.		0.493	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040	
MT1E	4493	hgsc.bcm.edu	37	16	56660821	56660821	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr16:56660821G>T	ENST00000306061.6	+	3	501	c.124G>T	c.(124-126)Gcc>Tcc	p.A42S	MT1E_ENST00000330439.6_3'UTR|MT1E_ENST00000568293.1_Missense_Mutation_p.A20S	NM_175617.3	NP_783316.2	P04732	MT1E_HUMAN	metallothionein 1E	42	Alpha.				cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)										CGTGGGCTGTGCCAAGTGTGC	0.592																																					p.A42S		Atlas-SNP	.											.	MT1E	7	.	0			c.G124T						.						142.0	136.0	138.0					16																	56660821		2198	4300	6498	SO:0001583	missense	4493	exon3			GGCTGTGCCAAGT	BC009699	CCDS10764.2	16q13	2008-08-11	2007-03-02		ENSG00000169715	ENSG00000169715		"""Metallothioneins"""	7397	protein-coding gene	gene with protein product		156351		MT1		6089206, 2581970	Standard	XM_005255956		Approved	MTD	uc002ejl.3	P04732	OTTHUMG00000133014	ENST00000306061.6:c.124G>T	chr16.hg19:g.56660821G>T	ENSP00000307706:p.Ala42Ser	43.0	0.0		39.0	23.0	NM_175617	A2RRF7|Q86YX4|Q8TD51	Missense_Mutation	SNP	ENST00000306061.6	hg19	CCDS10764.2	.	.	.	.	.	.	.	.	.	.	G	11.00	1.509995	0.27036	.	.	ENSG00000169715	ENST00000306061	T	0.09445	2.98	2.39	1.39	0.22231	Metallothionein domain, vertebrate (1);Metallothionein domain (1);	.	.	.	.	T	0.07638	0.0192	.	.	.	0.80722	D	1	B	0.17038	0.02	B	0.18871	0.023	T	0.21280	-1.0250	8	0.40728	T	0.16	.	5.6138	0.17420	0.2906:0.0:0.7094:0.0	.	42	P04732	MT1E_HUMAN	S	42	ENSP00000307706:A42S	ENSP00000307706:A42S	A	+	1	0	MT1E	55218322	0.288000	0.24324	0.995000	0.50966	0.831000	0.47069	0.203000	0.17315	0.327000	0.23409	0.306000	0.20318	GCC	.	.		0.592	MT1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256600.1	NM_175617	
KCNG4	93107	hgsc.bcm.edu	37	16	84270675	84270675	+	Silent	SNP	G	G	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr16:84270675G>A	ENST00000308251.4	-	2	485	c.417C>T	c.(415-417)tgC>tgT	p.C139C	KCNG4_ENST00000568181.1_Silent_p.C139C	NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	139					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.C139C(2)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						AGGACAGCGCGCACATCTCCT	0.652																																					p.C139C		Atlas-SNP	.											KCNG4,rectum,carcinoma,0,2	KCNG4	71	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C417T						.						47.0	49.0	48.0					16																	84270675		2200	4300	6500	SO:0001819	synonymous_variant	93107	exon2			CAGCGCGCACATC	AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.417C>T	chr16.hg19:g.84270675G>A		64.0	1.0		68.0	33.0	NM_172347	Q96H24	Silent	SNP	ENST00000308251.4	hg19	CCDS10945.1																																																																																			.	.		0.652	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347	
KIAA0513	9764	hgsc.bcm.edu	37	16	85114999	85114999	+	Splice_Site	SNP	G	G	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr16:85114999G>A	ENST00000566428.1	+	9	1611		c.e9+1		KIAA0513_ENST00000258180.3_Splice_Site|KIAA0513_ENST00000538274.1_Splice_Site			O60268	K0513_HUMAN	KIAA0513							cytoplasm (GO:0005737)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(9)|pancreas(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.234)		CCACTACCAGGTAGGAGCAAA	0.537																																					.		Atlas-SNP	.											.	KIAA0513	43	.	0			c.980+1G>A						.						49.0	37.0	41.0					16																	85114999		2195	4294	6489	SO:0001630	splice_region_variant	9764	exon9			TACCAGGTAGGAG	AB011085	CCDS32499.1, CCDS67091.1, CCDS73919.1	16q24.1	2012-11-29			ENSG00000135709	ENSG00000135709			29058	protein-coding gene	gene with protein product		611675				9628581	Standard	XM_005256265		Approved		uc002fiu.3	O60268	OTTHUMG00000176597	ENST00000566428.1:c.980+1G>A	chr16.hg19:g.85114999G>A		64.0	0.0		73.0	30.0	NM_014732	B4DSS5|D3DUM2|Q8N6G0	Splice_Site	SNP	ENST00000566428.1	hg19	CCDS32499.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.516209	0.85495	.	.	ENSG00000135709	ENST00000538274;ENST00000258180	.	.	.	4.75	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7052	0.85370	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIAA0513	83672500	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.068000	0.93961	2.350000	0.79820	0.561000	0.74099	.	.	.		0.537	KIAA0513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432736.1	NM_014732	Intron
ALKBH5	54890	hgsc.bcm.edu	37	17	18088100	18088100	+	Silent	SNP	C	C	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr17:18088100C>T	ENST00000399138.4	+	1	548	c.543C>T	c.(541-543)gtC>gtT	p.V181V	RP11-258F1.1_ENST00000583062.1_RNA|RP11-258F1.1_ENST00000577847.1_RNA|ALKBH5_ENST00000541285.1_Intron	NM_017758.3	NP_060228.3	Q6P6C2	ALKB5_HUMAN	AlkB family member 5, RNA demethylase	181					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|oxidative single-stranded RNA demethylation (GO:0035553)|response to hypoxia (GO:0001666)|spermatogenesis (GO:0007283)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidative RNA demethylase activity (GO:0035515)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|skin(1)	10	all_neural(463;0.228)					AGCACCGCGTCATCCCCGAGG	0.677																																					p.V181V	Ovarian(166;154 1953 40235 46283 46309)	Atlas-SNP	.											.	ALKBH5	24	.	0			c.C543T						.						36.0	42.0	40.0					17																	18088100		2094	4200	6294	SO:0001819	synonymous_variant	54890	exon1			CCGCGTCATCCCC	AK000315	CCDS42272.1	17p11.2	2014-07-23	2014-07-23	2006-02-09	ENSG00000091542	ENSG00000091542	1.14.11.-	"""Alkylation repair homologs"""	25996	protein-coding gene	gene with protein product		613303	"""oxoglutarate and iron-dependent oxygenase domain containing"", ""alkB, alkylation repair homolog 5 (E. coli)"""	OFOXD1		11997338, 24778178	Standard	NM_017758		Approved	FLJ20308	uc010cpw.3	Q6P6C2	OTTHUMG00000059397	ENST00000399138.4:c.543C>T	chr17.hg19:g.18088100C>T		47.0	0.0		81.0	37.0	NM_017758	B4DVJ4|D3DXC6|Q9NXD6	Silent	SNP	ENST00000399138.4	hg19	CCDS42272.1																																																																																			.	.		0.677	ALKBH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132069.3	NM_017758	
TMEM132E	124842	hgsc.bcm.edu	37	17	32964875	32964875	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr17:32964875T>A	ENST00000321639.5	+	10	2907	c.2579T>A	c.(2578-2580)cTg>cAg	p.L860Q		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	860						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		CAAGGAGAGCTGTCGCCGCCA	0.697																																					p.L860Q		Atlas-SNP	.											.	TMEM132E	122	.	0			c.T2579A						.						25.0	27.0	26.0					17																	32964875		2166	4225	6391	SO:0001583	missense	124842	exon10			GAGAGCTGTCGCC	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.2579T>A	chr17.hg19:g.32964875T>A	ENSP00000316532:p.Leu860Gln	28.0	0.0		33.0	18.0	NM_207313	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	hg19	CCDS11283.1	.	.	.	.	.	.	.	.	.	.	T	12.41	1.930269	0.34096	.	.	ENSG00000181291	ENST00000321639	T	0.06449	3.3	4.73	4.73	0.59995	.	0.000000	0.64402	D	0.000001	T	0.18841	0.0452	L	0.55743	1.74	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.01309	-1.1389	10	0.30854	T	0.27	-31.6467	13.5748	0.61868	0.0:0.0:0.0:1.0	.	860	Q6IEE7	T132E_HUMAN	Q	860	ENSP00000316532:L860Q	ENSP00000316532:L860Q	L	+	2	0	TMEM132E	29988988	1.000000	0.71417	1.000000	0.80357	0.035000	0.12851	6.101000	0.71479	1.993000	0.58246	0.523000	0.50628	CTG	.	.		0.697	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313	
KRT27	342574	hgsc.bcm.edu	37	17	38937443	38937443	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr17:38937443A>T	ENST00000301656.3	-	2	564	c.524T>A	c.(523-525)cTa>cAa	p.L175Q		NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				TACTTACTTTAGTCTGAAGTC	0.338																																					p.L175Q		Atlas-SNP	.											.	KRT27	41	.	0			c.T524A						.						89.0	77.0	81.0					17																	38937443		2203	4299	6502	SO:0001583	missense	342574	exon2			TACTTTAGTCTGA	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30841	protein-coding gene	gene with protein product			"""keratin 25C"""	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.524T>A	chr17.hg19:g.38937443A>T	ENSP00000301656:p.Leu175Gln	92.0	0.0		100.0	29.0	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	hg19	CCDS11375.1	.	.	.	.	.	.	.	.	.	.	A	16.90	3.249692	0.59212	.	.	ENSG00000171446	ENST00000301656	D	0.82711	-1.64	5.58	5.58	0.84498	Filament (1);	0.273139	0.26359	N	0.024826	D	0.84946	0.5585	L	0.56769	1.78	0.09310	N	0.999999	P	0.37233	0.588	P	0.46685	0.524	T	0.79811	-0.1646	10	0.54805	T	0.06	.	13.7809	0.63081	1.0:0.0:0.0:0.0	.	175	Q7Z3Y8	K1C27_HUMAN	Q	175	ENSP00000301656:L175Q	ENSP00000301656:L175Q	L	-	2	0	KRT27	36190969	0.034000	0.19679	0.223000	0.23860	0.962000	0.63368	3.090000	0.50191	2.248000	0.74166	0.528000	0.53228	CTA	.	.		0.338	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537	
KCNJ16	3773	hgsc.bcm.edu	37	17	68128987	68128987	+	Silent	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr17:68128987T>A	ENST00000589377.1	+	2	922	c.759T>A	c.(757-759)atT>atA	p.I253I	KCNJ16_ENST00000283936.1_Silent_p.I253I|KCNJ16_ENST00000585558.1_Silent_p.I288I|KCNJ16_ENST00000586462.1_Silent_p.I292I|KCNJ16_ENST00000392671.1_Silent_p.I253I|KCNJ16_ENST00000392670.1_Silent_p.I253I	NM_001270422.1	NP_001257351.1	Q9NPI9	KCJ16_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 16	253					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	32	Breast(10;2.96e-09)					CGGTAACTATTGTCCATGAAA	0.438																																					p.I253I		Atlas-SNP	.											.	KCNJ16	72	.	0			c.T759A						.						125.0	117.0	120.0					17																	68128987		2203	4300	6503	SO:0001819	synonymous_variant	3773	exon6			AACTATTGTCCAT	AF153815	CCDS11687.1, CCDS74141.1	17q24.3	2011-07-05				ENSG00000153822		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6262	protein-coding gene	gene with protein product		605722				11240146, 16382105	Standard	NM_018658		Approved	Kir5.1, BIR9	uc002jio.4	Q9NPI9		ENST00000589377.1:c.759T>A	chr17.hg19:g.68128987T>A		62.0	0.0		83.0	41.0	NM_001270422		Silent	SNP	ENST00000589377.1	hg19	CCDS11687.1																																																																																			.	.		0.438	KCNJ16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450880.1	NM_018658	
