#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
MMACHC	25974	hgsc.bcm.edu	37	1	45974808	45974808	+	Missense_Mutation	SNP	C	C	T	rs201601241		TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr1:45974808C>T	ENST00000401061.4	+	4	1050	c.770C>T	c.(769-771)cCc>cTc	p.P257L		NM_015506.2	NP_056321.2	Q9Y4U1	MMAC_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblC type, with homocystinuria	257					cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8	Acute lymphoblastic leukemia(166;0.155)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACACCCGCCCCCAAGAAGCCT	0.627																																					p.P257L		Atlas-SNP	.											.	MMACHC	22	.	0			c.C770T						.	C	LEU/PRO	0,3692		0,0,1846	89.0	100.0	96.0		770	2.5	0.0	1		96	1,8173		0,1,4086	yes	missense	MMACHC	NM_015506.2	98	0,1,5932	TT,TC,CC		0.0122,0.0,0.0084	benign	257/283	45974808	1,11865	1846	4087	5933	SO:0001583	missense	25974	exon4			CCGCCCCCAAGAA		CCDS41324.1	1p34.1	2011-05-12			ENSG00000132763	ENSG00000132763			24525	protein-coding gene	gene with protein product		609831				16311595	Standard	NM_015506		Approved	DKFZP564I122, cblC	uc009vxv.3	Q9Y4U1	OTTHUMG00000007742	ENST00000401061.4:c.770C>T	chr1.hg19:g.45974808C>T	ENSP00000383840:p.Pro257Leu	80.0	0.0		87.0	45.0	NM_015506	Q5T157|Q9BRQ7	Missense_Mutation	SNP	ENST00000401061.4	hg19	CCDS41324.1	.	.	.	.	.	.	.	.	.	.	C	9.169	1.020625	0.19433	0.0	1.22E-4	ENSG00000132763	ENST00000401061	D	0.94793	-3.52	3.43	2.48	0.30137	.	0.891026	0.09188	N	0.836537	D	0.90086	0.6903	L	0.29908	0.895	0.09310	N	1	B	0.22414	0.069	B	0.23419	0.046	T	0.82186	-0.0582	10	0.62326	D	0.03	-0.5441	8.8392	0.35131	0.0:0.7705:0.2295:0.0	.	257	Q9Y4U1	MMAC_HUMAN	L	257	ENSP00000383840:P257L	ENSP00000383840:P257L	P	+	2	0	MMACHC	45747395	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	0.560000	0.23500	0.753000	0.32945	0.563000	0.77884	CCC	.	.		0.627	MMACHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020864.2	NM_015506	
TTC24	164118	hgsc.bcm.edu	37	1	156551636	156551636	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr1:156551636G>A	ENST00000368237.3	+	1	480	c.480G>A	c.(478-480)atG>atA	p.M160I	TTC24_ENST00000368236.3_Missense_Mutation_p.M160I			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	160										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	20	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGGCAAAAATGGGAGCCTGCT	0.642																																					p.M160I		Atlas-SNP	.											.	TTC24	46	.	0			c.G480A						.						10.0	12.0	11.0					1																	156551636		692	1589	2281	SO:0001583	missense	164118	exon2			AAAAATGGGAGCC		CCDS53379.1	1q22	2013-01-10			ENSG00000187862	ENSG00000187862		"""Tetratricopeptide (TTC) repeat domain containing"""	32348	protein-coding gene	gene with protein product							Standard	NM_001105669		Approved		uc021pbf.1	A2A3L6	OTTHUMG00000033202	ENST00000368237.3:c.480G>A	chr1.hg19:g.156551636G>A	ENSP00000357220:p.Met160Ile	94.0	0.0		145.0	93.0	NM_001105669	Q5T3H7	Missense_Mutation	SNP	ENST00000368237.3	hg19	CCDS53379.1	.	.	.	.	.	.	.	.	.	.	G	3.502	-0.101525	0.06967	.	.	ENSG00000187862	ENST00000368236;ENST00000368237	T;T	0.61392	0.11;0.11	4.83	3.9	0.45041	.	0.000000	0.52532	D	0.000063	T	0.18676	0.0448	N	0.08118	0	0.26334	N	0.977478	.	.	.	.	.	.	T	0.14337	-1.0476	8	0.25106	T	0.35	-11.7295	11.0461	0.47859	0.093:0.0:0.907:0.0	.	.	.	.	I	160	ENSP00000357219:M160I;ENSP00000357220:M160I	ENSP00000357219:M160I	M	+	3	0	TTC24	154818260	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.548000	0.60718	1.230000	0.43646	0.462000	0.41574	ATG	.	.		0.642	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384	
ATP1A2	477	hgsc.bcm.edu	37	1	160094210	160094210	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr1:160094210A>G	ENST00000361216.3	+	6	709	c.620A>G	c.(619-621)cAt>cGt	p.H207R	ATP1A2_ENST00000392233.3_Missense_Mutation_p.H207R	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	207					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			ATCTCTTCTCATGGCTGTAAG	0.562																																					p.H207R		Atlas-SNP	.											.	ATP1A2	167	.	0			c.A620G						.						87.0	68.0	75.0					1																	160094210		2203	4300	6503	SO:0001583	missense	477	exon6			CTTCTCATGGCTG	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"""ATPases / P-type"""	800	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-2"", ""sodium pump subunit alpha-2"", ""sodium-potassium ATPase catalytic subunit alpha-2"""	182340	"""migraine, hemiplegic 2"", ""ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"""	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.620A>G	chr1.hg19:g.160094210A>G	ENSP00000354490:p.His207Arg	79.0	0.0		124.0	37.0	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	hg19	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	A	12.78	2.039126	0.35989	.	.	ENSG00000018625	ENST00000538123;ENST00000361216;ENST00000392233	D;D	0.90324	-2.65;-2.65	5.27	5.27	0.74061	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.201617	0.51477	D	0.000097	T	0.72195	0.3430	N	0.16862	0.45	0.40150	D	0.976937	B;B	0.14012	0.0;0.009	B;B	0.13407	0.003;0.009	T	0.68903	-0.5286	10	0.13470	T	0.59	.	14.1697	0.65500	1.0:0.0:0.0:0.0	.	52;207	B4DHD7;P50993	.;AT1A2_HUMAN	R	52;207;207	ENSP00000354490:H207R;ENSP00000376066:H207R	ENSP00000354490:H207R	H	+	2	0	ATP1A2	158360834	0.996000	0.38824	0.981000	0.43875	0.986000	0.74619	5.342000	0.65970	1.997000	0.58415	0.533000	0.62120	CAT	.	.		0.562	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702	
CACNA1E	777	hgsc.bcm.edu	37	1	181693620	181693620	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr1:181693620G>T	ENST00000367573.2	+	17	2089	c.2089G>T	c.(2089-2091)Gtg>Ttg	p.V697L	CACNA1E_ENST00000526775.1_Missense_Mutation_p.V697L|CACNA1E_ENST00000367567.4_Missense_Mutation_p.V304L|CACNA1E_ENST00000360108.3_Missense_Mutation_p.V697L|CACNA1E_ENST00000358338.5_Missense_Mutation_p.V648L|CACNA1E_ENST00000367570.1_Missense_Mutation_p.V697L|CACNA1E_ENST00000357570.5_Missense_Mutation_p.V648L	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	697					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						GCTACTGAATGTGTTCTTGGC	0.473																																					p.V697L		Atlas-SNP	.											.	CACNA1E	778	.	0			c.G2089T						.						142.0	131.0	134.0					1																	181693620		1980	4164	6144	SO:0001583	missense	777	exon17			CTGAATGTGTTCT	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.2089G>T	chr1.hg19:g.181693620G>T	ENSP00000356545:p.Val697Leu	50.0	0.0		99.0	51.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	15.48	2.844899	0.51164	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.97041	-4.22;-4.22;-4.22;-4.22;-4.22;-4.22;-4.22	4.86	3.95	0.45737	.	0.241030	0.41823	D	0.000805	D	0.92922	0.7748	N	0.21583	0.68	0.51012	D	0.999904	B;B	0.20261	0.043;0.043	B;B	0.20384	0.029;0.029	D	0.89313	0.3634	10	0.35671	T	0.21	.	12.7227	0.57152	0.0809:0.0:0.9191:0.0	.	697;697	Q15878-2;Q15878-3	.;.	L	697;697;648;648;304;697;697	ENSP00000356542:V697L;ENSP00000434814:V697L;ENSP00000350183:V648L;ENSP00000351101:V648L;ENSP00000356539:V304L;ENSP00000353222:V697L;ENSP00000356545:V697L	ENSP00000350183:V648L	V	+	1	0	CACNA1E	179960243	1.000000	0.71417	0.995000	0.50966	0.802000	0.45316	9.675000	0.98638	1.162000	0.42619	0.462000	0.41574	GTG	.	.		0.473	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
USH2A	7399	hgsc.bcm.edu	37	1	216011440	216011440	+	Silent	SNP	T	T	C			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr1:216011440T>C	ENST00000307340.3	-	47	9650	c.9264A>G	c.(9262-9264)gaA>gaG	p.E3088E	USH2A_ENST00000366943.2_Silent_p.E3088E	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3088	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.		E -> K (in dbSNP:rs56056328). {ECO:0000269|PubMed:18273898}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTGTGCAGACTTCAACCTGCA	0.383										HNSCC(13;0.011)																											p.E3088E		Atlas-SNP	.											.	USH2A	1168	.	0			c.A9264G						.						179.0	165.0	170.0					1																	216011440		2203	4300	6503	SO:0001819	synonymous_variant	7399	exon47			GCAGACTTCAACC	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.9264A>G	chr1.hg19:g.216011440T>C		138.0	0.0		211.0	63.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.383	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
GPR137B	7107	hgsc.bcm.edu	37	1	236306038	236306038	+	Missense_Mutation	SNP	C	C	A	rs199613305		TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr1:236306038C>A	ENST00000366592.3	+	1	207	c.116C>A	c.(115-117)cCc>cAc	p.P39H	GPR137B_ENST00000366591.4_Missense_Mutation_p.P39H	NM_003272.3	NP_003263.1	O60478	G137B_HUMAN	G protein-coupled receptor 137B	39						integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|membrane (GO:0016020)				endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.197)|Prostate(94;0.219)|Acute lymphoblastic leukemia(190;0.226)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			GCCGTGCCCCCCTACGTGAAG	0.711																																					p.P39H		Atlas-SNP	.											.	GPR137B	57	.	0			c.C116A						.						61.0	44.0	50.0					1																	236306038		2203	4300	6503	SO:0001583	missense	7107	exon1			TGCCCCCCTACGT	AF027826	CCDS1609.1	1q42-q43	2012-08-10	2006-01-26	2006-01-26	ENSG00000077585	ENSG00000077585			11862	protein-coding gene	gene with protein product		604658	"""transmembrane 7 superfamily member 1 (upregulated in kidney)"""	TM7SF1		9521871	Standard	NM_003272		Approved		uc001hxq.3	O60478	OTTHUMG00000037994	ENST00000366592.3:c.116C>A	chr1.hg19:g.236306038C>A	ENSP00000355551:p.Pro39His	54.0	0.0		100.0	60.0	NM_003272	Q53EK7|Q5TAE6|Q6FHI3	Missense_Mutation	SNP	ENST00000366592.3	hg19	CCDS1609.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.086274	0.76642	.	.	ENSG00000077585	ENST00000366592;ENST00000366591;ENST00000391852	T;T	0.14266	2.52;2.52	4.8	2.89	0.33648	.	0.053259	0.85682	D	0.000000	T	0.32071	0.0817	M	0.77103	2.36	0.53005	D	0.999969	D	0.69078	0.997	D	0.63192	0.912	T	0.02477	-1.1153	10	0.56958	D	0.05	-14.0193	10.022	0.42048	0.0:0.7855:0.1385:0.0761	.	39	O60478	G137B_HUMAN	H	39;39;38	ENSP00000355551:P39H;ENSP00000355550:P39H	ENSP00000355550:P39H	P	+	2	0	GPR137B	234372661	1.000000	0.71417	0.967000	0.41034	0.893000	0.52053	5.645000	0.67909	0.437000	0.26423	-0.510000	0.04470	CCC	.	C|0.999;T|0.001		0.711	GPR137B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092761.1	NM_003272	
PXDN	7837	hgsc.bcm.edu	37	2	1667507	1667507	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr2:1667507G>T	ENST00000252804.4	-	12	1487	c.1437C>A	c.(1435-1437)caC>caA	p.H479Q	PXDN_ENST00000483018.1_5'Flank	NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	479	Ig-like C2-type 3.				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)			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)		ACAGGACCAGGTGCCGCCGGT	0.602																																					p.H479Q		Atlas-SNP	.											.	PXDN	255	.	0			c.C1437A						.						59.0	67.0	65.0					2																	1667507		2037	4177	6214	SO:0001583	missense	7837	exon12			GACCAGGTGCCGC	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.1437C>A	chr2.hg19:g.1667507G>T	ENSP00000252804:p.His479Gln	23.0	0.0		52.0	19.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	hg19	CCDS46221.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.34|17.34	3.364925|3.364925	0.61513|0.61513	.|.	.|.	ENSG00000130508|ENSG00000130508	ENST00000252804|ENST00000433670	T|.	0.67698|.	-0.28|.	5.79|5.79	1.52|1.52	0.23074|0.23074	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.49338|0.49338	0.1551|0.1551	L|L	0.31157|0.31157	0.91|0.91	0.45580|0.45580	D|D	0.998529|0.998529	D;D|.	0.76494|.	0.998;0.999|.	D;D|.	0.77557|.	0.935;0.99|.	T|T	0.30966|0.30966	-0.9960|-0.9960	10|5	0.27785|.	T|.	0.31|.	-66.3747|-66.3747	11.3772|11.3772	0.49735|0.49735	0.3991:0.0:0.6009:0.0|0.3991:0.0:0.6009:0.0	.|.	479;479|.	Q92626-2;Q92626|.	.;PXDN_HUMAN|.	Q|N	479|475	ENSP00000252804:H479Q|.	ENSP00000252804:H479Q|.	H|T	-|-	3|2	2|0	PXDN|PXDN	1646514|1646514	0.946000|0.946000	0.32159|0.32159	1.000000|1.000000	0.80357|0.80357	0.930000|0.930000	0.56654|0.56654	0.119000|0.119000	0.15626|0.15626	0.387000|0.387000	0.25024|0.25024	-0.137000|-0.137000	0.14449|0.14449	CAC|ACC	.	.		0.602	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
MFSD9	84804	hgsc.bcm.edu	37	2	103340215	103340215	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr2:103340215T>C	ENST00000258436.5	-	5	624	c.581A>G	c.(580-582)gAg>gGg	p.E194G		NM_032718.3	NP_116107.3	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing 9	194					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(3)|large_intestine(7)|liver(1)|lung(6)|ovary(2)|skin(1)	20						AAACCCATCCTCTAATTCAGT	0.473																																					p.E194G		Atlas-SNP	.											.	MFSD9	56	.	0			c.A581G						.						82.0	81.0	81.0					2																	103340215		2203	4300	6503	SO:0001583	missense	84804	exon5			CCATCCTCTAATT		CCDS2063.1	2q12.1	2007-01-12			ENSG00000135953	ENSG00000135953			28158	protein-coding gene	gene with protein product							Standard	NM_032718		Approved	MGC11332	uc002tcb.2	Q8NBP5	OTTHUMG00000130781	ENST00000258436.5:c.581A>G	chr2.hg19:g.103340215T>C	ENSP00000258436:p.Glu194Gly	99.0	0.0		101.0	41.0	NM_032718	Q4ZG89|Q53TU0|Q96GQ4|Q9BRI8	Missense_Mutation	SNP	ENST00000258436.5	hg19	CCDS2063.1	.	.	.	.	.	.	.	.	.	.	T	13.28	2.188942	0.38707	.	.	ENSG00000135953	ENST00000258436	T	0.59224	0.28	4.99	4.99	0.66335	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.118515	0.56097	D	0.000037	T	0.40247	0.1109	N	0.19112	0.55	0.41948	D	0.990644	B	0.27068	0.167	B	0.30716	0.119	T	0.30446	-0.9978	10	0.02654	T	1	-29.2361	14.664	0.68893	0.0:0.0:0.0:1.0	.	194	Q8NBP5	MFSD9_HUMAN	G	194	ENSP00000258436:E194G	ENSP00000258436:E194G	E	-	2	0	MFSD9	102706647	0.999000	0.42202	0.028000	0.17463	0.087000	0.18053	7.543000	0.82106	1.856000	0.53863	0.383000	0.25322	GAG	.	.		0.473	MFSD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253295.2	NM_032718	
GPR148	344561	hgsc.bcm.edu	37	2	131486815	131486815	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr2:131486815G>A	ENST00000309926.4	+	1	173	c.91G>A	c.(91-93)Gca>Aca	p.A31T		NM_207364.2	NP_997247.2	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	31				CMPQAASNTSLGLGDLRVPSSMLYWLFLPSSLLAAA -> S S (in Ref. 2; AAP34196). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(15)|skin(3)|upper_aerodigestive_tract(1)	27	Colorectal(110;0.1)					CATGCCCCAAGCAGCCAGCAA	0.627																																					p.A31T		Atlas-SNP	.											.	GPR148	54	.	0			c.G91A						.						87.0	83.0	85.0					2																	131486815		2203	4300	6503	SO:0001583	missense	344561	exon1			CCCCAAGCAGCCA	AY255532	CCDS2163.1	2q21.2	2012-08-21			ENSG00000173302	ENSG00000173302		"""GPCR / Class A : Orphans"""	23623	protein-coding gene	gene with protein product						12679517	Standard	NM_207364		Approved	PGR6	uc002trv.2	Q8TDV2	OTTHUMG00000131655	ENST00000309926.4:c.91G>A	chr2.hg19:g.131486815G>A	ENSP00000308908:p.Ala31Thr	91.0	0.0		114.0	34.0	NM_207364	Q2M369|Q86SP7|Q86U87	Missense_Mutation	SNP	ENST00000309926.4	hg19	CCDS2163.1	.	.	.	.	.	.	.	.	.	.	.	4.650	0.120777	0.08881	.	.	ENSG00000173302	ENST00000309926	T	0.08282	3.11	2.41	-2.11	0.07187	.	1.636260	0.04504	U	0.381712	T	0.03520	0.0101	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.39683	-0.9602	10	0.13108	T	0.6	-0.6633	2.5715	0.04796	0.2756:0.0:0.2989:0.4255	.	31	Q8TDV2	GP148_HUMAN	T	31	ENSP00000308908:A31T	ENSP00000308908:A31T	A	+	1	0	GPR148	131203285	0.011000	0.17503	0.000000	0.03702	0.574000	0.36063	0.601000	0.24119	-0.581000	0.05937	0.462000	0.41574	GCA	.	.		0.627	GPR148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254552.3	XM_293092	
FMNL2	114793	hgsc.bcm.edu	37	2	153476054	153476054	+	Silent	SNP	A	A	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr2:153476054A>G	ENST00000288670.9	+	15	2026	c.1659A>G	c.(1657-1659)ccA>ccG	p.P553P	FMNL2_ENST00000475377.2_5'Flank	NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	553	Pro-rich.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						CACCTATGCCACCGCCGCCGC	0.582																																					p.P553P		Atlas-SNP	.											.	FMNL2	75	.	0			c.A1659G						.						14.0	13.0	14.0					2																	153476054		1424	3286	4710	SO:0001819	synonymous_variant	114793	exon15			TATGCCACCGCCG	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"""formin homology 2 domain containing 2"""	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.1659A>G	chr2.hg19:g.153476054A>G		20.0	0.0		50.0	10.0	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000288670.9	hg19	CCDS46429.1																																																																																			.	.		0.582	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905	
ALPP	250	hgsc.bcm.edu	37	2	233243546	233243546	+	Silent	SNP	C	C	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr2:233243546C>T	ENST00000392027.2	+	1	303	c.34C>T	c.(34-36)Ctg>Ttg	p.L12L	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	12					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		gctgctgctgctgctgGGCCT	0.642																																					p.L12L		Atlas-SNP	.											.	ALPP	53	.	0			c.C34T						.						48.0	53.0	51.0					2																	233243546		2203	4300	6503	SO:0001819	synonymous_variant	250	exon1			CTGCTGCTGCTGG	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.34C>T	chr2.hg19:g.233243546C>T		71.0	0.0		81.0	33.0	NM_001632	P05188|P06861|Q53S78|Q96DB7	Silent	SNP	ENST00000392027.2	hg19	CCDS2490.1																																																																																			.	.		0.642	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
ACOX2	8309	hgsc.bcm.edu	37	3	58510285	58510285	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr3:58510285G>A	ENST00000302819.5	-	11	1685	c.1394C>T	c.(1393-1395)aCg>aTg	p.T465M	ACOX2_ENST00000481527.1_5'Flank|ACOX2_ENST00000459701.2_Missense_Mutation_p.T451M	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	465					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		TCTCTGTGGCGTGGAGCCAGG	0.617																																					p.T465M		Atlas-SNP	.											.	ACOX2	53	.	0			c.C1394T						.						88.0	79.0	82.0					3																	58510285		2203	4300	6503	SO:0001583	missense	8309	exon11			TGTGGCGTGGAGC	X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"""trihydroxycoprostanoyl-CoA oxidase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"""	601641	"""acyl-Coenzyme A oxidase 2, branched chain"""			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.1394C>T	chr3.hg19:g.58510285G>A	ENSP00000307697:p.Thr465Met	72.0	0.0		79.0	26.0	NM_003500	A6NF16|B2R8U5	Missense_Mutation	SNP	ENST00000302819.5	hg19	CCDS33775.1	.	.	.	.	.	.	.	.	.	.	G	9.495	1.101656	0.20632	.	.	ENSG00000168306	ENST00000459701;ENST00000302819	T;T	0.15139	2.46;2.45	4.85	2.97	0.34412	Acyl-CoA dehydrogenase/oxidase C-terminal (1);	1.283950	0.05299	N	0.522624	T	0.09158	0.0226	N	0.08118	0	0.09310	N	1	P	0.42296	0.775	B	0.36666	0.23	T	0.24012	-1.0172	10	0.37606	T	0.19	-44.5598	6.526	0.22301	0.0957:0.0:0.7274:0.1769	.	465	Q99424	ACOX2_HUMAN	M	451;465	ENSP00000418562:T451M;ENSP00000307697:T465M	ENSP00000307697:T465M	T	-	2	0	ACOX2	58485325	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.264000	0.18497	0.519000	0.28406	0.484000	0.47621	ACG	.	.		0.617	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1		
VEPH1	79674	hgsc.bcm.edu	37	3	156983419	156983419	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr3:156983419C>A	ENST00000362010.2	-	13	2468	c.2161G>T	c.(2161-2163)Gga>Tga	p.G721*	VEPH1_ENST00000392833.2_Nonsense_Mutation_p.G676*|RP11-550I24.2_ENST00000487238.1_RNA|RP11-550I24.2_ENST00000488040.1_RNA|VEPH1_ENST00000543418.1_Nonsense_Mutation_p.G676*|VEPH1_ENST00000392832.2_Nonsense_Mutation_p.G721*|RP11-550I24.2_ENST00000475102.1_RNA	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	721	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			TTAAGTTTTCCTTCTATGAGA	0.368																																					p.G721X		Atlas-SNP	.											.	VEPH1	129	.	0			c.G2161T						.						144.0	133.0	137.0					3																	156983419		2203	4300	6503	SO:0001587	stop_gained	79674	exon13			GTTTTCCTTCTAT	AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"""Pleckstrin homology (PH) domain containing"""	25735	protein-coding gene	gene with protein product		609594	"""ventricular zone expressed PH domain homolog 1 (zebrafish)"""			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.2161G>T	chr3.hg19:g.156983419C>A	ENSP00000354919:p.Gly721*	93.0	0.0		134.0	53.0	NM_001167912	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Nonsense_Mutation	SNP	ENST00000362010.2	hg19	CCDS3179.1	.	.	.	.	.	.	.	.	.	.	C	42	9.820790	0.99272	.	.	ENSG00000197415	ENST00000392833;ENST00000362010;ENST00000543418;ENST00000392832	.	.	.	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-11.2672	19.5283	0.95215	0.0:1.0:0.0:0.0	.	.	.	.	X	676;721;676;721	.	ENSP00000354919:G721X	G	-	1	0	VEPH1	158466113	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.672000	0.83956	2.596000	0.87737	0.655000	0.94253	GGA	.	.		0.368	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621	