LAMA1	284217	hgsc.bcm.edu	37	18	6978215	6978215	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr18:6978215A>T	ENST00000389658.3	-	43	6263	c.6170T>A	c.(6169-6171)cTg>cAg	p.L2057Q		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2057	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GGAGTCCTGCAGAAGCTGGTG	0.587																																					p.L2057Q		Atlas-SNP	.											.	LAMA1	458	.	0			c.T6170A						.						231.0	201.0	211.0					18																	6978215		2203	4300	6503	SO:0001583	missense	284217	exon43			TCCTGCAGAAGCT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.6170T>A	chr18.hg19:g.6978215A>T	ENSP00000374309:p.Leu2057Gln	75.0	0.0		64.0	30.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	A	19.93	3.917552	0.73098	.	.	ENSG00000101680	ENST00000389658	T	0.51325	0.71	5.65	5.65	0.86999	Laminin II (1);	0.272595	0.28748	N	0.014265	T	0.61311	0.2337	M	0.65975	2.015	0.09310	N	1	D	0.55800	0.973	P	0.56163	0.793	T	0.57271	-0.7840	10	0.35671	T	0.21	.	16.183	0.81925	1.0:0.0:0.0:0.0	.	2057	P25391	LAMA1_HUMAN	Q	2057	ENSP00000374309:L2057Q	ENSP00000374309:L2057Q	L	-	2	0	LAMA1	6968215	0.999000	0.42202	0.048000	0.18961	0.021000	0.10359	6.242000	0.72376	2.282000	0.76494	0.533000	0.62120	CTG	.	.		0.587	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
DYNAP	284254	hgsc.bcm.edu	37	18	52262216	52262216	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr18:52262216G>A	ENST00000321600.1	+	2	228	c.182G>A	c.(181-183)tGg>tAg	p.W61*	DYNAP_ENST00000585973.1_Intron	NM_173629.1	NP_775900.1	Q8N1N2	DYNAP_HUMAN	dynactin associated protein	61					activation of protein kinase B activity (GO:0032148)|cellular response to ergosterol (GO:1901625)|positive regulation of cell proliferation (GO:0008284)|regulation of apoptotic process (GO:0042981)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											TCCATATGCTGGTGTCTACCT	0.463																																					p.W61X		Atlas-SNP	.											.	.	.	.	0			c.G182A						.						196.0	181.0	186.0					18																	52262216		2203	4300	6503	SO:0001587	stop_gained	284254	exon2			TATGCTGGTGTCT	AK096425	CCDS11957.1	18q21.2	2012-10-24	2012-10-24	2012-10-24	ENSG00000178690	ENSG00000178690			26808	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 26"""	C18orf26		20978158	Standard	NM_173629		Approved	FLJ39106	uc002lfq.1	Q8N1N2	OTTHUMG00000132709	ENST00000321600.1:c.182G>A	chr18.hg19:g.52262216G>A	ENSP00000315265:p.Trp61*	92.0	0.0		92.0	52.0	NM_173629		Nonsense_Mutation	SNP	ENST00000321600.1	hg19	CCDS11957.1	.	.	.	.	.	.	.	.	.	.	.	14.85	2.657331	0.47467	.	.	ENSG00000178690	ENST00000321600	.	.	.	4.24	2.43	0.29744	.	0.628433	0.13361	N	0.393641	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.1587	5.2196	0.15362	0.1044:0.0:0.6932:0.2025	.	.	.	.	X	61	.	ENSP00000315265:W61X	W	+	2	0	C18orf26	50413214	0.014000	0.17966	0.003000	0.11579	0.086000	0.17979	1.058000	0.30504	0.725000	0.32318	-0.251000	0.11542	TGG	.	.		0.463	DYNAP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256007.1	NM_173629	
MATK	4145	hgsc.bcm.edu	37	19	3784140	3784140	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:3784140G>A	ENST00000310132.6	-	5	742	c.344C>T	c.(343-345)cCc>cTc	p.P115L	MATK_ENST00000585778.1_Missense_Mutation_p.P115L|MATK_ENST00000395040.2_Missense_Mutation_p.P74L|MATK_ENST00000395045.2_Missense_Mutation_p.P116L	NM_139355.2	NP_647612.1	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase	115					cell proliferation (GO:0008283)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	26		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTGAGCTTGGGGTCTGCGGA	0.682																																					p.P116L		Atlas-SNP	.											.	MATK	108	.	0			c.C347T						.						30.0	34.0	33.0					19																	3784140		2201	4298	6499	SO:0001583	missense	4145	exon5			AGCTTGGGGTCTG	L18974	CCDS12113.1, CCDS12114.1, CCDS42468.1	19p13.3	2013-02-14						"""SH2 domain containing"""	6906	protein-coding gene	gene with protein product	"""Csk-homologous kinase"", ""tyrosine-protein kinase CTK"", ""protein kinase HYL"", ""hematopoietic consensus tyrosine-lacking kinase"", ""tyrosylprotein kinase"", ""hydroxyaryl-protein kinase"", ""Csk-type protein tyrosine kinase"", ""HYL tyrosine kinase"", ""tyrosine kinase MATK"", ""leukocyte carboxyl-terminal src kinase related"""	600038				8288563, 7530249	Standard	NM_139355		Approved	HYLTK, CTK, HYL, Lsk, CHK, HHYLTK, DKFZp434N1212, MGC1708, MGC2101	uc002lyt.3	P42679		ENST00000310132.6:c.344C>T	chr19.hg19:g.3784140G>A	ENSP00000308734:p.Pro115Leu	35.0	0.0		41.0	21.0	NM_002378	B3KNZ9|Q9NST8	Missense_Mutation	SNP	ENST00000310132.6	hg19	CCDS12114.1	.	.	.	.	.	.	.	.	.	.	g	19.29	3.799137	0.70567	.	.	ENSG00000007264	ENST00000395045;ENST00000310132;ENST00000395040	T;T;T	0.16743	2.32;2.32;2.32	4.25	4.25	0.50352	Src homology-3 domain (1);	0.000000	0.85682	D	0.000000	T	0.30603	0.0770	L	0.39514	1.22	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	P;P;P	0.61940	0.896;0.896;0.896	T	0.06041	-1.0849	10	0.66056	D	0.02	-29.0344	16.0026	0.80306	0.0:0.0:1.0:0.0	.	115;116;115	F1T0G6;B3KNZ9;P42679	.;.;MATK_HUMAN	L	116;115;74	ENSP00000378485:P116L;ENSP00000308734:P115L;ENSP00000378481:P74L	ENSP00000308734:P115L	P	-	2	0	MATK	3735140	1.000000	0.71417	0.964000	0.40570	0.663000	0.39108	3.524000	0.53495	2.067000	0.61834	0.306000	0.20318	CCC	.	.		0.682	MATK-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453639.1	NM_139355	
MUC16	94025	hgsc.bcm.edu	37	19	9062327	9062327	+	Silent	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:9062327T>A	ENST00000397910.4	-	3	25322	c.25119A>T	c.(25117-25119)tcA>tcT	p.S8373S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8375	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGGGTGTCTCTGAGTCAGATA	0.478																																					p.S8373S		Atlas-SNP	.											.	MUC16	4315	.	0			c.A25119T						.						178.0	173.0	175.0					19																	9062327		2079	4206	6285	SO:0001819	synonymous_variant	94025	exon3			TGTCTCTGAGTCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.25119A>T	chr19.hg19:g.9062327T>A		68.0	0.0		66.0	25.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MUC16	94025	hgsc.bcm.edu	37	19	9082590	9082590	+	Silent	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:9082590A>T	ENST00000397910.4	-	1	9428	c.9225T>A	c.(9223-9225)gcT>gcA	p.A3075A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3076	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AAAGTGTCAGAGCTGAAGTCT	0.498																																					p.A3075A		Atlas-SNP	.											.	MUC16	4315	.	0			c.T9225A						.						154.0	156.0	156.0					19																	9082590		1948	4136	6084	SO:0001819	synonymous_variant	94025	exon1			TGTCAGAGCTGAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.9225T>A	chr19.hg19:g.9082590A>T		103.0	0.0		155.0	66.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF486	90649	hgsc.bcm.edu	37	19	20307961	20307961	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:20307961A>T	ENST00000335117.8	+	4	499	c.442A>T	c.(442-444)Act>Tct	p.T148S	CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	148					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						ATGTTTGACAACTACCCAGAG	0.318																																					p.T148S		Atlas-SNP	.											.	ZNF486	74	.	0			c.A442T						.						69.0	75.0	73.0					19																	20307961		2187	4294	6481	SO:0001583	missense	90649	exon4			TTGACAACTACCC	BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"""Zinc fingers, C2H2-type"", ""-"""	20807	protein-coding gene	gene with protein product			"""KRAB domain only 2"""	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.442A>T	chr19.hg19:g.20307961A>T	ENSP00000335042:p.Thr148Ser	174.0	0.0		249.0	94.0	NM_052852	Q0VG00	Missense_Mutation	SNP	ENST00000335117.8	hg19	CCDS46029.1	.	.	.	.	.	.	.	.	.	.	a	6.228	0.410191	0.11812	.	.	ENSG00000256229	ENST00000545779;ENST00000335117	T	0.47528	0.84	0.149	0.149	0.14863	.	.	.	.	.	T	0.40171	0.1106	L	0.43923	1.385	0.21355	N	0.999719	P	0.45078	0.85	P	0.46208	0.507	T	0.23332	-1.0191	8	0.27082	T	0.32	.	.	.	.	.	148	Q96H40	ZN486_HUMAN	S	187;148	ENSP00000335042:T148S	ENSP00000335042:T148S	T	+	1	0	ZNF486	20168961	0.001000	0.12720	0.052000	0.19188	0.052000	0.14988	1.065000	0.30592	0.166000	0.19597	0.164000	0.16699	ACT	.	.		0.318	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852	
ZNF568	374900	hgsc.bcm.edu	37	19	37440867	37440867	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:37440867T>A	ENST00000333987.7	+	7	1318	c.812T>A	c.(811-813)aTt>aAt	p.I271N	ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000415168.1_Missense_Mutation_p.I207N|ZNF568_ENST00000427117.1_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	271					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CATCAGAAAATTCATACTGGG	0.363																																					p.I271N		Atlas-SNP	.											.	ZNF568	106	.	0			c.T812A						.						37.0	41.0	39.0					19																	37440867		2123	4245	6368	SO:0001583	missense	374900	exon7			AGAAAATTCATAC	BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"""Zinc fingers, C2H2-type"", ""-"""	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.812T>A	chr19.hg19:g.37440867T>A	ENSP00000334685:p.Ile271Asn	80.0	0.0		112.0	49.0	NM_198539	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	hg19	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	T	14.59	2.580163	0.46006	.	.	ENSG00000198453	ENST00000333987;ENST00000415168	T;T	0.09073	3.02;3.02	3.95	3.95	0.45737	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.37483	N	0.002071	T	0.19087	0.0458	L	0.56769	1.78	0.58432	D	0.999999	D	0.57571	0.98	D	0.65573	0.936	T	0.00555	-1.1673	10	0.87932	D	0	.	6.0896	0.19987	0.0:0.1155:0.0:0.8845	.	271	Q3ZCX4	ZN568_HUMAN	N	271;207	ENSP00000334685:I271N;ENSP00000394514:I207N	ENSP00000334685:I271N	I	+	2	0	ZNF568	42132707	0.000000	0.05858	0.724000	0.30704	0.999000	0.98932	-0.359000	0.07632	1.775000	0.52247	0.533000	0.62120	ATT	.	.		0.363	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539	
PLD3	23646	hgsc.bcm.edu	37	19	40877640	40877640	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:40877640A>T	ENST00000409587.1	+	9	1136	c.739A>T	c.(739-741)Atc>Ttc	p.I247F	PLD3_ENST00000409419.1_Missense_Mutation_p.I247F|PLD3_ENST00000409281.1_Missense_Mutation_p.I247F|PLD3_ENST00000356508.5_Missense_Mutation_p.I247F|PLD3_ENST00000409735.4_Missense_Mutation_p.I247F			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	247					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			CCTGACCAAGATCTTTGAGGC	0.587																																					p.I247F		Atlas-SNP	.											.	PLD3	71	.	0			c.A739T						.						100.0	67.0	78.0					19																	40877640		2203	4300	6503	SO:0001583	missense	23646	exon9			ACCAAGATCTTTG	BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"""phospholipase D3"""			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.739A>T	chr19.hg19:g.40877640A>T	ENSP00000387050:p.Ile247Phe	74.0	0.0		86.0	31.0	NM_012268	Q92853|Q9BW87	Missense_Mutation	SNP	ENST00000409587.1	hg19	CCDS33027.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.176795	0.78564	.	.	ENSG00000105223	ENST00000409419;ENST00000409587;ENST00000356508;ENST00000536031;ENST00000409735;ENST00000409281	T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67	5.77	4.7	0.59300	Phospholipase D/viral envelope (1);	0.106329	0.64402	D	0.000005	T	0.65749	0.2721	M	0.83223	2.63	0.80722	D	1	D	0.67145	0.996	D	0.71414	0.973	T	0.68796	-0.5314	10	0.56958	D	0.05	-11.9012	7.2566	0.26179	0.872:0.0:0.128:0.0	.	247	Q8IV08	PLD3_HUMAN	F	247;247;247;228;247;247	ENSP00000386293:I247F;ENSP00000387050:I247F;ENSP00000348901:I247F;ENSP00000386938:I247F;ENSP00000387022:I247F	ENSP00000348901:I247F	I	+	1	0	PLD3	45569480	1.000000	0.71417	1.000000	0.80357	0.658000	0.38924	4.239000	0.58694	2.215000	0.71742	0.459000	0.35465	ATC	.	.		0.587	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268	
LIG1	3978	hgsc.bcm.edu	37	19	48643272	48643273	+	Missense_Mutation	DNP	CC	CC	AA			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:48643272_48643273CC>AA	ENST00000263274.7	-	12	1461_1462	c.1042_1043GG>TT	c.(1042-1044)GGc>TTc	p.G348F	LIG1_ENST00000427526.2_Missense_Mutation_p.G317F|LIG1_ENST00000536218.1_Missense_Mutation_p.G280F	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	348					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	ATCACCCACGCCAAGCTCCAGG	0.634								Nucleotide excision repair (NER)																													p.G348V|p.G348C		Atlas-SNP	.											.	LIG1	151	.	0			c.G1043T|c.G1042T						.																																			SO:0001583	missense	3978	exon12			CCCACGCCAAGCT|CCACGCCAAGCTC		CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.1042_1043delinsAA	chr19.hg19:g.48643272_48643273delinsAA	ENSP00000263274:p.Gly348Phe	54.0	0.0		85.0	27.0|26.0	NM_000234	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	hg19	CCDS12711.1																																																																																			.	.		0.634	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234	
KIR2DL3	3804	hgsc.bcm.edu	37	19	55263853	55263853	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:55263853A>T	ENST00000342376.3	+	8	939	c.908A>T	c.(907-909)tAt>tTt	p.Y303F	KIR3DL1_ENST00000541392.1_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR2DL3_ENST00000434419.2_Intron|KIR3DL1_ENST00000402254.2_Intron	NM_015868.2	NP_056952.2	P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3	303					immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		GAGGTGACATATGCACAGTTG	0.488																																					p.Y303F		Atlas-SNP	.											.	KIR2DL3	68	.	0			c.A908T						.						212.0	218.0	216.0					19																	55263853		2049	4015	6064	SO:0001583	missense	3804	exon8			TGACATATGCACA	L41268	CCDS33107.1	19q13.4	2013-01-29				ENSG00000243772		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6331	protein-coding gene	gene with protein product		604938				7749980, 8662091	Standard	XM_006725426		Approved	cl-6, nkat2, nkat2a, nkat2b, p58, CD158B2		P43628	OTTHUMG00000065887	ENST00000342376.3:c.908A>T	chr19.hg19:g.55263853A>T	ENSP00000342215:p.Tyr303Phe	113.0	0.0		130.0	66.0	NM_015868	O43472|P78402|Q14944|Q14945|Q9UM51|Q9UQ70	Missense_Mutation	SNP	ENST00000342376.3	hg19	CCDS33107.1	.	.	.	.	.	.	.	.	.	.	A	12.08	1.830010	0.32329	.	.	ENSG00000243772	ENST00000342376	T	0.00584	6.4	1.06	1.06	0.20224	.	.	.	.	.	T	0.03053	0.0090	H	0.94847	3.59	0.09310	N	0.999999	P;D;D	0.54964	0.927;0.969;0.969	D;P;P	0.67725	0.953;0.45;0.45	T	0.25328	-1.0135	9	0.87932	D	0	.	4.3665	0.11227	1.0:0.0:0.0:0.0	.	205;303;303	P43628-2;P43628;E3NZD8	.;KI2L3_HUMAN;.	F	303	ENSP00000342215:Y303F	ENSP00000342215:Y303F	Y	+	2	0	KIR2DL3	59955665	0.220000	0.23631	0.049000	0.19019	0.074000	0.17049	1.289000	0.33307	0.739000	0.32628	0.248000	0.18094	TAT	.	.		0.488	KIR2DL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000141150.1		
NLRP5	126206	hgsc.bcm.edu	37	19	56538847	56538847	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:56538847G>T	ENST00000390649.3	+	7	1248	c.1248G>T	c.(1246-1248)aaG>aaT	p.K416N		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	416	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		GCACAGAGAAGCTCAAGTCAG	0.557																																					p.K416N		Atlas-SNP	.											.	NLRP5	217	.	0			c.G1248T						.						48.0	49.0	49.0					19																	56538847		2091	4209	6300	SO:0001583	missense	126206	exon7			AGAGAAGCTCAAG	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.1248G>T	chr19.hg19:g.56538847G>T	ENSP00000375063:p.Lys416Asn	58.0	0.0		90.0	20.0	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	hg19	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.219706	0.39201	.	.	ENSG00000171487	ENST00000390649	T	0.78364	-1.17	3.35	1.01	0.19927	.	1.816140	0.03225	N	0.178137	T	0.78629	0.4313	L	0.54965	1.715	0.09310	N	1	B	0.30526	0.283	B	0.39465	0.3	T	0.63497	-0.6624	10	0.45353	T	0.12	.	9.1235	0.36801	0.0:0.443:0.557:0.0	.	416	P59047	NALP5_HUMAN	N	416	ENSP00000375063:K416N	ENSP00000375063:K416N	K	+	3	2	NLRP5	61230659	0.026000	0.19158	0.007000	0.13788	0.005000	0.04900	-0.017000	0.12590	0.352000	0.24053	0.655000	0.94253	AAG	.	.		0.557	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
ZNF667	63934	hgsc.bcm.edu	37	19	56953879	56953879	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:56953879T>A	ENST00000504904.3	-	7	1204	c.485A>T	c.(484-486)cAt>cTt	p.H162L	ZNF667_ENST00000292069.6_Missense_Mutation_p.H162L|ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Missense_Mutation_p.H290L			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	162					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		AATGTTCTGATGAAGTTTAAG	0.373																																					p.H162L		Atlas-SNP	.											.	ZNF667	95	.	0			c.A485T						.						83.0	87.0	86.0					19																	56953879		2203	4299	6502	SO:0001583	missense	63934	exon5			TTCTGATGAAGTT		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"""Zinc fingers, C2H2-type"", ""-"""	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.485A>T	chr19.hg19:g.56953879T>A	ENSP00000439402:p.His162Leu	109.0	0.0		139.0	60.0	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Missense_Mutation	SNP	ENST00000504904.3	hg19	CCDS12944.1	.	.	.	.	.	.	.	.	.	.	T	14.82	2.650751	0.47362	.	.	ENSG00000198046	ENST00000342634;ENST00000504904;ENST00000292069;ENST00000360227	D;D;D	0.86865	-2.18;-2.18;-2.18	4.86	4.86	0.63082	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45867	D	0.000339	D	0.95906	0.8667	H	0.98333	4.205	0.47659	D	0.999487	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.995	D	0.96963	0.9703	10	0.87932	D	0	-9.2598	12.4411	0.55625	0.0:0.0:0.0:1.0	.	290;162	E7EPS0;Q5HYK9	.;ZN667_HUMAN	L	290;162;162;36	ENSP00000344699:H290L;ENSP00000439402:H162L;ENSP00000292069:H162L	ENSP00000292069:H162L	H	-	2	0	ZNF667	61645691	1.000000	0.71417	0.752000	0.31206	0.002000	0.02628	5.373000	0.66162	2.037000	0.60232	0.477000	0.44152	CAT	.	.		0.373	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103	
CHGB	1114	hgsc.bcm.edu	37	20	5904188	5904188	+	Silent	SNP	G	G	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr20:5904188G>A	ENST00000378961.4	+	4	1602	c.1398G>A	c.(1396-1398)gaG>gaA	p.E466E		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	466						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						CGTGGAAAGAGCTGGACAGAA	0.522																																					p.E466E		Atlas-SNP	.											.	CHGB	112	.	0			c.G1398A						.						98.0	101.0	100.0					20																	5904188		2203	4300	6503	SO:0001819	synonymous_variant	1114	exon4			GAAAGAGCTGGAC		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.1398G>A	chr20.hg19:g.5904188G>A		55.0	0.0		92.0	40.0	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Silent	SNP	ENST00000378961.4	hg19	CCDS13092.1																																																																																			.	.		0.522	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
PLCB1	23236	hgsc.bcm.edu	37	20	8713899	8713899	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr20:8713899A>G	ENST00000338037.6	+	19	1930	c.1903A>G	c.(1903-1905)Ata>Gta	p.I635V	PLCB1_ENST00000378637.2_Missense_Mutation_p.I635V|PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378641.3_Missense_Mutation_p.I635V	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	635	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						GGCTATGCAAATAAATATGGG	0.393																																					p.P635A		Atlas-SNP	.											.	PLCB1	394	.	0			c.C1903G						.						123.0	117.0	119.0					20																	8713899		2203	4300	6503	SO:0001583	missense	23236	exon19			ATGCAAATAAATA	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.1903A>G	chr20.hg19:g.8713899A>G	ENSP00000338185:p.Ile635Val	90.0	0.0		110.0	56.0	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	hg19	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	A	13.25	2.181469	0.38511	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000441163;ENST00000535719	T;T;T	0.66460	-0.21;-0.21;-0.21	5.19	4.03	0.46877	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.127350	0.53938	D	0.000041	T	0.47600	0.1454	N	0.13299	0.325	0.33361	D	0.57238	B;B	0.18013	0.014;0.025	B;B	0.26416	0.069;0.041	T	0.56038	-0.8045	10	0.46703	T	0.11	.	7.9853	0.30207	0.7282:0.1385:0.0:0.1333	.	635;635	Q9NQ66;Q9NQ66-2	PLCB1_HUMAN;.	V	635;635;635;555;555	ENSP00000367908:I635V;ENSP00000338185:I635V;ENSP00000367904:I635V	ENSP00000338185:I635V	I	+	1	0	PLCB1	8661899	1.000000	0.71417	0.579000	0.28588	0.975000	0.68041	2.337000	0.43947	2.075000	0.62263	0.528000	0.53228	ATA	.	.		0.393	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		