ATP11B	23200	hgsc.bcm.edu	37	3	182597383	182597383	+	Silent	SNP	C	C	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr3:182597383C>T	ENST00000323116.5	+	20	2612	c.2352C>T	c.(2350-2352)tgC>tgT	p.C784C		NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	784					aminophospholipid transport (GO:0015917)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|ion transmembrane transporter activity (GO:0015075)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			TGGAAGTTTGCAGAAATTGTT	0.388																																					p.C784C		Atlas-SNP	.											.	ATP11B	115	.	0			c.C2352T						.						111.0	110.0	111.0					3																	182597383		2203	4300	6503	SO:0001819	synonymous_variant	23200	exon20			AGTTTGCAGAAAT	AF156548	CCDS33896.1	3q27	2010-04-20	2007-09-19		ENSG00000058063	ENSG00000058063		"""ATPases / P-type"""	13553	protein-coding gene	gene with protein product		605869	"""ATPase, Class VI, type 11B"""			10231032, 11015572	Standard	NM_014616		Approved	ATPIF, ATPIR, KIAA0956	uc003flb.3	Q9Y2G3	OTTHUMG00000158295	ENST00000323116.5:c.2352C>T	chr3.hg19:g.182597383C>T		281.0	1.0		360.0	147.0	NM_014616	Q96FN1|Q9UKK7	Silent	SNP	ENST00000323116.5	hg19	CCDS33896.1	.	.	.	.	.	.	.	.	.	.	C	4.653	0.121436	0.08881	.	.	ENSG00000058063	ENST00000498086	.	.	.	4.78	1.57	0.23409	.	.	.	.	.	T	0.55114	0.1900	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47736	-0.9094	4	.	.	.	.	7.7193	0.28723	0.0:0.5112:0.0:0.4888	.	.	.	.	V	585	.	.	A	+	2	0	ATP11B	184080077	1.000000	0.71417	1.000000	0.80357	0.467000	0.32768	0.736000	0.26130	0.533000	0.28675	0.585000	0.79938	GCA	.	.		0.388	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	NM_014616	
FAM157A	728262	hgsc.bcm.edu	37	3	197880167	197880167	+	lincRNA	SNP	G	G	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr3:197880167G>A	ENST00000437428.2	+	0	47							C9JC47	F157A_HUMAN	family with sequence similarity 157, member A											NS(1)|skin(1)	2						agcagcagcagcagcaACTGG	0.527																																					p.Q82Q		Atlas-SNP	.											.	FAM157A	4	.	0			c.G246A						.						2.0	6.0	5.0					3																	197880167		369	1057	1426			728262	exon2			GCAGCAGCAGCAA			3q29	2013-01-30			ENSG00000236438	ENSG00000236438			34079	other	unknown							Standard	NM_001145248		Approved		uc011bup.1	C9JC47			chr3.hg19:g.197880167G>A		386.0	0.0		422.0	22.0	NM_001145248		Silent	SNP	ENST00000437428.2	hg19																																																																																				.	.		0.527	FAM157A-001	KNOWN	not_best_in_genome_evidence|mRNA_end_NF|basic	lincRNA	lincRNA	OTTHUMT00000340078.2	NM_001145248	
KIT	3815	hgsc.bcm.edu	37	4	55602719	55602719	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr4:55602719C>T	ENST00000288135.5	+	18	2637	c.2540C>T	c.(2539-2541)aCg>aTg	p.T847M		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	847	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		T -> P (in PBT). {ECO:0000269|PubMed:9699740}.		actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGTGTATACACGTTTGAAAGT	0.408		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.T847M		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	KIT,colon,carcinoma,0,1	KIT	7396	.	0			c.C2540T						.						172.0	168.0	169.0					4																	55602719		2203	4300	6503	SO:0001583	missense	3815	exon18	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	TATACACGTTTGA	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2540C>T	chr4.hg19:g.55602719C>T	ENSP00000288135:p.Thr847Met	119.0	0.0		65.0	46.0	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	hg19	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.724516	0.68959	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.90900	-2.75;-2.75	5.7	5.7	0.88788	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000012	D	0.95360	0.8494	M	0.73753	2.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.994	D	0.95354	0.8449	10	0.87932	D	0	.	19.8411	0.96685	0.0:1.0:0.0:0.0	.	843;847	P10721-2;P10721	.;KIT_HUMAN	M	847;843	ENSP00000288135:T847M;ENSP00000390987:T843M	ENSP00000288135:T847M	T	+	2	0	KIT	55297476	1.000000	0.71417	0.990000	0.47175	0.158000	0.22134	7.695000	0.84257	2.683000	0.91414	0.655000	0.94253	ACG	.	.		0.408	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
COQ2	27235	hgsc.bcm.edu	37	4	84191021	84191021	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr4:84191021C>A	ENST00000311469.4	-	5	903	c.904G>T	c.(904-906)Gcc>Tcc	p.A302S	COQ2_ENST00000311461.7_Missense_Mutation_p.A252S|COQ2_ENST00000439031.2_Missense_Mutation_p.A265S	NM_015697.7	NP_056512.5	Q96H96	COQ2_HUMAN	coenzyme Q2 4-hydroxybenzoate polyprenyltransferase	252					cell death (GO:0008219)|glycerol metabolic process (GO:0006071)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	4-hydroxybenzoate decaprenyltransferase activity (GO:0002083)|4-hydroxybenzoate nonaprenyltransferase activity (GO:0047293)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)	8		Hepatocellular(203;0.114)				ACCTGATGGGCATAAATAGTA	0.328																																					p.A302S		Atlas-SNP	.											.	COQ2	22	.	0			c.G904T						.						56.0	51.0	52.0					4																	84191021		1819	4089	5908	SO:0001583	missense	27235	exon5			GATGGGCATAAAT		CCDS47090.1, CCDS47090.2	4q21.23	2013-05-23	2013-05-23				2.5.1.39		25223	protein-coding gene	gene with protein product	"""4-hydroxybenzoate polyprenyltransferase"""	609825	"""coenzyme Q2 homolog, prenyltransferase (yeast)"""			15153069, 17332895	Standard	NM_015697		Approved	CL640, FLJ26072	uc003hog.3	Q96H96		ENST00000311469.4:c.904G>T	chr4.hg19:g.84191021C>A	ENSP00000310873:p.Ala302Ser	441.0	2.0		214.0	159.0	NM_015697	O95331|Q1JQ78|Q684R2	Missense_Mutation	SNP	ENST00000311469.4	hg19	CCDS47090.2	.	.	.	.	.	.	.	.	.	.	C	19.31	3.802644	0.70682	.	.	ENSG00000173085	ENST00000311469;ENST00000439031;ENST00000311461	D;D;D	0.92099	-2.97;-2.97;-2.97	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.97081	0.9046	M	0.92412	3.305	0.80722	D	1	D;D	0.56746	0.971;0.977	D;P	0.67382	0.951;0.794	D	0.96789	0.9581	10	0.56958	D	0.05	0.1232	19.6509	0.95805	0.0:1.0:0.0:0.0	.	252;252	E2QRG7;Q96H96	.;COQ2_HUMAN	S	302;265;252	ENSP00000310873:A302S;ENSP00000409275:A265S;ENSP00000311835:A252S	ENSP00000311835:A252S	A	-	1	0	COQ2	84410045	1.000000	0.71417	1.000000	0.80357	0.215000	0.24574	7.587000	0.82613	2.941000	0.99782	0.655000	0.94253	GCC	.	.		0.328	COQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363027.3	NM_015697	
AFF1	4299	hgsc.bcm.edu	37	4	88035865	88035865	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr4:88035865G>T	ENST00000307808.6	+	11	2279	c.1859G>T	c.(1858-1860)aGc>aTc	p.S620I	AFF1_ENST00000544085.1_Missense_Mutation_p.S258I|AFF1_ENST00000395146.4_Missense_Mutation_p.S627I	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	620					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		TCACGGACCAGCCTGCAGGGG	0.607																																					p.S627I		Atlas-SNP	.											.	AFF1	102	.	0			c.G1880T						.						35.0	42.0	40.0					4																	88035865		2201	4298	6499	SO:0001583	missense	4299	exon12			GGACCAGCCTGCA	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2"", ""pre-B-cell monocytic leukemia partner 1"""	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.1859G>T	chr4.hg19:g.88035865G>T	ENSP00000305689:p.Ser620Ile	215.0	0.0		163.0	124.0	NM_001166693	B4DTU1|E9PBM3	Missense_Mutation	SNP	ENST00000307808.6	hg19	CCDS3616.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.705590	0.48412	.	.	ENSG00000172493	ENST00000395146;ENST00000541943;ENST00000307808;ENST00000544085	T;T;T	0.64803	-0.12;-0.12;-0.12	5.93	3.89	0.44902	.	2.212320	0.01226	N	0.008224	T	0.59998	0.2235	N	0.25647	0.755	0.09310	N	1	P;P;P	0.42161	0.772;0.772;0.772	B;B;B	0.44224	0.444;0.444;0.444	T	0.55509	-0.8130	10	0.35671	T	0.21	2.0044	12.8761	0.57991	0.071:0.119:0.81:0.0	.	627;620;620	E9PBM3;Q14C88;P51825	.;.;AFF1_HUMAN	I	627;279;620;258	ENSP00000378578:S627I;ENSP00000305689:S620I;ENSP00000440843:S258I	ENSP00000305689:S620I	S	+	2	0	AFF1	88254889	0.972000	0.33761	0.033000	0.17914	0.036000	0.12997	4.358000	0.59442	1.509000	0.48786	0.561000	0.74099	AGC	.	.		0.607	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935	
TLL1	7092	hgsc.bcm.edu	37	4	166986934	166986934	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr4:166986934T>C	ENST00000061240.2	+	16	2754	c.2107T>C	c.(2107-2109)Tcc>Ccc	p.S703P	TLL1_ENST00000507499.1_Missense_Mutation_p.S726P	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	703	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		AGTGATCACATCCCAGTTCAA	0.398																																					p.S703P		Atlas-SNP	.											.	TLL1	194	.	0			c.T2107C						.						149.0	145.0	146.0					4																	166986934		2203	4299	6502	SO:0001583	missense	7092	exon16			ATCACATCCCAGT	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2107T>C	chr4.hg19:g.166986934T>C	ENSP00000061240:p.Ser703Pro	173.0	0.0		100.0	80.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	hg19	CCDS3811.1	.	.	.	.	.	.	.	.	.	.	T	18.96	3.733051	0.69189	.	.	ENSG00000038295	ENST00000061240;ENST00000507499	T;T	0.41400	1.0;1.0	5.97	5.97	0.96955	CUB (5);	0.000000	0.85682	U	0.000000	T	0.74846	0.3770	H	0.94808	3.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82575	-0.0389	10	0.87932	D	0	.	16.4608	0.84044	0.0:0.0:0.0:1.0	.	726;703	E9PD25;O43897	.;TLL1_HUMAN	P	703;726	ENSP00000061240:S703P;ENSP00000426082:S726P	ENSP00000061240:S703P	S	+	1	0	TLL1	167206384	1.000000	0.71417	0.449000	0.26957	0.174000	0.22865	7.997000	0.88414	2.288000	0.76882	0.533000	0.62120	TCC	.	.		0.398	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1		
TRIP13	9319	hgsc.bcm.edu	37	5	908114	908114	+	Silent	SNP	G	G	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:908114G>A	ENST00000166345.3	+	8	1040	c.684G>A	c.(682-684)ctG>ctA	p.L228L		NM_004237.3	NP_004228.1	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	228					double-strand break repair (GO:0006302)|female meiosis I (GO:0007144)|male meiosis I (GO:0007141)|oocyte maturation (GO:0001556)|oogenesis (GO:0048477)|reciprocal meiotic recombination (GO:0007131)|regulation of RNA biosynthetic process (GO:2001141)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	18			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			GTGGCAAGCTGGTAACCAAGA	0.502																																					p.L228L		Atlas-SNP	.											.	TRIP13	41	.	0			c.G684A						.						161.0	141.0	148.0					5																	908114		2203	4300	6503	SO:0001819	synonymous_variant	9319	exon8			CAAGCTGGTAACC	L40384	CCDS3858.1	5p15	2010-04-21			ENSG00000071539	ENSG00000071539		"""ATPases / AAA-type"""	12307	protein-coding gene	gene with protein product	"""thyroid receptor interacting protein 13"""	604507				7776974	Standard	NM_004237		Approved	16E1BP	uc003jbr.3	Q15645	OTTHUMG00000090349	ENST00000166345.3:c.684G>A	chr5.hg19:g.908114G>A		93.0	0.0		146.0	29.0	NM_004237	C9K0T3|D3DTC0|O15324	Silent	SNP	ENST00000166345.3	hg19	CCDS3858.1	.	.	.	.	.	.	.	.	.	.	.	10.07	1.250794	0.22880	.	.	ENSG00000071539	ENST00000513435	.	.	.	5.62	2.74	0.32292	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-9.828	6.6383	0.22895	0.1613:0.0:0.6395:0.1992	.	.	.	.	X	224	.	.	W	+	2	0	TRIP13	961114	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.625000	0.24477	1.521000	0.48983	0.655000	0.94253	TGG	.	.		0.502	TRIP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206721.2	NM_004237	
ICE1	23379	hgsc.bcm.edu	37	5	5462390	5462390	+	Silent	SNP	G	G	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:5462390G>A	ENST00000296564.7	+	13	3165	c.2943G>A	c.(2941-2943)ggG>ggA	p.G981G		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		981					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						AGGGAGATGGGCAGAAGCAAA	0.483																																					p.G981G		Atlas-SNP	.											.	KIAA0947	301	.	0			c.G2943A						.						34.0	36.0	35.0					5																	5462390		2049	4232	6281	SO:0001819	synonymous_variant	23379	exon13			AGATGGGCAGAAG																												ENST00000296564.7:c.2943G>A	chr5.hg19:g.5462390G>A		104.0	0.0		103.0	52.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	hg19	CCDS47187.1																																																																																			.	.		0.483	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1		
ZFR	51663	hgsc.bcm.edu	37	5	32417841	32417841	+	Silent	SNP	T	T	C			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:32417841T>C	ENST00000265069.8	-	4	579	c.477A>G	c.(475-477)caA>caG	p.Q159Q		NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	159	Ala-rich.				multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		GTTGGTAGTATTGCTTACTAT	0.438																																					p.Q159Q		Atlas-SNP	.											.	ZFR	98	.	0			c.A477G						.						124.0	123.0	124.0					5																	32417841		2203	4300	6503	SO:0001819	synonymous_variant	51663	exon4			GTAGTATTGCTTA	AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.477A>G	chr5.hg19:g.32417841T>C		68.0	0.0		68.0	23.0	NM_016107	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Silent	SNP	ENST00000265069.8	hg19	CCDS34139.1																																																																																			.	.		0.438	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1		
ADAMTS6	11174	hgsc.bcm.edu	37	5	64521991	64521991	+	IGR	SNP	A	A	C			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:64521991A>C								ADAMTS6 (27399 upstream) : ADAMTS6 (71043 downstream)																							GAGCACGTTCAGTGTAGAAAT	0.443																																					p.T663T		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.T1989G						.						103.0	96.0	98.0					5																	64521991		2203	4300	6503	SO:0001628	intergenic_variant	11174	exon16			ACGTTCAGTGTAG																													chr5.hg19:g.64521991A>C		175.0	0.0		192.0	87.0	NM_197941		Silent	SNP		hg19																																																																																				.	.	0	0.443								
OCLN	100506658	hgsc.bcm.edu	37	5	68849479	68849479	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:68849479A>G	ENST00000355237.2	+	9	1986	c.1550A>G	c.(1549-1551)tAt>tGt	p.Y517C	OCLN_ENST00000380766.2_Missense_Mutation_p.Y463C|OCLN_ENST00000542132.1_Missense_Mutation_p.Y195C|OCLN_ENST00000538151.1_Missense_Mutation_p.Y266C|OCLN_ENST00000396442.2_Missense_Mutation_p.Y517C|OCLN_ENST00000514370.1_3'UTR	NM_002538.3	NP_002529.1	Q16625	OCLN_HUMAN	occludin	517					apoptotic process (GO:0006915)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|protein complex assembly (GO:0006461)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethionine metabolic process (GO:0046500)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)|structural molecule activity (GO:0005198)|thiopurine S-methyltransferase activity (GO:0008119)			endometrium(2)|large_intestine(1)|liver(1)|prostate(1)|skin(1)	6		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		GTTGGAGACTATGATAGACAG	0.368																																					p.Y517C		Atlas-SNP	.											.	OCLN	22	.	0			c.A1550G						.						83.0	89.0	87.0					5																	68849479		2203	4299	6502	SO:0001583	missense	100506658	exon9			GAGACTATGATAG	U49184	CCDS4006.1, CCDS54864.1	5q13.1	2014-06-13			ENSG00000197822	ENSG00000197822			8104	protein-coding gene	gene with protein product	"""tight junction protein occludin TM4 minus"", ""phosphatase 1, regulatory subunit 115"""	602876				8601611	Standard	NM_002538		Approved	PPP1R115	uc003jwu.3	Q16625	OTTHUMG00000099356	ENST00000355237.2:c.1550A>G	chr5.hg19:g.68849479A>G	ENSP00000347379:p.Tyr517Cys	1057.0	0.0		1059.0	387.0	NM_001205254	B5BU70|D2DU64|D2DU65|D2IGC0|D2IGC1|E2CYV9|Q5U1V4|Q8N6K1	Missense_Mutation	SNP	ENST00000355237.2	hg19	CCDS4006.1	.	.	.	.	.	.	.	.	.	.	A	17.91	3.504575	0.64410	.	.	ENSG00000197822	ENST00000355237;ENST00000396442;ENST00000380766;ENST00000538151;ENST00000542132	T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17	5.6	5.6	0.85130	Occludin/RNA polymerase II elongation factor, ELL domain (1);	0.117665	0.64402	D	0.000013	T	0.65512	0.2698	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72424	-0.4298	10	0.87932	D	0	-22.6701	14.837	0.70192	1.0:0.0:0.0:0.0	.	517	Q16625	OCLN_HUMAN	C	517;517;463;266;195	ENSP00000347379:Y517C;ENSP00000379719:Y517C;ENSP00000370143:Y463C;ENSP00000445940:Y266C;ENSP00000440000:Y195C	ENSP00000347379:Y517C	Y	+	2	0	OCLN	68885235	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.483000	0.73617	2.144000	0.66660	0.451000	0.29950	TAT	.	.		0.368	OCLN-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216794.1	NM_002538	
PAPD4	167153	hgsc.bcm.edu	37	5	78938692	78938692	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:78938692A>G	ENST00000296783.3	+	8	1009	c.710A>G	c.(709-711)cAt>cGt	p.H237R	PAPD4_ENST00000504233.1_Missense_Mutation_p.H237R|PAPD4_ENST00000453514.1_Missense_Mutation_p.H237R|PAPD4_ENST00000423041.2_Missense_Mutation_p.H233R|PAPD4_ENST00000428308.2_Missense_Mutation_p.H237R			Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	237					hematopoietic progenitor cell differentiation (GO:0002244)|histone mRNA catabolic process (GO:0071044)|mRNA processing (GO:0006397)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|nuclear RNA-directed RNA polymerase complex (GO:0031380)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)			biliary_tract(1)|breast(2)|endometrium(4)|kidney(3)|large_intestine(9)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)		GAAGCACGGCATATACTCACC	0.323																																					p.H237R		Atlas-SNP	.											.	PAPD4	51	.	0			c.A710G						.						104.0	92.0	96.0					5																	78938692		2203	4300	6503	SO:0001583	missense	167153	exon8			CACGGCATATACT	AL833136	CCDS4048.1, CCDS75265.1, CCDS75266.1	5q14.1	2014-03-21			ENSG00000164329	ENSG00000164329			26776	protein-coding gene	gene with protein product	"""TUTase2"""	614121				12477932	Standard	NM_173797		Approved	FLJ38499, GLD2, TUT2	uc003kgb.2	Q6PIY7	OTTHUMG00000108163	ENST00000296783.3:c.710A>G	chr5.hg19:g.78938692A>G	ENSP00000296783:p.His237Arg	92.0	0.0		86.0	28.0	NM_173797	Q86WZ2|Q8N927	Missense_Mutation	SNP	ENST00000296783.3	hg19	CCDS4048.1	.	.	.	.	.	.	.	.	.	.	A	13.59	2.281545	0.40394	.	.	ENSG00000164329	ENST00000453514;ENST00000423041;ENST00000504233;ENST00000428308;ENST00000296783	T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05	5.88	5.88	0.94601	.	0.241752	0.49305	D	0.000143	T	0.24353	0.0590	N	0.12920	0.275	0.41035	D	0.985189	B;B;B	0.12630	0.0;0.002;0.006	B;B;B	0.12837	0.0;0.008;0.002	T	0.12993	-1.0526	10	0.09338	T	0.73	-15.6384	12.0969	0.53761	0.9314:0.0:0.0686:0.0	.	237;233;237	Q6PIY7;Q6PIY7-2;D6RAF2	GLD2_HUMAN;.;.	R	237;233;237;237;237	ENSP00000397563:H237R;ENSP00000393412:H233R;ENSP00000421966:H237R;ENSP00000396861:H237R;ENSP00000296783:H237R	ENSP00000296783:H237R	H	+	2	0	PAPD4	78974448	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.724000	0.61972	2.248000	0.74166	0.477000	0.44152	CAT	.	.		0.323	PAPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226967.1	NM_173797	
CMYA5	202333	hgsc.bcm.edu	37	5	79031059	79031059	+	Silent	SNP	A	A	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:79031059A>G	ENST00000446378.2	+	2	6502	c.6471A>G	c.(6469-6471)acA>acG	p.T2157T		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2157					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		ATCCACCTACACAACCAAAGG	0.453																																					p.T2157T		Atlas-SNP	.											.	CMYA5	643	.	0			c.A6471G						.						76.0	73.0	74.0					5																	79031059		1877	4107	5984	SO:0001819	synonymous_variant	202333	exon2			ACCTACACAACCA	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.6471A>G	chr5.hg19:g.79031059A>G		266.0	1.0		305.0	119.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.		0.453	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
RASA1	5921	hgsc.bcm.edu	37	5	86659193	86659193	+	Nonsense_Mutation	SNP	T	T	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:86659193T>G	ENST00000274376.6	+	11	2046	c.1482T>G	c.(1480-1482)taT>taG	p.Y494*	RASA1_ENST00000456692.2_Nonsense_Mutation_p.Y317*|RASA1_ENST00000512763.1_Nonsense_Mutation_p.Y327*|RASA1_ENST00000506290.1_Nonsense_Mutation_p.Y328*	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	494	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		AAAATTTATATTTTATCTTAG	0.294																																					p.Y494X		Atlas-SNP	.											.	RASA1	213	.	0			c.T1482G						.						51.0	55.0	54.0					5																	86659193		2203	4297	6500	SO:0001587	stop_gained	5921	exon11			TTTATATTTTATC		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	9871	protein-coding gene	gene with protein product	"""capillary malformation-arteriovenous malformation"""	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.1482T>G	chr5.hg19:g.86659193T>G	ENSP00000274376:p.Tyr494*	88.0	0.0		101.0	35.0	NM_002890	B2R6W3|Q9UDI1	Nonsense_Mutation	SNP	ENST00000274376.6	hg19	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	T	41	8.944730	0.99012	.	.	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	.	.	.	5.58	3.23	0.37069	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.6399	0.33970	0.0:0.2207:0.0:0.7793	.	.	.	.	X	494;527;317;327;328	.	ENSP00000274376:Y494X	Y	+	3	2	RASA1	86694949	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	1.653000	0.37323	0.941000	0.37499	-0.605000	0.04089	TAT	.	.		0.294	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890	