CRNKL1	51340	hgsc.bcm.edu	37	20	20033133	20033133	+	Nonsense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr20:20033133T>A	ENST00000377340.2	-	2	368	c.337A>T	c.(337-339)Aga>Tga	p.R113*	CRNKL1_ENST00000536226.1_5'Flank|C20orf26_ENST00000377309.2_5'Flank|C20orf26_ENST00000377306.1_5'Flank|C20orf26_ENST00000389656.3_5'Flank|CRNKL1_ENST00000377327.4_Nonsense_Mutation_p.R101*|C20orf26_ENST00000245957.5_5'Flank	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	113					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						CTTTGACCTCTCGCTTGAGCC	0.597																																					p.R113X		Atlas-SNP	.											.	CRNKL1	101	.	0			c.A337T						.						79.0	76.0	77.0					20																	20033133		2203	4300	6503	SO:0001587	stop_gained	51340	exon2			GACCTCTCGCTTG	AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"""SYF3 pre-mRNA-splicing factor"""	610952	"""crooked neck (Drosophila Crn homolog)-like 1"", ""Crn, crooked neck-like 1 (Drosophila)"", ""crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"""				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.337A>T	chr20.hg19:g.20033133T>A	ENSP00000366557:p.Arg113*	81.0	0.0		100.0	34.0	NM_016652	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Nonsense_Mutation	SNP	ENST00000377340.2	hg19	CCDS33446.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.012309	0.75046	.	.	ENSG00000101343	ENST00000377327;ENST00000377340	.	.	.	5.38	-10.8	0.00216	.	1.951080	0.02912	N	0.136770	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0425	1.2283	0.01938	0.3008:0.1367:0.1404:0.4221	.	.	.	.	X	101;113	.	ENSP00000366544:R101X	R	-	1	2	CRNKL1	19981133	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-1.371000	0.02573	-3.650000	0.00126	-1.292000	0.01352	AGA	.	.		0.597	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1		
RALGAPA2	57186	hgsc.bcm.edu	37	20	20563863	20563863	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr20:20563863A>T	ENST00000202677.7	-	20	2545	c.2538T>A	c.(2536-2538)agT>agA	p.S846R		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	846					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						CACTGTTGGTACTTTCACCTG	0.433																																					p.S846R		Atlas-SNP	.											.	RALGAPA2	274	.	0			c.T2538A						.						80.0	77.0	78.0					20																	20563863		1903	4124	6027	SO:0001583	missense	57186	exon20			GTTGGTACTTTCA	AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 74"""	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.2538T>A	chr20.hg19:g.20563863A>T	ENSP00000202677:p.Ser846Arg	77.0	0.0		88.0	41.0	NM_020343	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Missense_Mutation	SNP	ENST00000202677.7	hg19	CCDS46584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.20|14.20	2.464979|2.464979	0.43839|0.43839	.|.	.|.	ENSG00000188559|ENSG00000188559	ENST00000202677|ENST00000430436	T|.	0.70282|.	-0.47|.	6.07|6.07	2.66|2.66	0.31614|0.31614	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.62877|0.62877	0.2464|0.2464	M|M	0.68317|0.68317	2.08|2.08	0.40371|0.40371	D|D	0.979341|0.979341	D;B|.	0.56746|.	0.977;0.053|.	P;B|.	0.54312|.	0.748;0.019|.	T|T	0.60265|0.60265	-0.7297|-0.7297	10|5	0.23891|.	T|.	0.37|.	.|.	9.32|9.32	0.37957|0.37957	0.7959:0.0:0.2041:0.0|0.7959:0.0:0.2041:0.0	.|.	684;846|.	A8MSM5;Q2PPJ7|.	.;RGPA2_HUMAN|.	R|E	846|663	ENSP00000202677:S846R|.	ENSP00000202677:S846R|.	S|V	-|-	3|2	2|0	RALGAPA2|RALGAPA2	20511863|20511863	1.000000|1.000000	0.71417|0.71417	0.984000|0.984000	0.44739|0.44739	0.949000|0.949000	0.60115|0.60115	2.317000|2.317000	0.43770|0.43770	0.539000|0.539000	0.28788|0.28788	0.533000|0.533000	0.62120|0.62120	AGT|GTA	.	.		0.433	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343	
SRSF6	6431	hgsc.bcm.edu	37	20	42089474	42089474	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr20:42089474A>G	ENST00000244020.3	+	6	912	c.806A>G	c.(805-807)tAt>tGt	p.Y269C		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	269	Arg/Ser-rich (RS domain).				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)	p.Y269C(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						AAGGATGAGTATGAGAAATCT	0.453																																					p.Y269C		Atlas-SNP	.											SRSF6_ENST00000244020,NS,carcinoma,0,1	SRSF6	37	.	1	Substitution - Missense(1)	lung(1)	c.A806G						.						55.0	56.0	56.0					20																	42089474		2203	4300	6503	SO:0001583	missense	6431	exon6			ATGAGTATGAGAA	U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10788	protein-coding gene	gene with protein product	"""pre-mRNA splicing factor SRP55"", ""SR splicing factor 6"""	601944	"""splicing factor, arginine/serine-rich 6"""	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.806A>G	chr20.hg19:g.42089474A>G	ENSP00000244020:p.Tyr269Cys	111.0	0.0		136.0	20.0	NM_006275	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Missense_Mutation	SNP	ENST00000244020.3	hg19	CCDS13318.1	.	.	.	.	.	.	.	.	.	.	A	7.519	0.656340	0.14580	.	.	ENSG00000124193	ENST00000244020	T	0.11169	2.8	5.83	4.75	0.60458	.	0.350840	0.26784	N	0.022505	T	0.09774	0.0240	L	0.36672	1.1	0.20873	N	0.999833	B	0.28512	0.214	B	0.26693	0.072	T	0.17961	-1.0352	10	0.48119	T	0.1	.	11.4682	0.50252	0.7846:0.2154:0.0:0.0	.	269	Q13247	SRSF6_HUMAN	C	269	ENSP00000244020:Y269C	ENSP00000244020:Y269C	Y	+	2	0	SRSF6	41522888	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.101000	0.50283	2.217000	0.71921	0.477000	0.44152	TAT	.	.		0.453	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275	
ZNF334	55713	hgsc.bcm.edu	37	20	45130663	45130663	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr20:45130663C>T	ENST00000347606.4	-	5	1497	c.1315G>A	c.(1315-1317)Gga>Aga	p.G439R	ZNF334_ENST00000457685.2_Missense_Mutation_p.G401R|ZNF334_ENST00000593880.1_Missense_Mutation_p.G462R	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	439					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G439R(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				AAAAATTTTCCACATTGACTG	0.378																																					p.G439R		Atlas-SNP	.											ZNF334,NS,carcinoma,0,1	ZNF334	101	.	1	Substitution - Missense(1)	kidney(1)	c.G1315A						.						115.0	113.0	114.0					20																	45130663		2203	4299	6502	SO:0001583	missense	55713	exon5			ATTTTCCACATTG	AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"""Zinc fingers, C2H2-type"", ""-"""	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.1315G>A	chr20.hg19:g.45130663C>T	ENSP00000255129:p.Gly439Arg	55.0	0.0		87.0	28.0	NM_018102	Q5T6U2|Q9NVW4	Missense_Mutation	SNP	ENST00000347606.4	hg19	CCDS33480.1	.	.	.	.	.	.	.	.	.	.	C	12.68	2.009792	0.35415	.	.	ENSG00000198185	ENST00000457685;ENST00000347606	T;T	0.22743	1.94;1.94	3.24	0.129	0.14739	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25044	0.0608	M	0.81239	2.535	0.35114	D	0.766422	B;B;B	0.26547	0.152;0.152;0.152	B;B;B	0.28232	0.087;0.087;0.087	T	0.18555	-1.0333	9	0.87932	D	0	.	7.0128	0.24871	0.0:0.6653:0.0:0.3347	.	401;439;462	B3KQ93;Q9HCZ1;Q8N3P8	.;ZN334_HUMAN;.	R	401;439	ENSP00000402582:G401R;ENSP00000255129:G439R	ENSP00000255129:G439R	G	-	1	0	ZNF334	44564070	0.296000	0.24398	0.009000	0.14445	0.977000	0.68977	0.397000	0.20883	-0.062000	0.13088	-0.216000	0.12614	GGA	.	.		0.378	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1		
IGSF5	150084	hgsc.bcm.edu	37	21	41151111	41151111	+	Silent	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr21:41151111A>T	ENST00000380588.4	+	5	916	c.813A>T	c.(811-813)ctA>ctT	p.L271L	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	271					single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				GACTTGGACTAGCAGGCACCA	0.488																																					p.L271L		Atlas-SNP	.											.	IGSF5	62	.	0			c.A813T						.						121.0	113.0	116.0					21																	41151111		2203	4300	6503	SO:0001819	synonymous_variant	150084	exon5			TGGACTAGCAGGC		CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5952	protein-coding gene	gene with protein product	"""junctional adhesion molecule 4"""	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.813A>T	chr21.hg19:g.41151111A>T		49.0	0.0		81.0	34.0	NM_001080444		Silent	SNP	ENST00000380588.4	hg19	CCDS33562.1																																																																																			.	.		0.488	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1		
CHEK2	11200	hgsc.bcm.edu	37	22	29130468	29130468	+	Missense_Mutation	SNP	T	T	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr22:29130468T>G	ENST00000405598.1	-	3	433	c.242A>C	c.(241-243)gAg>gCg	p.E81A	CHEK2_ENST00000544772.1_5'UTR|CHEK2_ENST00000402731.1_Missense_Mutation_p.E81A|CHEK2_ENST00000382580.2_Missense_Mutation_p.E81A|CHEK2_ENST00000382578.1_Missense_Mutation_p.E81A|CHEK2_ENST00000348295.3_Missense_Mutation_p.E81A|CHEK2_ENST00000382566.1_Missense_Mutation_p.E81A|CHEK2_ENST00000328354.6_Missense_Mutation_p.E81A|CHEK2_ENST00000404276.1_Missense_Mutation_p.E81A|CHEK2_ENST00000382565.1_Missense_Mutation_p.E81A|CHEK2_ENST00000403642.1_Missense_Mutation_p.E81A			O96017	CHK2_HUMAN	checkpoint kinase 2	81					cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						TTCTTGGTCCTCAGGTTCTTG	0.522			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.E81A		Atlas-SNP	.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	.	CHEK2	438	.	0			c.A242C						.						70.0	74.0	72.0					22																	29130468		2203	4300	6503	SO:0001583	missense	11200	exon2			TGGTCCTCAGGTT	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.242A>C	chr22.hg19:g.29130468T>G	ENSP00000386087:p.Glu81Ala	96.0	0.0		72.0	15.0	NM_145862	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	hg19	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	T	16.74	3.206881	0.58343	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000382565;ENST00000382566;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731;ENST00000447421;ENST00000439200;ENST00000398017	T;T;T;D;T;T;T;T;T;T;T;T;D	0.93488	0.84;-0.2;-0.26;-3.23;-0.12;-0.12;-0.12;2.27;-0.2;0.84;0.32;2.27;-2.27	5.41	5.41	0.78517	.	.	.	.	.	D	0.91703	0.7377	L	0.29908	0.895	0.40775	D	0.983123	D;D;D;D;P;D	0.60160	0.967;0.987;0.976;0.986;0.944;0.974	P;P;P;P;B;P	0.56163	0.716;0.754;0.541;0.793;0.437;0.793	D	0.89126	0.3506	9	0.09338	T	0.73	.	14.9223	0.70847	0.0:0.0:0.0:1.0	.	81;81;81;81;81;81	O96017-7;O96017-4;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	A	81;81;81;81;81;81;81;81;81;81;81;81;91	ENSP00000329012:E81A;ENSP00000372021:E81A;ENSP00000372006:E81A;ENSP00000372007:E81A;ENSP00000329178:E81A;ENSP00000385747:E81A;ENSP00000386087:E81A;ENSP00000372023:E81A;ENSP00000384919:E81A;ENSP00000384835:E81A;ENSP00000397478:E81A;ENSP00000408065:E81A;ENSP00000381099:E91A	ENSP00000329178:E81A	E	-	2	0	CHEK2	27460468	1.000000	0.71417	0.969000	0.41365	0.982000	0.71751	5.187000	0.65087	2.180000	0.69256	0.528000	0.53228	GAG	.	.		0.522	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735	