GALNT10	55568	hgsc.bcm.edu	37	5	153709146	153709146	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr5:153709146G>A	ENST00000297107.6	+	4	553	c.416G>A	c.(415-417)cGc>cAc	p.R139H	SAP30L-AS1_ENST00000519727.1_RNA|GALNT10_ENST00000425427.2_Missense_Mutation_p.R139H|GALNT10_ENST00000377661.2_Missense_Mutation_p.R139H	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	139					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.R139H(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			AACAGCAAGCGCTACCTGGAG	0.577																																					p.R139H		Atlas-SNP	.											GALNT10,NS,carcinoma,+1,2	GALNT10	70	.	1	Substitution - Missense(1)	large_intestine(1)	c.G416A						.						163.0	123.0	137.0					5																	153709146		2203	4300	6503	SO:0001583	missense	55568	exon4			GCAAGCGCTACCT	AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19873	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 10"""	608043	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)"""			12417297	Standard	NM_198321		Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.416G>A	chr5.hg19:g.153709146G>A	ENSP00000297107:p.Arg139His	70.0	0.0		88.0	20.0	NM_198321	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Missense_Mutation	SNP	ENST00000297107.6	hg19	CCDS4325.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.963195	0.53507	.	.	ENSG00000164574	ENST00000425427;ENST00000297107;ENST00000377661	T;T;T	0.59364	0.27;0.27;0.27	5.28	2.08	0.27032	.	2.769860	0.00906	N	0.002404	T	0.38692	0.1050	N	0.11845	0.185	0.80722	D	1	P;P;P	0.50369	0.572;0.763;0.934	B;B;B	0.36959	0.231;0.076;0.237	T	0.31779	-0.9931	10	0.46703	T	0.11	.	7.1293	0.25490	0.0943:0.0:0.3079:0.5979	.	139;139;139	Q86SR1-2;Q86SR1;Q86SR1-3	.;GLT10_HUMAN;.	H	139	ENSP00000415210:R139H;ENSP00000297107:R139H;ENSP00000366889:R139H	ENSP00000297107:R139H	R	+	2	0	GALNT10	153689339	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.988000	0.40697	0.566000	0.29273	0.655000	0.94253	CGC	.	.		0.577	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321	
CDYL	9425	hgsc.bcm.edu	37	6	4892318	4892318	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr6:4892318C>A	ENST00000328908.5	+	4	689	c.558C>A	c.(556-558)aaC>aaA	p.N186K	CDYL_ENST00000397588.3_Missense_Mutation_p.N132K|CDYL_ENST00000449732.2_De_novo_Start_InFrame|CDYL_ENST00000343762.5_De_novo_Start_InFrame|CDYL_ENST00000472453.1_Intron			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	186	Interaction with EZH2.				regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		GCCGGAAGAACATGGACCTAG	0.532																																					p.N132K		Atlas-SNP	.											.	CDYL	74	.	0			c.C396A						.						87.0	88.0	87.0					6																	4892318		2203	4300	6503	SO:0001583	missense	9425	exon2			GAAGAACATGGAC	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"""CDY-like, autosomal"", ""testis-specific chromodomain Y-like protein"""	603778	"""chromodomain protein, Y chromosome-like"""			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.558C>A	chr6.hg19:g.4892318C>A	ENSP00000330512:p.Asn186Lys	122.0	0.0		157.0	68.0	NM_004824	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	hg19		.	.	.	.	.	.	.	.	.	.	C	5.083	0.200884	0.09652	.	.	ENSG00000153046	ENST00000328908;ENST00000397588	T;T	0.54279	0.97;0.58	5.79	-5.41	0.02648	.	0.225483	0.44688	D	0.000439	T	0.18299	0.0439	L	0.33485	1.01	0.80722	D	1	B;B	0.11235	0.001;0.004	B;B	0.12837	0.008;0.005	T	0.17410	-1.0370	10	0.17369	T	0.5	.	15.693	0.77469	0.0:0.1478:0.0:0.8522	.	132;186	Q9Y232-2;Q9Y232	.;CDYL1_HUMAN	K	186;132	ENSP00000330512:N186K;ENSP00000380718:N132K	ENSP00000330512:N186K	N	+	3	2	CDYL	4837317	0.845000	0.29573	0.679000	0.29978	0.972000	0.66771	0.044000	0.13992	-1.004000	0.03421	-0.312000	0.09012	AAC	.	.		0.532	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824	
RGL2	5863	hgsc.bcm.edu	37	6	33266246	33266246	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr6:33266246C>T	ENST00000497454.1	-	2	637	c.142G>A	c.(142-144)Gag>Aag	p.E48K	RGL2_ENST00000437840.2_Intron|RGL2_ENST00000444031.2_Intron	NM_001243738.1|NM_004761.4	NP_001230667.1|NP_004752.1	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation stimulator-like 2	48					positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(2)|cervix(2)|endometrium(7)|kidney(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	34						tcttcttcctcctcctcttcc	0.632																																					p.E48K		Atlas-SNP	.											.	RGL2	58	.	0			c.G142A						.						3.0	4.0	4.0					6																	33266246		1981	3928	5909	SO:0001583	missense	5863	exon2			CTTCCTCCTCCTC		CCDS4774.1	6p21.3	2010-02-17	2004-06-11	2004-06-16	ENSG00000237441	ENSG00000237441			9769	protein-coding gene	gene with protein product		602306	"""RAB2, member RAS oncogene family-like"""	RAB2L		8976381	Standard	NM_001243738		Approved	KE1.5, HKE1.5	uc003odv.3	O15211	OTTHUMG00000031072	ENST00000497454.1:c.142G>A	chr6.hg19:g.33266246C>T	ENSP00000420211:p.Glu48Lys	445.0	1.0		430.0	200.0	NM_004761	B4DG72|Q5STK0|Q9Y3F3	Missense_Mutation	SNP	ENST00000497454.1	hg19	CCDS4774.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.976718	0.53720	.	.	ENSG00000237441	ENST00000497454;ENST00000425946	T	0.11277	2.79	4.83	4.83	0.62350	.	0.771349	0.11255	N	0.583161	T	0.01730	0.0055	N	0.05078	-0.115	0.80722	D	1	B	0.29531	0.247	B	0.25759	0.063	T	0.29610	-1.0006	10	0.06365	T	0.9	.	13.2872	0.60249	0.0:1.0:0.0:0.0	.	48	O15211	RGL2_HUMAN	K	48	ENSP00000420211:E48K	ENSP00000392918:E48K	E	-	1	0	RGL2	33374224	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.023000	0.49666	2.516000	0.84829	0.579000	0.79373	GAG	.	.		0.632	RGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076098.2		
KLHL7	55975	hgsc.bcm.edu	37	7	23212604	23212604	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr7:23212604A>C	ENST00000339077.5	+	10	1660	c.1417A>C	c.(1417-1419)Aat>Cat	p.N473H	KLHL7_ENST00000322231.7_Missense_Mutation_p.N451H|KLHL7_ENST00000539124.1_Missense_Mutation_p.N397H|KLHL7_ENST00000545443.1_Missense_Mutation_p.N451H|KLHL7_ENST00000542558.1_Missense_Mutation_p.N248H|KLHL7_ENST00000409689.1_Missense_Mutation_p.N425H|AC005082.1_ENST00000366347.4_Intron	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	473					protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AGCCAGGAAGAATCATGGGCT	0.373																																					p.N473H		Atlas-SNP	.											.	KLHL7	102	.	0			c.A1417C						.						284.0	265.0	272.0					7																	23212604		2203	4300	6503	SO:0001583	missense	55975	exon10			AGGAAGAATCATG		CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550		"""Kelch-like"", ""BTB/POZ domain containing"""	15646	protein-coding gene	gene with protein product	"""retinitis pigmentosa 42"""	611119	"""kelch-like 7 (Drosophila)"""			19520207	Standard	NM_001031710		Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.1417A>C	chr7.hg19:g.23212604A>C	ENSP00000343273:p.Asn473His	202.0	0.0		209.0	89.0	NM_001031710	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Missense_Mutation	SNP	ENST00000339077.5	hg19	CCDS34609.1	.	.	.	.	.	.	.	.	.	.	A	7.699	0.692648	0.15039	.	.	ENSG00000122550	ENST00000538858;ENST00000322231;ENST00000339077;ENST00000539124;ENST00000542558;ENST00000409689;ENST00000545443	T;T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13;-1.13	5.68	4.53	0.55603	Kelch-type beta propeller (1);	0.042337	0.85682	D	0.000000	T	0.75087	0.3802	N	0.16368	0.405	0.53005	D	0.999963	B;P;D	0.76494	0.422;0.856;0.999	B;P;P	0.61070	0.397;0.525;0.883	T	0.74309	-0.3707	10	0.38643	T	0.18	.	11.543	0.50677	0.9302:0.0:0.0698:0.0	.	248;473;451	B7Z3P9;Q8IXQ5;Q8IXQ5-2	.;KLHL7_HUMAN;.	H	314;451;473;397;248;425;451	ENSP00000322958:N451H;ENSP00000343273:N473H;ENSP00000441136:N397H;ENSP00000442367:N248H;ENSP00000386263:N425H;ENSP00000442366:N451H	ENSP00000322958:N451H	N	+	1	0	KLHL7	23179129	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.938000	0.92943	0.991000	0.38814	0.477000	0.44152	AAT	.	.		0.373	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846	
RFC2	5982	hgsc.bcm.edu	37	7	73654297	73654297	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr7:73654297T>C	ENST00000055077.3	-	7	724	c.664A>G	c.(664-666)Atc>Gtc	p.I222V	RFC2_ENST00000352131.3_Missense_Mutation_p.I188V	NM_181471.1	NP_852136.1	P35250	RFC2_HUMAN	replication factor C (activator 1) 2, 40kDa	222					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(3)	8						GCCGTGAAGATGATGGCTTCT	0.587																																					p.I222V		Atlas-SNP	.											.	RFC2	27	.	0			c.A664G						.						135.0	87.0	103.0					7																	73654297		2203	4300	6503	SO:0001583	missense	5982	exon7			TGAAGATGATGGC		CCDS5567.1, CCDS5568.1, CCDS75618.1	7q11.23	2010-04-21	2002-08-29		ENSG00000049541	ENSG00000049541		"""ATPases / AAA-type"""	9970	protein-coding gene	gene with protein product	"""activator 1"""	600404	"""replication factor C (activator 1) 2 (40kD)"""			1313560, 7774928	Standard	NM_181471		Approved	A1, RFC40	uc003uaj.3	P35250	OTTHUMG00000023239	ENST00000055077.3:c.664A>G	chr7.hg19:g.73654297T>C	ENSP00000055077:p.Ile222Val	121.0	0.0		112.0	38.0	NM_181471	B5BU07|D3DXG3|P32846|Q9BU93	Missense_Mutation	SNP	ENST00000055077.3	hg19	CCDS5568.1	.	.	.	.	.	.	.	.	.	.	T	8.748	0.920590	0.17982	.	.	ENSG00000049541	ENST00000352131;ENST00000055077	T;T	0.38887	1.11;1.11	5.19	0.151	0.14888	.	0.198965	0.53938	N	0.000054	T	0.16599	0.0399	N	0.13327	0.33	0.50467	D	0.999874	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.001	T	0.28808	-1.0032	10	0.02654	T	1	.	5.1254	0.14882	0.0:0.3123:0.1492:0.5384	.	188;188;222	P35250-2;Q75MT5;P35250	.;.;RFC2_HUMAN	V	188;222	ENSP00000275627:I188V;ENSP00000055077:I222V	ENSP00000055077:I222V	I	-	1	0	RFC2	73292233	1.000000	0.71417	0.854000	0.33618	0.955000	0.61496	2.210000	0.42816	0.066000	0.16515	0.459000	0.35465	ATC	.	.		0.587	RFC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252459.2	NM_181471	
CACNA2D1	781	hgsc.bcm.edu	37	7	81642821	81642821	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr7:81642821A>G	ENST00000356253.5	-	14	1483	c.1228T>C	c.(1228-1230)Tat>Cat	p.Y410H	CACNA2D1_ENST00000464354.1_5'UTR|MIR1255B1_ENST00000439234.1_RNA|MIR1255B1_ENST00000454066.1_RNA|CACNA2D1_ENST00000356860.3_Missense_Mutation_p.Y410H			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	410	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	ATTTCATAATAATAACCTGAA	0.189																																					p.Y410H		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.T1228C						.						8.0	8.0	8.0					7																	81642821		1827	3719	5546	SO:0001583	missense	781	exon14			CATAATAATAACC	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"""Calcium channel subunits"""	1399	protein-coding gene	gene with protein product		114204	"""long intergenic non-protein coding RNA 1112"""	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.1228T>C	chr7.hg19:g.81642821A>G	ENSP00000348589:p.Tyr410His	650.0	0.0		748.0	319.0	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	hg19		.	.	.	.	.	.	.	.	.	.	A	23.6	4.434542	0.83776	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253	T;T	0.14516	2.5;2.5	5.72	5.72	0.89469	.	0.052077	0.85682	D	0.000000	T	0.40247	0.1109	M	0.80616	2.505	0.80722	D	1	D	0.69078	0.997	D	0.72075	0.976	T	0.34900	-0.9810	10	0.87932	D	0	-19.3369	14.9805	0.71309	1.0:0.0:0.0:0.0	.	410	P54289-2	.	H	410	ENSP00000349320:Y410H;ENSP00000348589:Y410H	ENSP00000284088:Y410H	Y	-	1	0	CACNA2D1	81480757	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.811000	0.75221	2.183000	0.69458	0.383000	0.25322	TAT	.	.		0.189	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding			
PCLO	27445	hgsc.bcm.edu	37	7	82784467	82784467	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr7:82784467G>A	ENST00000333891.9	-	2	1827	c.1490C>T	c.(1489-1491)gCa>gTa	p.A497V	PCLO_ENST00000423517.2_Missense_Mutation_p.A497V	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGGGGGCTTTGCTGAGCCAGG	0.607																																					p.A497V		Atlas-SNP	.											.	PCLO	1506	.	0			c.C1490T						.						93.0	102.0	99.0					7																	82784467		1946	4134	6080	SO:0001583	missense	27445	exon2			GGCTTTGCTGAGC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.1490C>T	chr7.hg19:g.82784467G>A	ENSP00000334319:p.Ala497Val	23.0	0.0		32.0	9.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	4.487|4.487	0.090288|0.090288	0.08632|0.08632	.|.	.|.	ENSG00000186472|ENSG00000186472	ENST00000333891;ENST00000423517|ENST00000431819	T;T|.	0.16597|.	2.33;2.33|.	4.64|4.64	3.73|3.73	0.42828|0.42828	.|.	.|.	.|.	.|.	.|.	T|T	0.30262|0.30262	0.0759|0.0759	L|L	0.32530|0.32530	0.975|0.975	0.19775|0.19775	N|N	0.99996|0.99996	B;B|.	0.28850|.	0.225;0.225|.	B;B|.	0.30316|.	0.114;0.114|.	T|T	0.26780|0.26780	-1.0093|-1.0093	9|6	0.87932|0.72032	D|D	0|0.01	.|.	4.7611|4.7611	0.13108|0.13108	0.0841:0.1631:0.6057:0.1471|0.0841:0.1631:0.6057:0.1471	.|.	497;497|.	Q9Y6V0-5;Q9Y6V0-6|.	.;.|.	V|L	497|443	ENSP00000334319:A497V;ENSP00000388393:A497V|.	ENSP00000334319:A497V|ENSP00000403939:P443L	A|P	-|-	2|2	0|0	PCLO|PCLO	82622403|82622403	0.001000|0.001000	0.12720|0.12720	0.028000|0.028000	0.17463|0.17463	0.090000|0.090000	0.18270|0.18270	0.529000|0.529000	0.23019|0.23019	1.036000|1.036000	0.39998|0.39998	0.561000|0.561000	0.74099|0.74099	GCA|CCA	.	.		0.607	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
DOCK4	9732	hgsc.bcm.edu	37	7	111555875	111555875	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr7:111555875G>T	ENST00000437633.1	-	13	1407	c.1151C>A	c.(1150-1152)tCc>tAc	p.S384Y	DOCK4_ENST00000428084.1_Missense_Mutation_p.S384Y|DOCK4_ENST00000476846.1_5'UTR	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	384					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)	p.S372F(1)|p.S384F(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				CCTTGTTATGGATACTCCATG	0.373																																					p.S384Y		Atlas-SNP	.											DOCK4_ENST00000437633,NS,carcinoma,0,2	DOCK4	365	.	2	Substitution - Missense(2)	lung(2)	c.C1151A						.						58.0	53.0	55.0					7																	111555875		1820	4080	5900	SO:0001583	missense	9732	exon13			GTTATGGATACTC		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.1151C>A	chr7.hg19:g.111555875G>T	ENSP00000404179:p.Ser384Tyr	110.0	0.0		119.0	49.0	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	hg19	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.2|26.2	4.710821|4.710821	0.89112|0.89112	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000445943|ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250	.|T;T	.|0.03152	.|4.04;4.03	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.14614|0.14614	0.0353|0.0353	L|L	0.58101|0.58101	1.795|1.795	0.80722|0.80722	D|D	1|1	.|D;D	.|0.54047	.|0.964;0.964	.|P;P	.|0.59056	.|0.851;0.714	T|T	0.00002|0.00002	-1.2647|-1.2647	5|10	.|0.87932	.|D	.|0	.|.	19.3311|19.3311	0.94288|0.94288	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|384;384	.|Q149N5;Q8N1I0	.|.;DOCK4_HUMAN	T|Y	372|372;384;384;372;383	.|ENSP00000410746:S384Y;ENSP00000404179:S384Y	.|ENSP00000345432:S372Y	P|S	-|-	1|2	0|0	DOCK4|DOCK4	111343111|111343111	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	8.322000|8.322000	0.90000|0.90000	2.868000|2.868000	0.98415|0.98415	0.555000|0.555000	0.69702|0.69702	CCA|TCC	.	.		0.373	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	
CTTNBP2	83992	hgsc.bcm.edu	37	7	117431229	117431229	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr7:117431229G>A	ENST00000160373.3	-	4	2112	c.2021C>T	c.(2020-2022)tCa>tTa	p.S674L	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	674					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		TCTACAGGATGAGGCACTAAC	0.483																																					p.S674L		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.C2021T						.						118.0	110.0	113.0					7																	117431229		2203	4300	6503	SO:0001583	missense	83992	exon4			CAGGATGAGGCAC		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"""Ankyrin repeat domain containing"""	15679	protein-coding gene	gene with protein product		609772	"""cortactin binding protein 2"""	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.2021C>T	chr7.hg19:g.117431229G>A	ENSP00000160373:p.Ser674Leu	145.0	0.0		196.0	85.0	NM_033427	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	hg19	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.163486	0.78226	.	.	ENSG00000077063	ENST00000160373	T	0.68025	-0.3	5.68	5.68	0.88126	.	0.113271	0.64402	D	0.000007	T	0.77068	0.4076	M	0.76574	2.34	0.51767	D	0.999932	D	0.58620	0.983	P	0.51016	0.656	T	0.79472	-0.1789	10	0.72032	D	0.01	-0.725	20.153	0.98091	0.0:0.0:1.0:0.0	.	674	Q8WZ74	CTTB2_HUMAN	L	674	ENSP00000160373:S674L	ENSP00000160373:S674L	S	-	2	0	CTTNBP2	117218465	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.011000	0.93618	2.838000	0.97847	0.563000	0.77884	TCA	.	.		0.483	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427	
GPR124	25960	hgsc.bcm.edu	37	8	37699537	37699537	+	Silent	SNP	C	C	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr8:37699537C>T	ENST00000412232.2	+	19	3694	c.3681C>T	c.(3679-3681)acC>acT	p.T1227T	GPR124_ENST00000315215.7_Silent_p.T1010T	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	1227					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			ACAGCCCCACCGACAGCTACC	0.741																																					p.T1227T		Atlas-SNP	.											.	GPR124	85	.	0			c.C3681T						.						2.0	3.0	2.0					8																	37699537		1211	2420	3631	SO:0001819	synonymous_variant	25960	exon19			CCCCACCGACAGC	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17849	protein-coding gene	gene with protein product	"""tumor endothelial marker 5"""	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.3681C>T	chr8.hg19:g.37699537C>T		15.0	0.0		20.0	18.0	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Silent	SNP	ENST00000412232.2	hg19	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	C	8.908	0.958046	0.18507	.	.	ENSG00000020181	ENST00000416514	.	.	.	3.95	-2.01	0.07410	.	.	.	.	.	.	.	.	.	.	.	0.30433	N	0.776948	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-11.071	2.1908	0.03898	0.1036:0.3087:0.301:0.2867	.	.	.	.	X	1220	.	ENSP00000405145:R1220X	R	+	1	2	GPR124	37818695	0.000000	0.05858	0.743000	0.31040	0.816000	0.46133	-2.794000	0.00765	-0.266000	0.09339	0.313000	0.20887	CGA	.	.		0.741	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2		
CPQ	10404	hgsc.bcm.edu	37	8	97797377	97797377	+	Silent	SNP	A	A	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr8:97797377A>G	ENST00000220763.5	+	2	462	c.252A>G	c.(250-252)ctA>ctG	p.L84L		NM_016134.2	NP_057218.1	Q9Y646	CBPQ_HUMAN	carboxypeptidase Q	84					peptide catabolic process (GO:0043171)|proteolysis (GO:0006508)|thyroid hormone generation (GO:0006590)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)	carboxypeptidase activity (GO:0004180)|metal ion binding (GO:0046872)|metallodipeptidase activity (GO:0070573)|protein homodimerization activity (GO:0042803)										CCAAGAACCTAGAAAAAGCCA	0.488																																					p.L84L		Atlas-SNP	.											.	.	.	.	0			c.A252G						.						91.0	85.0	87.0					8																	97797377		2203	4300	6503	SO:0001819	synonymous_variant	10404	exon2			GAACCTAGAAAAA	AF107834	CCDS6273.1	8q22.2	2012-02-17			ENSG00000104324	ENSG00000104324			16910	protein-coding gene	gene with protein product	"""lysosomal dipeptidase"", ""Ser-Met dipeptidase"", ""plasma glutamate carboxypeptidase"""					10206990	Standard	NM_016134		Approved	LDP, PGCP	uc003yhw.3	Q9Y646	OTTHUMG00000164690	ENST00000220763.5:c.252A>G	chr8.hg19:g.97797377A>G		192.0	0.0		316.0	98.0	NM_016134	B2RD88|Q8NBZ1|Q9UNM8|Q9Y5X6	Silent	SNP	ENST00000220763.5	hg19	CCDS6273.1																																																																																			.	.		0.488	CPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379757.2	NM_016134	
ZHX2	22882	hgsc.bcm.edu	37	8	123964558	123964558	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr8:123964558G>A	ENST00000314393.4	+	3	1643	c.808G>A	c.(808-810)Gcc>Acc	p.A270T		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	270	Required for homodimerization.|Required for interaction with NFYA.|Required for repressor activity.				mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			ATACAACTCTGCCCTGGATAC	0.493																																					p.A270T	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.G808A						.						153.0	157.0	156.0					8																	123964558		2203	4300	6503	SO:0001583	missense	22882	exon3			AACTCTGCCCTGG	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.808G>A	chr8.hg19:g.123964558G>A	ENSP00000314709:p.Ala270Thr	103.0	0.0		196.0	48.0	NM_014943		Missense_Mutation	SNP	ENST00000314393.4	hg19	CCDS6336.1	.	.	.	.	.	.	.	.	.	.	G	17.98	3.521675	0.64747	.	.	ENSG00000178764	ENST00000314393	T	0.20738	2.05	5.93	5.93	0.95920	Homeobox (1);Homeodomain-like (1);	0.116646	0.64402	D	0.000017	T	0.31295	0.0792	M	0.76838	2.35	0.50813	D	0.999895	P	0.48503	0.911	B	0.39840	0.311	T	0.14896	-1.0456	10	0.45353	T	0.12	-25.4178	20.3437	0.98782	0.0:0.0:1.0:0.0	.	270	Q9Y6X8	ZHX2_HUMAN	T	270	ENSP00000314709:A270T	ENSP00000314709:A270T	A	+	1	0	ZHX2	124033739	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.802000	0.62539	2.821000	0.97095	0.555000	0.69702	GCC	.	.		0.493	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
TRPM6	140803	hgsc.bcm.edu	37	9	77454953	77454953	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr9:77454953T>G	ENST00000360774.1	-	5	768	c.531A>C	c.(529-531)gaA>gaC	p.E177D	TRPM6_ENST00000451710.3_Missense_Mutation_p.E177D|TRPM6_ENST00000361255.3_Missense_Mutation_p.E172D|TRPM6_ENST00000376864.4_Missense_Mutation_p.E177D|TRPM6_ENST00000359047.2_Missense_Mutation_p.E177D|TRPM6_ENST00000376872.3_Missense_Mutation_p.E177D|TRPM6_ENST00000376871.3_Missense_Mutation_p.E177D|TRPM6_ENST00000449912.2_Missense_Mutation_p.E172D	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	177					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						TATTGATGCCTTCAGTTATTA	0.463																																					p.E177D		Atlas-SNP	.											.	TRPM6	377	.	0			c.A531C						.						133.0	120.0	124.0					9																	77454953		2203	4300	6503	SO:0001583	missense	140803	exon5			GATGCCTTCAGTT	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.531A>C	chr9.hg19:g.77454953T>G	ENSP00000354006:p.Glu177Asp	98.0	0.0		67.0	49.0	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	hg19	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	T	12.01	1.808872	0.31961	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000376871;ENST00000449912;ENST00000361255;ENST00000376870;ENST00000376864;ENST00000359047	T;T;T;T;T;T;T;T	0.02974	4.09;4.09;4.09;4.09;4.09;4.09;4.09;4.09	5.86	5.86	0.93980	.	0.043658	0.85682	D	0.000000	T	0.03136	0.0092	L	0.33189	0.99	0.46927	D	0.999259	B;B;B;B;B;B	0.25007	0.003;0.003;0.023;0.002;0.021;0.116	B;B;B;B;B;B	0.19391	0.004;0.011;0.011;0.007;0.025;0.025	T	0.51172	-0.8739	10	0.48119	T	0.1	.	10.5821	0.45261	0.0:0.0715:0.0:0.9285	.	177;177;177;177;177;172	Q9BX84-7;Q9BX84-6;Q9BX84-5;Q96LV9;Q9BX84;Q9BX84-3	.;.;.;.;TRPM6_HUMAN;.	D	177;177;177;177;172;172;176;177;177	ENSP00000354006:E177D;ENSP00000407341:E177D;ENSP00000366068:E177D;ENSP00000366067:E177D;ENSP00000396672:E172D;ENSP00000354962:E172D;ENSP00000366060:E177D;ENSP00000351942:E177D	ENSP00000351942:E177D	E	-	3	2	TRPM6	76644773	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.098000	0.41757	2.240000	0.73641	0.533000	0.62120	GAA	.	.		0.463	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