MCM5	4174	hgsc.bcm.edu	37	22	35812706	35812706	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr22:35812706G>C	ENST00000216122.4	+	12	1643	c.1489G>C	c.(1489-1491)Gag>Cag	p.E497Q	MCM5_ENST00000382011.5_Missense_Mutation_p.E454Q	NM_006739.3	NP_006730.2	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	497	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29						CCGCTGGGATGAGACGAAGGG	0.567																																					p.E497Q		Atlas-SNP	.											.	MCM5	54	.	0			c.G1489C						.						118.0	92.0	101.0					22																	35812706		2203	4300	6503	SO:0001583	missense	4174	exon12			TGGGATGAGACGA		CCDS13915.1	22q13.1-q13.2	2007-04-04	2007-04-04		ENSG00000100297	ENSG00000100297			6948	protein-coding gene	gene with protein product		602696	"""minichromosome maintenance deficient (S. cerevisiae) 5 (cell division cycle 46)"", ""MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"""	CDC46		8751386, 10591208	Standard	NM_006739		Approved		uc003anu.4	P33992	OTTHUMG00000150961	ENST00000216122.4:c.1489G>C	chr22.hg19:g.35812706G>C	ENSP00000216122:p.Glu497Gln	69.0	0.0		63.0	25.0	NM_006739	O60785|Q14578|Q9BTJ4|Q9BWL8	Missense_Mutation	SNP	ENST00000216122.4	hg19	CCDS13915.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.892370	0.91889	.	.	ENSG00000100297	ENST00000216122;ENST00000382011	T;T	0.06528	3.29;3.29	5.77	4.73	0.59995	.	0.148087	0.64402	D	0.000010	T	0.13628	0.0330	L	0.37507	1.11	0.47547	D	0.999451	P;P;P;P	0.37276	0.589;0.589;0.589;0.589	P;P;P;P	0.50136	0.632;0.632;0.565;0.632	T	0.02676	-1.1125	10	0.87932	D	0	-27.8061	16.6228	0.84934	0.0:0.1302:0.8698:0.0	.	497;497;454;497	B1AHB0;Q53FG5;B1AHB1;P33992	.;.;.;MCM5_HUMAN	Q	497;454	ENSP00000216122:E497Q;ENSP00000371441:E454Q	ENSP00000216122:E497Q	E	+	1	0	MCM5	34142706	1.000000	0.71417	0.990000	0.47175	0.954000	0.61252	3.776000	0.55356	1.403000	0.46800	0.650000	0.86243	GAG	.	.		0.567	MCM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320661.3		
C22orf46	79640	hgsc.bcm.edu	37	22	42086739	42086739	+	Silent	SNP	T	T	G			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr22:42086739T>G	ENST00000402966.1	+	1	193	c.108T>G	c.(106-108)ccT>ccG	p.P36P	NHP2L1_ENST00000402458.1_5'Flank|NHP2L1_ENST00000355257.3_5'Flank|C22orf46_ENST00000472110.2_Intron|NHP2L1_ENST00000401959.1_5'Flank|NHP2L1_ENST00000463675.1_5'Flank	NM_001142964.1	NP_001136436.1	C9J442	CV046_HUMAN	chromosome 22 open reading frame 46	36						extracellular region (GO:0005576)											GCAGGGACCCTCAGTGCTGTG	0.622																																					p.P36P		Atlas-SNP	.											.	C22orf46	4	.	0			c.T108G						.						91.0	80.0	83.0					22																	42086739		692	1591	2283	SO:0001819	synonymous_variant	79640	exon1			GGACCCTCAGTGC	BC007210	CCDS46717.1	22q13.2	2011-01-25			ENSG00000184208	ENSG00000184208			26294	protein-coding gene	gene with protein product						12477932	Standard	NM_001142964		Approved	FLJ23584, CTA-216E10.6	uc003bax.1	C9J442	OTTHUMG00000151188	ENST00000402966.1:c.108T>G	chr22.hg19:g.42086739T>G		52.0	0.0		48.0	12.0	NM_001142964		Silent	SNP	ENST00000402966.1	hg19	CCDS46717.1																																																																																			.	.		0.622	C22orf46-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321678.2	NM_024588	
PHEX	5251	hgsc.bcm.edu	37	X	22056646	22056646	+	Missense_Mutation	SNP	A	A	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:22056646A>C	ENST00000379374.4	+	2	743	c.178A>C	c.(178-180)Atc>Ctc	p.I60L	PHEX_ENST00000537599.1_Missense_Mutation_p.I60L|PHEX_ENST00000535894.1_5'UTR	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN	phosphate regulating endopeptidase homolog, X-linked	60					bone mineralization (GO:0030282)|cell-cell signaling (GO:0007267)|cellular protein modification process (GO:0006464)|organophosphate metabolic process (GO:0019637)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(2)|large_intestine(12)|liver(1)|lung(19)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	42						GCCAGAATGCATCGAAGCGGG	0.418																																					p.I60L		Atlas-SNP	.											.	PHEX	95	.	0			c.A178C						.						230.0	204.0	213.0					X																	22056646		2203	4300	6503	SO:0001583	missense	5251	exon2			GAATGCATCGAAG	U82970	CCDS14204.1	Xp22.2-p22.1	2008-07-31	2008-07-31		ENSG00000102174	ENSG00000102174			8918	protein-coding gene	gene with protein product		300550	"""phosphate regulating gene with homologies to endopeptidases on the X chromosome (hypophosphatemia, vitamin D resistant rickets)"""	HYP, HPDR		7550339, 9070861	Standard	NM_000444		Approved	PEX, HPDR1, HYP1, XLH	uc004dah.3	P78562	OTTHUMG00000021241	ENST00000379374.4:c.178A>C	chrX.hg19:g.22056646A>C	ENSP00000368682:p.Ile60Leu	39.0	0.0		38.0	28.0	NM_000444	O00678|Q13646|Q2M325|Q93032|Q99827	Missense_Mutation	SNP	ENST00000379374.4	hg19	CCDS14204.1	.	.	.	.	.	.	.	.	.	.	A	15.01	2.705829	0.48412	.	.	ENSG00000102174	ENST00000379374;ENST00000537599	D;D	0.82081	-1.57;-1.57	5.58	1.82	0.25136	.	0.306400	0.39909	N	0.001234	T	0.67608	0.2911	N	0.14661	0.345	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.57283	-0.7838	10	0.66056	D	0.02	.	9.0666	0.36467	0.7843:0.0:0.2157:0.0	.	60;60	F5GXU4;P78562	.;PHEX_HUMAN	L	60	ENSP00000368682:I60L;ENSP00000440362:I60L	ENSP00000368682:I60L	I	+	1	0	PHEX	21966567	1.000000	0.71417	0.640000	0.29408	0.987000	0.75469	2.298000	0.43602	-0.031000	0.13781	-0.335000	0.08231	ATC	.	.		0.418	PHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056035.1	NM_000444	
KLHL15	80311	hgsc.bcm.edu	37	X	24006693	24006693	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:24006693C>A	ENST00000328046.8	-	4	1415	c.1160G>T	c.(1159-1161)aGa>aTa	p.R387I		NM_030624.2	NP_085127.2	Q96M94	KLH15_HUMAN	kelch-like family member 15	387					protein ubiquitination (GO:0016567)					autonomic_ganglia(1)|breast(1)|endometrium(8)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	22						ATCTCTGGTTCTGCCTGCTAC	0.433																																					p.R387I		Atlas-SNP	.											.	KLHL15	50	.	0			c.G1160T						.						158.0	133.0	141.0					X																	24006693		2203	4300	6503	SO:0001583	missense	80311	exon4			CTGGTTCTGCCTG	AB051464	CCDS35217.1	Xp22.1-p21	2013-01-30	2013-01-30		ENSG00000174010	ENSG00000174010		"""Kelch-like"", ""BTB/POZ domain containing"""	29347	protein-coding gene	gene with protein product			"""kelch-like 15 (Drosophila)"""			11214970, 14702039	Standard	NM_030624		Approved	KIAA1677	uc004dba.4	Q96M94	OTTHUMG00000021261	ENST00000328046.8:c.1160G>T	chrX.hg19:g.24006693C>A	ENSP00000332791:p.Arg387Ile	97.0	0.0		102.0	91.0	NM_030624	Q32MN3|Q8NDA3|Q96BM6|Q9C0I6	Missense_Mutation	SNP	ENST00000328046.8	hg19	CCDS35217.1	.	.	.	.	.	.	.	.	.	.	C	15.87	2.961028	0.53400	.	.	ENSG00000174010	ENST00000328046	T	0.78481	-1.18	5.49	5.49	0.81192	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.83899	0.5354	L	0.42487	1.325	0.80722	D	1	D	0.71674	0.998	D	0.65874	0.939	D	0.84113	0.0402	10	0.49607	T	0.09	.	18.6167	0.91305	0.0:1.0:0.0:0.0	.	387	Q96M94	KLH15_HUMAN	I	387	ENSP00000332791:R387I	ENSP00000332791:R387I	R	-	2	0	KLHL15	23916614	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.294000	0.78760	2.426000	0.82243	0.506000	0.49869	AGA	.	.		0.433	KLHL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056078.1	XM_040383	
DCAF8L1	139425	hgsc.bcm.edu	37	X	27999289	27999289	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:27999289T>A	ENST00000441525.1	-	1	277	c.163A>T	c.(163-165)Agg>Tgg	p.R55W		NM_001017930.1	NP_001017930.1	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	55										NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(24)|ovary(3)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	56						CCACCATCCCTGGTATCACCA	0.527																																					p.R55W		Atlas-SNP	.											.	DCAF8L1	121	.	0			c.A163T						.						135.0	99.0	111.0					X																	27999289		2202	4300	6502	SO:0001583	missense	139425	exon1			CATCCCTGGTATC		CCDS35222.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17	ENSG00000226372	ENSG00000226372		"""WD repeat domain containing"""	31810	protein-coding gene	gene with protein product			"""WD repeat domain 42B"""	WDR42B			Standard	NM_001017930		Approved		uc004dbx.1	A6NGE4	OTTHUMG00000021312	ENST00000441525.1:c.163A>T	chrX.hg19:g.27999289T>A	ENSP00000405222:p.Arg55Trp	93.0	0.0		108.0	91.0	NM_001017930	B3KXX1	Missense_Mutation	SNP	ENST00000441525.1	hg19	CCDS35222.1	.	.	.	.	.	.	.	.	.	.	T	10.30	1.312153	0.23821	.	.	ENSG00000226372	ENST00000441525	T	0.64618	-0.11	0.842	-1.08	0.09936	.	1.668810	0.04494	U	0.380061	T	0.55513	0.1925	L	0.50333	1.59	0.09310	N	1	D	0.59357	0.985	B	0.43754	0.43	T	0.50338	-0.8840	10	0.62326	D	0.03	.	4.4695	0.11704	0.0:0.0:0.3321:0.6679	.	55	A6NGE4	DC8L1_HUMAN	W	55	ENSP00000405222:R55W	ENSP00000405222:R55W	R	-	1	2	DCAF8L1	27909210	0.002000	0.14202	0.006000	0.13384	0.101000	0.19017	0.053000	0.14184	-0.346000	0.08312	0.235000	0.17854	AGG	.	.		0.527	DCAF8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056150.2	XM_066690	
CCNB3	85417	hgsc.bcm.edu	37	X	50053768	50053768	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:50053768A>T	ENST00000376042.1	+	6	2897	c.2599A>T	c.(2599-2601)Agc>Tgc	p.S867C	CCNB3_ENST00000376038.1_Intron|CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000276014.7_Missense_Mutation_p.S867C			Q8WWL7	CCNB3_HUMAN	cyclin B3	867					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					GGAGAAGCCCAGCATTGAGCA	0.537																																					p.S867C		Atlas-SNP	.											.	CCNB3	367	.	0			c.A2599T						.						45.0	38.0	40.0					X																	50053768		2203	4300	6503	SO:0001583	missense	85417	exon5			AAGCCCAGCATTG	AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.2599A>T	chrX.hg19:g.50053768A>T	ENSP00000365210:p.Ser867Cys	84.0	0.0		111.0	94.0	NM_033031	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	hg19	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	A	14.68	2.606232	0.46527	.	.	ENSG00000147082	ENST00000376042;ENST00000276014	T;T	0.35973	1.28;1.28	4.07	0.0577	0.14324	.	60.879100	0.00166	N	0.000000	T	0.32556	0.0833	L	0.38175	1.15	0.09310	N	1	D	0.60160	0.987	P	0.48189	0.57	T	0.11324	-1.0592	9	.	.	.	.	0.7114	0.00925	0.467:0.2082:0.1198:0.205	.	867	Q8WWL7	CCNB3_HUMAN	C	867	ENSP00000365210:S867C;ENSP00000276014:S867C	.	S	+	1	0	CCNB3	50070508	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.136000	0.10405	-0.081000	0.12662	0.430000	0.28490	AGC	.	.		0.537	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1		
GABRA3	2556	hgsc.bcm.edu	37	X	151336877	151336877	+	Silent	SNP	G	G	C			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:151336877G>C	ENST00000370314.4	-	10	1540	c.1302C>G	c.(1300-1302)ccC>ccG	p.P434P	GABRA3_ENST00000535043.1_Silent_p.P434P|RP11-329E24.6_ENST00000453915.1_RNA	NM_000808.3	NP_000799.1	P34903	GBRA3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 3	434					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(6)	37	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	AGGTGGCCTTGGGTGAAGCAA	0.532																																					p.P434P	NSCLC(142;2578 2613 10251 16743)	Atlas-SNP	.											.	GABRA3	97	.	0			c.C1302G						.						305.0	240.0	262.0					X																	151336877		2203	4300	6503	SO:0001819	synonymous_variant	2556	exon10			GGCCTTGGGTGAA		CCDS14706.1	Xq28	2012-06-22			ENSG00000011677	ENSG00000011677		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4077	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 3"""	305660					Standard	NM_000808		Approved		uc010ntk.1	P34903	OTTHUMG00000024183	ENST00000370314.4:c.1302C>G	chrX.hg19:g.151336877G>C		127.0	0.0		273.0	71.0	NM_000808	Q8TAF9	Silent	SNP	ENST00000370314.4	hg19	CCDS14706.1																																																																																			.	.		0.532	GABRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060921.1	NM_000808	
MECP2	4204	hgsc.bcm.edu	37	X	153295883	153295883	+	Missense_Mutation	SNP	T	T	A	rs267608630		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:153295883T>A	ENST00000303391.6	-	4	1645	c.1396A>T	c.(1396-1398)Atg>Ttg	p.M466L	MECP2_ENST00000460227.1_5'Flank|MECP2_ENST00000453960.2_Missense_Mutation_p.M478L	NM_004992.3	NP_004983.1	P51608	MECP2_HUMAN	methyl CpG binding protein 2	466				M -> V (in Ref. 7; CAD97991). {ECO:0000305}.	adult locomotory behavior (GO:0008344)|behavioral fear response (GO:0001662)|cardiolipin metabolic process (GO:0032048)|catecholamine secretion (GO:0050432)|cerebellum development (GO:0021549)|chromatin silencing (GO:0006342)|dendrite development (GO:0016358)|glucocorticoid metabolic process (GO:0008211)|glutamine metabolic process (GO:0006541)|histone acetylation (GO:0016573)|histone methylation (GO:0016571)|inositol metabolic process (GO:0006020)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone methylation (GO:0031061)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron maturation (GO:0042551)|pathogenesis (GO:0009405)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of cell proliferation (GO:0008284)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|proprioception (GO:0019230)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|startle response (GO:0001964)|synapse assembly (GO:0007416)|transcription, DNA-templated (GO:0006351)|ventricular system development (GO:0021591)|visual learning (GO:0008542)	cytosol (GO:0005829)|extracellular space (GO:0005615)|heterochromatin (GO:0000792)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|methyl-CpG binding (GO:0008327)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|siRNA binding (GO:0035197)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|prostate(2)|urinary_tract(1)	23	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGCCTTGGCATGGAGGATGAA	0.582																																					p.M478L		Atlas-SNP	.											.	MECP2	41	.	0			c.A1432T						.						253.0	219.0	230.0					X																	153295883		2203	4300	6503	SO:0001583	missense	4204	exon3			TTGGCATGGAGGA	AF158180	CCDS14741.1, CCDS48193.1	Xq28	2014-09-17	2014-06-18		ENSG00000169057	ENSG00000169057			6990	protein-coding gene	gene with protein product		300005	"""mental retardation, X-linked 16"", ""mental retardation, X-linked 79"", ""Rett syndrome"", ""methyl CpG binding protein 2 (Rett syndrome)"""	RTT, MRX16, MRX79		1606614, 10508514	Standard	NM_004992		Approved		uc004fjw.2	P51608	OTTHUMG00000024229	ENST00000303391.6:c.1396A>T	chrX.hg19:g.153295883T>A	ENSP00000301948:p.Met466Leu	48.0	0.0		116.0	52.0	NM_001110792	O15233|Q6QHH9|Q7Z384	Missense_Mutation	SNP	ENST00000303391.6	hg19	CCDS14741.1	.	.	.	.	.	.	.	.	.	.	T	12.35	1.911461	0.33721	.	.	ENSG00000169057	ENST00000303391;ENST00000453960	D;D	0.88354	-2.37;-2.36	5.67	4.48	0.54585	.	0.160656	0.56097	N	0.000025	T	0.77253	0.4103	N	0.19112	0.55	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.65442	-0.6167	10	0.23302	T	0.38	-12.9611	5.0745	0.14625	0.0:0.0937:0.1833:0.7231	.	478;466	P51608-2;P51608	.;MECP2_HUMAN	L	466;478	ENSP00000301948:M466L;ENSP00000395535:M478L	ENSP00000301948:M466L	M	-	1	0	MECP2	152949077	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.156000	0.31712	0.737000	0.32582	0.417000	0.27973	ATG	.	.		0.582	MECP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061144.1	NM_004992	
DNASE1L1	1774	hgsc.bcm.edu	37	X	153637534	153637534	+	Splice_Site	SNP	T	T	A			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:153637534T>A	ENST00000369809.1	-	3	458		c.e3-2		DNASE1L1_ENST00000393638.1_Intron|TAZ_ENST00000350743.4_5'Flank|TAZ_ENST00000475699.1_5'Flank|TAZ_ENST00000351413.4_5'Flank|TAZ_ENST00000369790.4_5'Flank|TAZ_ENST00000369776.4_5'Flank|TAZ_ENST00000299328.5_5'Flank	NM_001009932.1	NP_001009932.1	P49184	DNSL1_HUMAN	deoxyribonuclease I-like 1						DNA metabolic process (GO:0006259)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			lung(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGAATAGGGCTAGGAGGGGAA	0.617											OREG0003601	type=REGULATORY REGION|Gene=DNASE1L1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									.		Atlas-SNP	.											.	DNASE1L1	20	.	0			.						.																																			SO:0001630	splice_region_variant	1774	.			TAGGGCTAGGAGG	L40817	CCDS14747.1	Xq28	2008-02-05			ENSG00000013563	ENSG00000013563			2957	protein-coding gene	gene with protein product	"""DNase X"""	300081		DNL1L		8541839, 8654957	Standard	XM_005277829		Approved	DNAS1L1, XIB, DNASEX	uc004fkw.1	P49184	OTTHUMG00000033188	ENST00000369809.1:c.172-2A>T	chrX.hg19:g.153637534T>A		28.0	0.0	1757	73.0	30.0	.	D3DWW7|Q5HY41	Splice_Site	SNP	ENST00000369809.1	hg19	CCDS14747.1																																																																																			.	.		0.617	DNASE1L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Intron
CNNM1	26507	hgsc.bcm.edu	37	10	101124744	101124744	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr10:101124744delG	ENST00000356713.4	+	6	2450	c.2161delG	c.(2161-2163)ggafs	p.G721fs	CNNM1_ENST00000370534.4_Frame_Shift_Del_p.G356fs|CNNM1_ENST00000370528.3_Frame_Shift_Del_p.G650fs|CNNM1_ENST00000446890.1_Frame_Shift_Del_p.G650fs	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	721					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		AAGTCTGGCTGGATCTTCTGT	0.517																																					p.A720fs		Atlas-Indel,Pindel	.											.	CNNM1	101	.	0			c.2160delT						.						201.0	161.0	174.0					10																	101124744		2203	4300	6503	SO:0001589	frameshift_variant	26507	exon6			.	AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"""cyclin M1"""	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.2161delG	chr10.hg19:g.101124744delG	ENSP00000349147:p.Gly721fs	56.0	0.0		50.0	35.0	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Frame_Shift_Del	DEL	ENST00000356713.4	hg19	CCDS7478.2																																																																																			.	.		0.517	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348	
TTC28	23331	hgsc.bcm.edu	37	22	28426324	28426325	+	In_Frame_Ins	INS	-	-	TCA			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr22:28426324_28426325insTCA	ENST00000397906.2	-	13	4103_4104	c.3962_3963insTGA	c.(3961-3963)gaa>gaTGAa	p.1320_1321insD		NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	1320					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						TGTCTCCCGCTTCACTCTCTGT	0.51																																					p.E1321delinsDE		Atlas-Indel,Pindel	.											.	TTC28	84	.	0			c.3963_3964insTGA						.																																			SO:0001652	inframe_insertion	23331	exon13			.	AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.3960_3962dupTGA	chr22.hg19:g.28426325_28426327dupTCA	ENSP00000381003:p.Ser1320_Glu1321insAsp	112.0	0.0		99.0	24.0	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	In_Frame_Ins	INS	ENST00000397906.2	hg19	CCDS46678.1																																																																																			.	.		0.510	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
SLC10A1	6554	hgsc.bcm.edu	37	14	70245100	70245110	+	Frame_Shift_Del	DEL	AGCCCTTCTCC	AGCCCTTCTCC	-	rs376884319|rs201076064|rs202023002		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	AGCCCTTCTCC	AGCCCTTCTCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr14:70245100_70245110delAGCCCTTCTCC	ENST00000216540.4	-	4	1016_1026	c.883_893delGGAGAAGGGCT	c.(883-894)ggagaagggcttfs	p.GEGL295fs		NM_003049.3	NP_003040.1	Q14973	NTCP_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 1	295					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)	14				all cancers(60;0.00228)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0226)	Bumetanide(DB00887)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Ethinyl Estradiol(DB00977)|Indomethacin(DB00328)|Liothyronine(DB00279)|Liotrix(DB01583)|Pitavastatin(DB08860)|Probenecid(DB01032)|Progesterone(DB00396)|Testosterone(DB00624)|Ursodeoxycholic acid(DB01586)	AATGAGGAGAAGCCCTTCTCCAAGCTGGAAA	0.441																																					p.295_298del		Atlas-Indel,Pindel	.											.	SLC10A1	32	.	0			c.884_894del						.																																			SO:0001589	frameshift_variant	6554	exon4			.	L21893	CCDS9797.1	14q24.2	2013-07-18	2013-07-18		ENSG00000100652	ENSG00000100652		"""Solute carriers"""	10905	protein-coding gene	gene with protein product		182396				8132774	Standard	NM_003049		Approved	NTCP	uc001xlr.2	Q14973	OTTHUMG00000171236	ENST00000216540.4:c.883_893delGGAGAAGGGCT	chr14.hg19:g.70245100_70245110delAGCCCTTCTCC	ENSP00000216540:p.Gly295fs	94.0	0.0		100.0	26.0	NM_003049	B9EGB6|Q2TU29	Frame_Shift_Del	DEL	ENST00000216540.4	hg19	CCDS9797.1																																																																																			.	.		0.441	SLC10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412464.1		
TMEM184A	202915	hgsc.bcm.edu	37	7	1586662	1586663	+	In_Frame_Ins	INS	-	-	GCC	rs3837151|rs3779607	byFrequency	TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:1586662_1586663insGCC	ENST00000297477.5	-	9	1483_1484	c.1167_1168insGGC	c.(1165-1170)cccagc>cccGGCagc	p.389_390PS>PGS	TMEM184A_ENST00000449955.1_5'Flank	NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	389			S -> G (in dbSNP:rs3779607). {ECO:0000269|PubMed:15489334}.		germ-line sex determination (GO:0018992)|regulation of protein localization (GO:0032880)|regulation of secretion (GO:0051046)	early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)		GAGCCGCCGCTGGGGTGGGTGC	0.703																																					p.S390delinsGS		Atlas-INDEL	.											.,1	TMEM184A	35	.	0			c.1168_1169insGGC						.			1912,2170		535,842,664						-3.6	0.0		dbSNP_132	17	3872,4214		1028,1816,1199	no	coding	TMEM184A	NM_001097620.1		1563,2658,1863	A1A1,A1R,RR		47.8852,46.8398,47.5345				5784,6384				SO:0001652	inframe_insertion	202915	exon9			.		CCDS43537.1	7p22.3	2008-05-02			ENSG00000164855	ENSG00000164855			28797	protein-coding gene	gene with protein product						12477932	Standard	NM_001097620		Approved	MGC9712	uc003skv.4	Q6ZMB5	OTTHUMG00000119025	ENST00000297477.5:c.1167_1168insGGC	chr7.hg19:g.1586662_1586663insGCC	ENSP00000297477:p.Pro389_Ser390insGly	10.0	0.0		18.0	11.0	NM_001097620	Q8TBQ6	In_Frame_Ins	INS	ENST00000297477.5	hg19	CCDS43537.1																																																																																			.	.		0.703	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689	