EPB41L4B	54566	hgsc.bcm.edu	37	9	111962537	111962537	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr9:111962537T>A	ENST00000374566.3	-	20	2541	c.2024A>T	c.(2023-2025)aAg>aTg	p.K675M		NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	675					actomyosin structure organization (GO:0031032)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)	structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCTTGTTAACTTCCTCACTCG	0.408																																					p.K675M		Atlas-SNP	.											.	EPB41L4B	111	.	0			c.A2024T						.						83.0	81.0	82.0					9																	111962537		1867	4108	5975	SO:0001583	missense	54566	exon20			GTTAACTTCCTCA	AB032179	CCDS43859.1, CCDS43860.1	9q22.1-q22.3	2008-02-05			ENSG00000095203	ENSG00000095203			19818	protein-coding gene	gene with protein product		610340				10783258	Standard	NM_018424		Approved	EHM2	uc004bdz.1	Q9H329	OTTHUMG00000020470	ENST00000374566.3:c.2024A>T	chr9.hg19:g.111962537T>A	ENSP00000363694:p.Lys675Met	116.0	0.0		84.0	70.0	NM_019114	Q5T4G5|Q5T4G6|Q9H328|Q9P2V3	Missense_Mutation	SNP	ENST00000374566.3	hg19	CCDS43859.1	.	.	.	.	.	.	.	.	.	.	T	19.39	3.818518	0.71028	.	.	ENSG00000095203	ENST00000262536;ENST00000374566	D	0.86497	-2.13	5.61	4.48	0.54585	.	0.224284	0.22947	N	0.053711	D	0.83954	0.5366	L	0.47716	1.5	0.80722	D	1	D	0.56287	0.975	P	0.46629	0.522	T	0.82975	-0.0190	10	0.72032	D	0.01	.	7.6322	0.28247	0.0:0.0975:0.0:0.9025	.	675	Q9H329	E41LB_HUMAN	M	360;675	ENSP00000363694:K675M	ENSP00000262536:K360M	K	-	2	0	EPB41L4B	111002358	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.811000	0.47986	0.967000	0.38186	0.533000	0.62120	AAG	.	.		0.408	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1	NM_018424	
GDF2	2658	hgsc.bcm.edu	37	10	48413997	48413997	+	Missense_Mutation	SNP	C	C	A	rs201711410	byFrequency	TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr10:48413997C>A	ENST00000249598.1	-	2	1030	c.871G>T	c.(871-873)Ggc>Tgc	p.G291C		NM_016204.1	NP_057288.1	Q9UK05	GDF2_HUMAN	growth differentiation factor 2	291					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to BMP stimulus (GO:0071773)|growth (GO:0040007)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of DNA replication (GO:0008156)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	28						TCTGTGGAGCCGTCCTTGGAC	0.617																																					p.G291C		Atlas-SNP	.											.	GDF2	77	.	0			c.G871T						.						85.0	72.0	76.0					10																	48413997		2203	4300	6503	SO:0001583	missense	2658	exon2			TGGAGCCGTCCTT	AF156891	CCDS73118.1	10q11.22	2014-05-06			ENSG00000128802	ENSG00000263761		"""Endogenous ligands"""	4217	protein-coding gene	gene with protein product		605120				10849432	Standard	NM_016204		Approved	BMP-9, BMP9	uc001jfa.1	Q9UK05	OTTHUMG00000188320	ENST00000249598.1:c.871G>T	chr10.hg19:g.48413997C>A	ENSP00000249598:p.Gly291Cys	75.0	0.0		85.0	29.0	NM_016204	Q5VSQ9|Q9Y571	Missense_Mutation	SNP	ENST00000249598.1	hg19	CCDS7219.1	.	.	.	.	.	.	.	.	.	.	C	9.640	1.138643	0.21123	.	.	ENSG00000128802	ENST00000249598	T	0.79033	-1.23	5.46	-7.65	0.01281	.	1.295450	0.04583	N	0.395367	T	0.70815	0.3267	L	0.43152	1.355	0.09310	N	1	D	0.54772	0.968	P	0.45610	0.487	T	0.72097	-0.4393	10	0.87932	D	0	.	10.4445	0.44486	0.0:0.4232:0.0881:0.4888	.	291	Q9UK05	GDF2_HUMAN	C	291	ENSP00000249598:G291C	ENSP00000249598:G291C	G	-	1	0	GDF2	48034003	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.437000	0.06914	-1.226000	0.02574	-0.373000	0.07131	GGC	.	C|1.000;T|0.000		0.617	GDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047891.1	NM_016204	
CC2D2B	387707	hgsc.bcm.edu	37	10	97787105	97787105	+	Intron	SNP	G	G	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr10:97787105G>A	ENST00000344386.3	+	9	944				ENTPD1-AS1_ENST00000458228.1_RNA|ENTPD1-AS1_ENST00000449197.1_RNA|CC2D2B_ENST00000371198.2_3'UTR|ENTPD1-AS1_ENST00000454638.1_RNA|ENTPD1-AS1_ENST00000451364.1_RNA|RP11-690P14.4_ENST00000475252.2_3'UTR|ENTPD1-AS1_ENST00000452728.1_RNA|ENTPD1-AS1_ENST00000416301.1_RNA|CC2D2B_ENST00000410012.2_Missense_Mutation_p.E326K	NM_001001732.3	NP_001001732.2	Q6DHV5	C2D2B_HUMAN	coiled-coil and C2 domain containing 2B											large_intestine(1)|lung(7)|ovary(1)|urinary_tract(1)	10		Colorectal(252;0.158)		Epithelial(162;7.08e-08)|all cancers(201;2.71e-06)		TGTTTCATCTGAAGGAGATAA	0.318																																					p.E326K		Atlas-SNP	.											.	CC2D2B	46	.	0			c.G976A						.						189.0	153.0	164.0					10																	97787105		692	1591	2283	SO:0001627	intron_variant	387707	exon11			TCATCTGAAGGAG	BC075861	CCDS41555.1, CCDS53560.1	10q23.33	2008-11-06	2007-10-19	2007-10-19	ENSG00000188649	ENSG00000188649			31666	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 130"""	C10orf130			Standard	NM_001001732		Approved	bA248J23.4	uc010qop.2	Q6DHV5	OTTHUMG00000018820	ENST00000344386.3:c.781-4472G>A	chr10.hg19:g.97787105G>A		134.0	0.0		179.0	81.0	NM_001159747	A2A3E9|B4DYD4|E9PCC3|Q5VUS0	Missense_Mutation	SNP	ENST00000344386.3	hg19	CCDS41555.1	.	.	.	.	.	.	.	.	.	.	G	8.009	0.757107	0.15846	.	.	ENSG00000188649	ENST00000451649;ENST00000410012	T	0.71579	-0.58	5.8	5.8	0.92144	.	.	.	.	.	T	0.54775	0.1879	N	0.20986	0.625	0.23144	N	0.998228	B	0.14012	0.009	B	0.12156	0.007	T	0.35450	-0.9788	9	0.13853	T	0.58	.	10.9752	0.47461	0.0844:0.0:0.9156:0.0	.	326	E9PCC3	.	K	326	ENSP00000386988:E326K	ENSP00000386988:E326K	E	+	1	0	CC2D2B	97777095	0.958000	0.32768	0.998000	0.56505	0.033000	0.12548	1.366000	0.34193	2.741000	0.93983	0.650000	0.86243	GAA	.	.		0.318	CC2D2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049573.3	NM_001001732	
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118225668	118225668	+	Silent	SNP	A	A	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr10:118225668A>G	ENST00000369230.3	+	8	1061	c.915A>G	c.(913-915)acA>acG	p.T305T		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	305					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		GATCCTACACATCTTTTAAAG	0.323																																					p.T305T		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.A915G						.						96.0	92.0	93.0					10																	118225668		2202	4299	6501	SO:0001819	synonymous_variant	119548	exon8			CTACACATCTTTT	BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.915A>G	chr10.hg19:g.118225668A>G		81.0	0.0		92.0	44.0	NM_001011709		Silent	SNP	ENST00000369230.3	hg19	CCDS31292.1																																																																																			.	.		0.323	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
UBQLNL	143630	hgsc.bcm.edu	37	11	5537631	5537631	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr11:5537631C>G	ENST00000380184.1	-	1	304	c.41G>C	c.(40-42)aGt>aCt	p.S14T	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	14										endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		TGGACATCCACTCTGGGACAT	0.532																																					p.S14T		Atlas-SNP	.											.	UBQLNL	74	.	0			c.G41C						.						80.0	78.0	79.0					11																	5537631		2201	4297	6498	SO:0001583	missense	143630	exon1			CATCCACTCTGGG	AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"""Ubiquilin family"""	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.41G>C	chr11.hg19:g.5537631C>G	ENSP00000369531:p.Ser14Thr	61.0	0.0		75.0	30.0	NM_145053	Q6ZRU1|Q96EK3|Q96MB0	Missense_Mutation	SNP	ENST00000380184.1	hg19	CCDS31385.1	.	.	.	.	.	.	.	.	.	.	C	6.287	0.421012	0.11928	.	.	ENSG00000175518	ENST00000380184;ENST00000538889	T	0.45668	0.89	4.94	-2.31	0.06765	.	0.608853	0.15582	N	0.254825	T	0.29190	0.0726	L	0.53249	1.67	0.09310	N	1	B	0.33694	0.421	B	0.32864	0.154	T	0.20538	-1.0272	10	0.62326	D	0.03	.	2.462	0.04544	0.1469:0.2338:0.4326:0.1867	.	14	Q8IYU4	UBQLN_HUMAN	T	14	ENSP00000369531:S14T	ENSP00000369531:S14T	S	-	2	0	UBQLNL	5494207	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-1.132000	0.03235	-0.257000	0.09459	0.650000	0.86243	AGT	.	.		0.532	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053	
MMP20	9313	hgsc.bcm.edu	37	11	102477304	102477304	+	Silent	SNP	C	C	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr11:102477304C>T	ENST00000260228.2	-	6	927	c.915G>A	c.(913-915)gtG>gtA	p.V305V	RP11-817J15.2_ENST00000544115.1_RNA|MMP20_ENST00000544938.1_5'UTR|RP11-817J15.2_ENST00000542119.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	324					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	CCAGCATTGTCACAGCGTCAA	0.582																																					p.V305V		Atlas-SNP	.											.	MMP20	52	.	0			c.G915A						.						128.0	111.0	117.0					11																	102477304		2203	4299	6502	SO:0001819	synonymous_variant	9313	exon6			CATTGTCACAGCG	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"""enamelysin"""	604629	"""matrix metalloproteinase 20 (enamelysin)"""			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.915G>A	chr11.hg19:g.102477304C>T		167.0	0.0		165.0	31.0	NM_004771	D3DUA8|Q9H3Q0	Silent	SNP	ENST00000260228.2	hg19	CCDS8318.1																																																																																			.	.		0.582	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1		
ROBO4	54538	hgsc.bcm.edu	37	11	124766129	124766129	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr11:124766129T>C	ENST00000306534.3	-	4	1129	c.644A>G	c.(643-645)cAt>cGt	p.H215R	ROBO4_ENST00000526899.1_5'UTR|ROBO4_ENST00000533054.1_Missense_Mutation_p.H70R	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	215	Ig-like C2-type 2.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GCTCTCCCTATGTCCTGCGCT	0.622																																					p.H215R		Atlas-SNP	.											.	ROBO4	130	.	0			c.A644G						.						86.0	84.0	85.0					11																	124766129		2201	4299	6500	SO:0001583	missense	54538	exon4			TCCCTATGTCCTG	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.644A>G	chr11.hg19:g.124766129T>C	ENSP00000304945:p.His215Arg	49.0	0.0		47.0	4.0	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	hg19	CCDS8455.1	.	.	.	.	.	.	.	.	.	.	T	3.912	-0.019822	0.07634	.	.	ENSG00000154133	ENST00000306534;ENST00000374963;ENST00000533054	T;T	0.65732	-0.17;-0.17	5.04	-3.63	0.04529	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.453940	0.04684	N	0.412847	T	0.26846	0.0657	N	0.01277	-0.915	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.15896	-1.0421	10	0.11182	T	0.66	.	5.3946	0.16263	0.0:0.2943:0.2597:0.4461	.	105;215	Q8WZ75-3;Q8WZ75	.;ROBO4_HUMAN	R	215;105;70	ENSP00000304945:H215R;ENSP00000437129:H70R	ENSP00000304945:H215R	H	-	2	0	ROBO4	124271339	0.000000	0.05858	0.004000	0.12327	0.057000	0.15508	-0.431000	0.06965	-0.760000	0.04677	0.528000	0.53228	CAT	.	.		0.622	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