BTBD8	284697	hgsc.bcm.edu	37	1	92554445	92554445	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:92554445delT	ENST00000342818.3	+	2	576	c.340delT	c.(340-342)tttfs	p.F114fs	BTBD8_ENST00000370382.3_Frame_Shift_Del_p.F114fs|BTBD8_ENST00000540648.1_Frame_Shift_Del_p.F114fs	NM_183242.3	NP_899065.2	Q5XKL5	BTBD8_HUMAN	BTB (POZ) domain containing 8	114	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.					nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)	16		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)		ATTTAGAACGTTTTTACAGTA	0.274																																					p.T113fs		Atlas-Indel,Pindel	.											.	BTBD8	32	.	0			c.339delG						.						85.0	79.0	81.0					1																	92554445		2202	4299	6501	SO:0001589	frameshift_variant	284697	exon2			.	AY346333	CCDS737.1	1p22.1	2013-01-08			ENSG00000189195	ENSG00000189195		"""BTB/POZ domain containing"""	21019	protein-coding gene	gene with protein product						14654994	Standard	NM_183242		Approved		uc001doo.3	Q5XKL5	OTTHUMG00000010289	ENST00000342818.3:c.340delT	chr1.hg19:g.92554445delT	ENSP00000343686:p.Phe114fs	107.0	0.0		90.0	49.0	NM_183242	Q6V9S5	Frame_Shift_Del	DEL	ENST00000342818.3	hg19	CCDS737.1																																																																																			.	.		0.274	BTBD8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028372.1	NM_183242	
RYR3	6263	hgsc.bcm.edu	37	15	34109120	34109120	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr15:34109120delG	ENST00000389232.4	+	75	10630	c.10560delG	c.(10558-10560)gagfs	p.E3521fs	RYR3_ENST00000415757.3_Frame_Shift_Del_p.E3516fs	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3521					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TAGAAACAGAGGAGTATTCCT	0.458																																					p.E3520fs		Atlas-Indel,Pindel	.											.	RYR3	760	.	0			c.10559delA						.						70.0	67.0	68.0					15																	34109120		1865	4108	5973	SO:0001589	frameshift_variant	6263	exon75			.		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.10560delG	chr15.hg19:g.34109120delG	ENSP00000373884:p.Glu3521fs	94.0	0.0		110.0	42.0	NM_001036	O15175|Q15412	Frame_Shift_Del	DEL	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.		0.458	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
PDE1C	5137	hgsc.bcm.edu	37	7	31855598	31855599	+	Frame_Shift_Del	DEL	CA	CA	-			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:31855598_31855599delCA	ENST00000396191.1	-	15	2207_2208	c.1752_1753delTG	c.(1750-1755)agtgacfs	p.SD584fs	PDE1C_ENST00000321453.7_Frame_Shift_Del_p.SD584fs|PDE1C_ENST00000396193.1_Frame_Shift_Del_p.SD644fs|PDE1C_ENST00000479980.1_5'UTR|PDE1C_ENST00000396182.2_Frame_Shift_Del_p.SD584fs|PDE1C_ENST00000396184.3_Frame_Shift_Del_p.SD584fs	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	584					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	CGAGGGTTGTCACTTTTGTTTG	0.48																																					p.645_645del		Atlas-Indel,Pindel	.											.	PDE1C	465	.	0			c.1933_1934del						.																																			SO:0001589	frameshift_variant	5137	exon16			.	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1752_1753delTG	chr7.hg19:g.31855598_31855599delCA	ENSP00000379494:p.Ser584fs	112.0	0.0		161.0	48.0	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Frame_Shift_Del	DEL	ENST00000396191.1	hg19	CCDS55099.1																																																																																			.	.		0.480	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
NFRKB	4798	hgsc.bcm.edu	37	11	129751620	129751644	+	Splice_Site	DEL	AAAAAAGAGCATCTTACCTCGACTT	AAAAAAGAGCATCTTACCTCGACTT	-			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	AAAAAAGAGCATCTTACCTCGACTT	AAAAAAGAGCATCTTACCTCGACTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:129751620_129751644delAAAAAAGAGCATCTTACCTCGACTT	ENST00000446488.3	-	11	1399_1422	c.1296_1319delAAGTCGAGGTAAGATGCTCTTTTTT	c.(1294-1320)caaagtcgaggtaagatgctctttttt>cat	p.QSRGKMLFF432fs	NFRKB_ENST00000304521.5_Splice_Site_p.QSRGKMLFF432fs|NFRKB_ENST00000524746.1_Splice_Site_p.QSRGKMLFF432fs|NFRKB_ENST00000524794.1_Splice_Site_p.QSRGKMLFF457fs	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	432	Winged-helix like domain.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)	p.R464P(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		AGAGCATCTTACCTCGACTTTCTCCAGCAAGATACTGCAGGGCTG	0.48											OREG0021512	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.463_465del		Atlas-Indel,Pindel	.											.	NFRKB	101	.	1	Substitution - Missense(1)	lung(1)	c.1387_1393del						.																																			SO:0001630	splice_region_variant	4798	exon10			.		CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"""INO80 complex subunits"""	7802	protein-coding gene	gene with protein product	"""nuclear factor related to kappa B binding protein"", ""DNA-binding protein R kappa B"", ""INO80 complex subunit G"""	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.1318+1AAGTCGAGGTAAGATGCTCTTTTTT>-	chr11.hg19:g.129751620_129751644delAAAAAAGAGCATCTTACCTCGACTT		80.0	0.0	1574	76.0	11.0	NM_006165	Q12869|Q15312|Q9H048	Frame_Shift_Del	DEL	ENST00000446488.3	hg19	CCDS44770.1																																																																																			.	.		0.480	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165	Frame_Shift_Del
ACVR2A	92	hgsc.bcm.edu	37	2	148653984	148653984	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:148653984delG	ENST00000241416.7	+	2	806	c.170delG	c.(169-171)cggfs	p.R58fs	ACVR2A_ENST00000535787.1_5'UTR|AC009480.3_ENST00000402410.2_RNA|ACVR2A_ENST00000404590.1_Frame_Shift_Del_p.R58fs	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	58					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		AAAGATAAACGGCGGCATTGT	0.388																																					p.R57fs		Atlas-INDEL	.											ACVR2A,colon,carcinoma,0,1	ACVR2A	125	.	0			c.169delC						.						177.0	173.0	175.0					2																	148653984		2203	4300	6503	SO:0001589	frameshift_variant	92	exon2			.		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"""activin A receptor, type II"""	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.170delG	chr2.hg19:g.148653984delG	ENSP00000241416:p.Arg58fs	74.0	0.0		95.0	23.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Frame_Shift_Del	DEL	ENST00000241416.7	hg19	CCDS33301.1																																																																																			.	.		0.388	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616	
JARID2	3720	hgsc.bcm.edu	37	6	15496721	15496722	+	Frame_Shift_Ins	INS	-	-	G	rs554145993		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr6:15496721_15496722insG	ENST00000341776.2	+	7	1509_1510	c.1265_1266insG	c.(1264-1269)gtggggfs	p.VG422fs	JARID2_ENST00000541660.1_Frame_Shift_Ins_p.VG384fs|JARID2_ENST00000397311.3_Frame_Shift_Ins_p.VG250fs	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	422					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				ACTAAGGAGGTGGGGGGGCGGC	0.668																																					p.V422fs		Atlas-INDEL	.											.,1	JARID2	135	.	0			c.1265_1266insG						.																																			SO:0001589	frameshift_variant	3720	exon7			.	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"""jumonji (mouse) homolog"", ""Jumonji, AT rich interactive domain 2"""	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.1272dupG	chr6.hg19:g.15496728_15496728dupG	ENSP00000341280:p.Val422fs	58.0	0.0		75.0	11.0	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Frame_Shift_Ins	INS	ENST00000341776.2	hg19	CCDS4533.1																																																																																			.	.		0.668	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
FCRL2	79368	hgsc.bcm.edu	37	1	157740434	157740434	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:157740434delG	ENST00000361516.3	-	3	123	c.75delC	c.(73-75)cccfs	p.P25fs	FCRL2_ENST00000368181.4_Frame_Shift_Del_p.P25fs|FCRL2_ENST00000469986.1_5'Flank|FCRL2_ENST00000392274.3_Frame_Shift_Del_p.P25fs	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	25	Ig-like C2-type 1.				cell-cell signaling (GO:0007267)|positive regulation of signal transduction (GO:0009967)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			AGACAGAAGAGGGCGCCACAA	0.483																																					p.S26fs		Atlas-Indel,Pindel	.											.	FCRL2	104	.	0			c.76delT						.						40.0	39.0	39.0					1																	157740434		2203	4300	6503	SO:0001589	frameshift_variant	79368	exon3			.	AF319438	CCDS1168.1	1q23.1	2013-01-14	2002-01-14	2005-03-23	ENSG00000132704	ENSG00000132704		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14875	protein-coding gene	gene with protein product		606509	"""SH2 domain-containing phosphatase anchor protein 1"""	SPAP1		11162587	Standard	NM_030764		Approved	FCRH2, IRTA4, CD307b	uc001fre.2	Q96LA5	OTTHUMG00000019399	ENST00000361516.3:c.75delC	chr1.hg19:g.157740434delG	ENSP00000355157:p.Pro25fs	49.0	0.0		59.0	27.0	NM_030764	A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Frame_Shift_Del	DEL	ENST00000361516.3	hg19	CCDS1168.1																																																																																			.	.		0.483	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051408.2	NM_030764	
OR2F2	135948	hgsc.bcm.edu	37	7	143633139	143633139	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr7:143633139delA	ENST00000408955.2	+	1	881	c.814delA	c.(814-816)aagfs	p.K272fs		NM_001004685.1	NP_001004685.1	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F, member 2	272						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(19)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	32	Melanoma(164;0.0903)					CCTTCAAGAGAAGCTGATCTC	0.498																																					p.E271fs		Atlas-Indel,Pindel	.											.	OR2F2	63	.	0			c.813delG						.						100.0	102.0	101.0					7																	143633139		2197	4300	6497	SO:0001589	frameshift_variant	135948	exon1			.		CCDS43666.1	7q33-q35	2012-08-09			ENSG00000221910	ENSG00000221910		"""GPCR / Class A : Olfactory receptors"""	8247	protein-coding gene	gene with protein product							Standard	NM_001004685		Approved	OR7-1	uc011ktv.2	O95006	OTTHUMG00000157768	ENST00000408955.2:c.814delA	chr7.hg19:g.143633139delA	ENSP00000386222:p.Lys272fs	91.0	0.0		150.0	87.0	NM_001004685	A4D2G0|Q6IFP8	Frame_Shift_Del	DEL	ENST00000408955.2	hg19	CCDS43666.1																																																																																			.	.		0.498	OR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349570.1		
FTCD	10841	hgsc.bcm.edu	37	21	47566181	47566181	+	Splice_Site	DEL	C	C	-	rs374048282		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr21:47566181delC	ENST00000291670.5	-	8	1010	c.967delG	c.(967-969)gag>ag	p.E323fs	FTCD_ENST00000397748.1_Splice_Site_p.E323fs|FTCD_ENST00000359679.2_Splice_Site_p.E323fs|FTCD_ENST00000355384.2_Splice_Site_p.E323fs|FTCD_ENST00000498355.2_5'UTR|FTCD_ENST00000397743.1_Splice_Site_p.E323fs|FTCD_ENST00000397746.3_Splice_Site_p.E323fs	NM_006657.2	NP_006648.1	O95954	FTCD_HUMAN	formimidoyltransferase cyclodeaminase	323	Formiminotransferase C-subdomain. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|cytoskeleton organization (GO:0007010)|folic acid-containing compound metabolic process (GO:0006760)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	folic acid binding (GO:0005542)|formimidoyltetrahydrofolate cyclodeaminase activity (GO:0030412)|glutamate formimidoyltransferase activity (GO:0030409)			endometrium(1)|large_intestine(2)|lung(9)|pancreas(1)|prostate(3)|skin(3)	19	Breast(49;0.214)			Colorectal(79;0.235)	Tetrahydrofolic acid(DB00116)	GAGGCTCACTCGATGATCCGC	0.697																																					p.E323fs		Atlas-Indel,Pindel	.											.	FTCD	59	.	0			c.968delA						.						68.0	67.0	67.0					21																	47566181		2159	4279	6438	SO:0001630	splice_region_variant	10841	exon8			.	U91541	CCDS13731.1	21q22.3	2013-06-10	2013-06-10		ENSG00000160282	ENSG00000160282	2.1.2.5, 4.3.1.4		3974	protein-coding gene	gene with protein product		606806	"""formiminotransferase cyclodeaminase"""			10029623, 10773664	Standard	NM_006657		Approved		uc002zif.3	O95954	OTTHUMG00000090488	ENST00000291670.5:c.968+1G>-	chr21.hg19:g.47566181delC		100.0	0.0		113.0	51.0	NM_206965	B9EGD0|Q86V03|Q9HCT4|Q9HCT5|Q9HCT6|Q9UHJ2	Frame_Shift_Del	DEL	ENST00000291670.5	hg19	CCDS13731.1																																																																																			.	.		0.697	FTCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206962.1	NM_006657	Frame_Shift_Del
WT1-AS	51352	hgsc.bcm.edu	37	11	32461618	32461619	+	RNA	INS	-	-	AAAAAAAA	rs561416904|rs558926734|rs71063728|rs544079703		TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr11:32461618_32461619insAAAAAAAA	ENST00000395900.1	+	0	2496_2497				WT1-AS_ENST00000478367.1_RNA|WT1-AS_ENST00000426618.2_RNA|WT1-AS_ENST00000442957.1_RNA|WT1-AS_ENST00000494911.1_RNA|WT1-AS_ENST00000525436.1_RNA	NR_023920.1		Q06250	WIT1_HUMAN	WT1 antisense RNA											endometrium(1)|large_intestine(2)|lung(2)|prostate(1)	6						TCTGCACCTGTaaaaaaaaaaa	0.297																																					.		Atlas-INDEL	.											.	WT1-AS	7	.	0			.						.																																					51352	.			.	BC002734		11p13	2012-10-19	2012-08-15	2012-01-25	ENSG00000183242	ENSG00000183242		"""Long non-coding RNAs"", ""-"""	18135	non-coding RNA	RNA, long non-coding	"""Wilms tumor associated protein"""	607899	"""Wilms tumor upstream neighbor 1"", ""WT1 antisense RNA (non-protein coding)"""	WIT1		2173145, 8406502, 17210670	Standard	NR_120546		Approved	WIT-1, WT1AS, WT1-AS1	uc010red.2	Q06250	OTTHUMG00000039557		chr11.hg19:g.32461619_32461626dupAAAAAAAA		96.0	0.0		121.0	10.0	.	Q4KMY0|Q96A27	RNA	INS	ENST00000395900.1	hg19																																																																																				.	.		0.297	WT1-AS-001	KNOWN	basic	antisense	antisense	OTTHUMT00000095437.1	NR_023920	
C19orf48	84798	hgsc.bcm.edu	37	19	51301354	51301354	+	Stop_Codon_Del	DEL	A	A	-			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr19:51301354delA	ENST00000598463.1	-	0	1450				C19orf48_ENST00000345523.4_Stop_Codon_Del|C19orf48_ENST00000391812.1_Stop_Codon_Del|C19orf48_ENST00000595794.1_5'Flank|SNORD88A_ENST00000408314.1_RNA|C19orf48_ENST00000596655.1_Stop_Codon_Del|SNORD88B_ENST00000408454.1_RNA			Q6RUI8	CS048_HUMAN	chromosome 19 open reading frame 48											endometrium(1)|kidney(1)|lung(1)|ovary(1)	4		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00531)|GBM - Glioblastoma multiforme(134;0.0145)		AATGCAGCTCAAACCAGGAGC	0.627																																					p.X118X		Atlas-Indel,Pindel	.											.	C19orf48	11	.	0			c.353delG						.						83.0	85.0	85.0					19																	51301354		2203	4300	6503	SO:0001567	stop_retained_variant	84798	exon5			.	BC037227	CCDS12803.1	19q13.33	2012-10-26			ENSG00000167747	ENSG00000167747			29667	protein-coding gene	gene with protein product	"""multidrug resistance-related protein"""					12452007	Standard	NM_001290154		Approved	MGC13170	uc002ptg.3	Q6RUI8		Exception_encountered	chr19.hg19:g.51301354delA	Exception_encountered	33.0	0.0		52.0	27.0	NM_199249		In_Frame_Del	DEL	ENST00000598463.1	hg19	CCDS12803.1																																																																																			.	.		0.627	C19orf48-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464107.1	NM_032712	
SAMD11	148398	hgsc.bcm.edu	37	1	878348	878348	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr1:878348delG	ENST00000342066.3	+	11	1557	c.1474delG	c.(1474-1476)ggafs	p.G493fs		NM_152486.2	NP_689699	Q96NU1	SAM11_HUMAN	sterile alpha motif domain containing 11	493					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.74e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000472)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		AGCTCCAGCTGGAGGGGCCGG	0.687																																					p.A491fs		Atlas-Indel,Pindel	.											.	SAMD11	34	.	0			c.1473delT						.						4.0	5.0	4.0					1																	878348		2043	4093	6136	SO:0001589	frameshift_variant	148398	exon11			.	BC024295	CCDS2.2	1p36.33	2013-01-10			ENSG00000187634	ENSG00000187634		"""Sterile alpha motif (SAM) domain containing"""	28706	protein-coding gene	gene with protein product						12477932	Standard	NM_152486		Approved	MGC45873	uc001abw.1	Q96NU1	OTTHUMG00000040719	ENST00000342066.3:c.1474delG	chr1.hg19:g.878348delG	ENSP00000342313:p.Gly493fs	93.0	0.0		61.0	27.0	NM_152486	A2AA76|I7FV78|I7FV81|I7G0Z6|Q5SV96|Q5SV99|Q5SVA0|Q8N195|Q8TB59	Frame_Shift_Del	DEL	ENST00000342066.3	hg19	CCDS2.2																																																																																			.	.		0.687	SAMD11-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276866.2	NM_152486	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33053994	33054040	+	Stop_Codon_Del	DEL	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	-	rs201552902|rs150818884|rs67523850	byFrequency	TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr6:33053994_33054040delTTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	ENST00000418931.2	+	0	873_897					NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)	p.R255P(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						CTTTCATTTCAGTTCAACGAGGATCTGCATAAACAGGTAATATTCCTGCTTTGATTTCCTTGTGGGG	0.429																																					p.253_259del		Pindel	.											.	HLA-DPB1	28	.	1	Substitution - Missense(1)	cervix(1)	c.758_775del						.																																			SO:0001567	stop_retained_variant	3115	exon5			.		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	Exception_encountered	chr6.hg19:g.33053994_33054040delTTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA		59.0	0.0		76.0	10.0	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	In_Frame_Del	DEL	ENST00000418931.2	hg19	CCDS4765.1																																																																																			.	.		0.429	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
PHKA1	5255	hgsc.bcm.edu	37	X	71804110	71804110	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chrX:71804110delT	ENST00000373542.4	-	30	3445	c.3286delA	c.(3286-3288)accfs	p.T1097fs	PHKA1_ENST00000339490.3_Frame_Shift_Del_p.T1084fs|PHKA1_ENST00000541944.1_Frame_Shift_Del_p.T1025fs|PHKA1_ENST00000373539.3_Frame_Shift_Del_p.T1114fs|PHKA1_ENST00000373545.3_Frame_Shift_Del_p.T1055fs	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	1097					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					TCTCTAGTGGTAGAGGAAGGA	0.393																																					p.T1096fs		Pindel	.											.	PHKA1	129	.	0			c.3287delC						.						118.0	94.0	103.0					X																	71804110		2203	4300	6503	SO:0001589	frameshift_variant	5255	exon30			.		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.3286delA	chrX.hg19:g.71804110delT	ENSP00000362643:p.Thr1097fs	267.0	0.0		313.0	115.0	NM_002637	B7ZL05|B7ZL07|Q2M3D7	Frame_Shift_Del	DEL	ENST00000373542.4	hg19	CCDS14421.1																																																																																			.	.		0.393	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1		
ACVR2A	92	hgsc.bcm.edu	37	2	148653985	148653987	+	In_Frame_Del	DEL	GCG	GCG	-			TCGA-G3-A7M5-01A-11D-A33Q-10	TCGA-G3-A7M5-10A-01D-A33Q-10	GCG	GCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce4d27a-466f-4333-8ea0-4342edd2f3e7	39e7b768-f7c4-48c0-9ba7-66a6ed5464ff	g.chr2:148653985_148653987delGCG	ENST00000241416.7	+	2	807_809	c.171_173delGCG	c.(169-174)cggcgg>cgg	p.57_58RR>R	ACVR2A_ENST00000535787.1_5'UTR|AC009480.3_ENST00000402410.2_RNA|ACVR2A_ENST00000404590.1_In_Frame_Del_p.57_58RR>R	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	57					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		AAGATAAACGGCGGCATTGTTTT	0.394																																					p.57_58del		Pindel	.											.	ACVR2A	125	.	0			c.170_172del						.																																			SO:0001651	inframe_deletion	92	exon2			.		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"""activin A receptor, type II"""	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.171_173delGCG	chr2.hg19:g.148653985_148653987delGCG	ENSP00000241416:p.Arg58del	73.0	0.0		96.0	15.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	In_Frame_Del	DEL	ENST00000241416.7	hg19	CCDS33301.1																																																																																			.	.		0.394	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616	