KCNC2	3747	hgsc.bcm.edu	37	12	75601377	75601377	+	Silent	SNP	C	C	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr12:75601377C>A	ENST00000549446.1	-	2	1067	c.387G>T	c.(385-387)gtG>gtT	p.V129V	KCNC2_ENST00000350228.2_Silent_p.V129V|KCNC2_ENST00000341669.3_Silent_p.V129V|KCNC2_ENST00000540018.1_Silent_p.V129V|KCNC2_ENST00000393288.2_Silent_p.V129V|KCNC2_ENST00000550433.1_Silent_p.V129V|KCNC2_ENST00000548513.1_Silent_p.V129V|KCNC2_ENST00000298972.1_Silent_p.V129V	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	129					action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	GCGGCCCGCACACGTCTGCGG	0.682																																					p.V129V		Atlas-SNP	.											.	KCNC2	239	.	0			c.G387T						.						31.0	35.0	34.0					12																	75601377		2202	4299	6501	SO:0001819	synonymous_variant	3747	exon2			CCCGCACACGTCT	AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.387G>T	chr12.hg19:g.75601377C>A		435.0	1.0		526.0	229.0	NM_139137	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Silent	SNP	ENST00000549446.1	hg19	CCDS9007.1																																																																																			.	.		0.682	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748	
MED13L	23389	hgsc.bcm.edu	37	12	116675396	116675396	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr12:116675396A>T	ENST00000281928.3	-	2	393	c.187T>A	c.(187-189)Tgt>Agt	p.C63S	MED13L_ENST00000551197.1_5'UTR	NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	63						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		GCTTGCAGACAGCGGATGAAA	0.473																																					p.C63S		Atlas-SNP	.											.	MED13L	193	.	0			c.T187A						.						176.0	157.0	164.0					12																	116675396		2203	4300	6503	SO:0001583	missense	23389	exon2			GCAGACAGCGGAT	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.187T>A	chr12.hg19:g.116675396A>T	ENSP00000281928:p.Cys63Ser	224.0	0.0		216.0	87.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	hg19	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.079561	0.76528	.	.	ENSG00000123066	ENST00000281928;ENST00000548743	T;T	0.80304	-1.36;-1.36	5.57	5.57	0.84162	Mediator complex, subunit Med13, N-terminal, metazoa/fungi (1);	0.000000	0.64402	D	0.000001	D	0.89815	0.6824	M	0.84683	2.71	0.54753	D	0.999985	P	0.37594	0.601	P	0.54965	0.765	D	0.90760	0.4664	10	0.72032	D	0.01	.	15.7209	0.77710	1.0:0.0:0.0:0.0	.	63	Q71F56	MD13L_HUMAN	S	63;53	ENSP00000281928:C63S;ENSP00000448553:C53S	ENSP00000281928:C63S	C	-	1	0	MED13L	115159779	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.279000	0.95777	2.123000	0.65237	0.459000	0.35465	TGT	.	.		0.473	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
UBC	7316	hgsc.bcm.edu	37	12	125397187	125397187	+	Silent	SNP	G	G	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr12:125397187G>A	ENST00000536769.1	-	1	2707	c.1131C>T	c.(1129-1131)ctC>ctT	p.L377L	UBC_ENST00000546120.1_Silent_p.L301L|MIR5188_ENST00000583467.1_RNA|UBC_ENST00000536661.1_5'Flank|UBC_ENST00000339647.5_Silent_p.L377L|UBC_ENST00000538617.1_Intron			P0CG48	UBC_HUMAN	ubiquitin C	377	Ubiquitin-like 5. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)			breast(3)|endometrium(4)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		TCCCACCTCTGAGACGGAGCA	0.522																																					p.L377L		Atlas-SNP	.											.	UBC	79	.	0			c.C1131T						.						226.0	213.0	217.0					12																	125397187		2203	4300	6503	SO:0001819	synonymous_variant	7316	exon2			ACCTCTGAGACGG		CCDS9260.1	12q24.3	2008-09-08			ENSG00000150991	ENSG00000150991			12468	protein-coding gene	gene with protein product	"""polyubiquitin-C"""	191340				1315303, 11872750	Standard	NM_021009		Approved		uc001ugs.4	P0CG48		ENST00000536769.1:c.1131C>T	chr12.hg19:g.125397187G>A		257.0	0.0		225.0	48.0	NM_021009	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000536769.1	hg19	CCDS9260.1																																																																																			.	.		0.522	UBC-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400177.1	NM_021009	
C15orf57	90416	hgsc.bcm.edu	37	15	40849416	40849416	+	Splice_Site	SNP	T	T	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr15:40849416T>A	ENST00000358005.3	-	3	673	c.400A>T	c.(400-402)Agc>Tgc	p.S134C	C15orf57_ENST00000416810.2_Splice_Site_p.S134C|C15orf57_ENST00000561011.1_Splice_Site_p.R134W|C15orf57_ENST00000558750.1_Splice_Site_p.S143C|C15orf57_ENST00000559911.1_Splice_Site_p.R134W|C15orf57_ENST00000560305.1_Splice_Site_p.S134C|C15orf57_ENST00000558113.1_Splice_Site_p.R134W|C15orf57_ENST00000558871.1_Missense_Mutation_p.R134W|RP11-111A22.1_ENST00000561460.1_RNA	NM_001080791.1|NM_052849.2	NP_001074260.1|NP_443081.1	Q9BV29	CO057_HUMAN	chromosome 15 open reading frame 57	134										endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	9						ATCGATTACCTCTCATCAGAA	0.428																																					p.S143C		Atlas-SNP	.											.	C15orf57	20	.	0			c.A427T						.						113.0	101.0	105.0					15																	40849416		2203	4300	6503	SO:0001630	splice_region_variant	90416	exon3			ATTACCTCTCATC	BC012189	CCDS10060.1, CCDS42022.1, CCDS73706.1	15q15.1	2008-05-30	2008-05-30	2008-05-30	ENSG00000128891	ENSG00000128891			28295	protein-coding gene	gene with protein product			"""coiled-coil domain containing 32"""	CCDC32		12477932	Standard	NM_001080791		Approved	MGC20481	uc001zma.1	Q9BV29	OTTHUMG00000129993	ENST00000358005.3:c.401+1A>T	chr15.hg19:g.40849416T>A		112.0	0.0		131.0	56.0	NM_001080791	A8KAL4|Q86TC4|Q8N788|Q8NAR7	Missense_Mutation	SNP	ENST00000358005.3	hg19	CCDS10060.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.936732	0.92458	.	.	ENSG00000128891	ENST00000358005;ENST00000416810	T	0.54866	0.55	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.70518	0.3233	M	0.62723	1.935	0.36270	D	0.855147	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.78119	-0.2328	10	0.72032	D	0.01	-14.7446	15.9681	0.79991	0.0:0.0:0.0:1.0	.	134;143	Q9BV29;Q9BV29-2	CO057_HUMAN;.	C	134;143	ENSP00000350695:S134C	ENSP00000350695:S134C	S	-	1	0	C15orf57	38636708	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	5.502000	0.66956	2.170000	0.68504	0.454000	0.30748	AGC	.	.		0.428	C15orf57-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252259.2	NM_052849	Missense_Mutation
GOLGA6A	342096	hgsc.bcm.edu	37	15	74364639	74364639	+	Missense_Mutation	SNP	G	G	C	rs200350318		TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr15:74364639G>C	ENST00000290438.3	-	14	1553	c.1513C>G	c.(1513-1515)Caa>Gaa	p.Q505E	RN7SL429P_ENST00000479090.2_RNA	NM_001038640.2	NP_001033729.2	Q9NYA3	GOG6A_HUMAN	golgin A6 family, member A	505						Golgi apparatus (GO:0005794)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|liver(1)|lung(6)|prostate(1)|urinary_tract(1)	16						TCCAGATGTTGTCCTCCATCT	0.632																																					p.Q505E		Atlas-SNP	.											GOLGA6A,NS,carcinoma,0,1	GOLGA6A	28	.	0			c.C1513G						.	C	GLU/GLN	13,2839		0,13,1413	43.0	76.0	64.0		1513	-1.8	0.0	15		64	41,5189		0,41,2574	no	missense	GOLGA6A	NM_001038640.2	29	0,54,3987	CC,CG,GG		0.7839,0.4558,0.6682	benign	505/694	74364639	54,8028	1426	2615	4041	SO:0001583	missense	342096	exon14			GATGTTGTCCTCC	AF263742	CCDS32290.1	15q24.1	2013-05-10	2010-02-12	2009-09-28	ENSG00000159289	ENSG00000159289			13567	protein-coding gene	gene with protein product		610288	"""golgi autoantigen, golgin subfamily a, member 6"", ""golgi autoantigen, golgin subfamily a, 6"", ""golgi autoantigen, golgin subfamily a, 6A"""	GOLGA6		11161787	Standard	NM_001038640		Approved	GLP	uc002axa.1	Q9NYA3	OTTHUMG00000173035	ENST00000290438.3:c.1513C>G	chr15.hg19:g.74364639G>C	ENSP00000290438:p.Gln505Glu	31.0	2.0		32.0	7.0	NM_001038640	A8K959|Q9NYA7	Missense_Mutation	SNP	ENST00000290438.3	hg19	CCDS32290.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.871708	0.00062	0.004558	0.007839	ENSG00000159289	ENST00000290438	T	0.17213	2.29	0.887	-1.77	0.07982	.	.	.	.	.	T	0.02193	0.0068	N	0.00677	-1.265	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22068	-1.0227	9	0.02654	T	1	.	5.0871	0.14689	0.1703:0.3999:0.4298:0.0	.	505	Q9NYA3	GOG6A_HUMAN	E	505	ENSP00000290438:Q505E	ENSP00000290438:Q505E	Q	-	1	0	GOLGA6A	72151692	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.799000	0.00762	-2.200000	0.00747	-2.001000	0.00444	CAA	.	G|0.999;C|0.001		0.632	GOLGA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421835.1	XM_292357	
FURIN	5045	hgsc.bcm.edu	37	15	91423324	91423324	+	Splice_Site	SNP	A	A	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr15:91423324A>T	ENST00000268171.3	+	13	1656	c.1377A>T	c.(1375-1377)aaA>aaT	p.K459N		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	459					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)			TCCTGCACAGAGACATCGGGA	0.692																																					p.K459N		Atlas-SNP	.											.	FURIN	85	.	0			c.A1377T						.						38.0	38.0	38.0					15																	91423324		2198	4298	6496	SO:0001630	splice_region_variant	5045	exon13			GCACAGAGACATC	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.1377-1A>T	chr15.hg19:g.91423324A>T		76.0	0.0		110.0	45.0	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Missense_Mutation	SNP	ENST00000268171.3	hg19	CCDS10364.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.27|14.27	2.484282|2.484282	0.44147|0.44147	.|.	.|.	ENSG00000140564|ENSG00000140564	ENST00000535252|ENST00000268171	.|T	.|0.62941	.|-0.01	4.65|4.65	2.76|2.76	0.32466|0.32466	.|Galactose-binding domain-like (1);	0.200094|0.200094	0.52532|0.52532	D|D	0.000066|0.000066	T|T	0.49745|0.49745	0.1575|0.1575	L|L	0.44542|0.44542	1.39|1.39	0.80722|0.80722	D|D	1|1	.|B	.|0.19817	.|0.039	.|B	.|0.18263	.|0.021	T|T	0.34875|0.34875	-0.9811|-0.9811	6|9	.|.	.|.	.|.	.|.	10.0037|10.0037	0.41944|0.41944	0.1667:0.0:0.8333:0.0|0.1667:0.0:0.8333:0.0	.|.	.|459	.|P09958	.|FURIN_HUMAN	M|N	58|459	.|ENSP00000268171:K459N	.|.	K|K	+|+	2|3	0|2	FURIN|FURIN	89224328|89224328	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.475000|0.475000	0.33008|0.33008	2.481000|2.481000	0.45215|0.45215	0.558000|0.558000	0.29135|0.29135	-0.425000|-0.425000	0.05940|0.05940	AAG|AAA	.	.		0.692	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569	Missense_Mutation
PRMT7	54496	hgsc.bcm.edu	37	16	68358647	68358647	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr16:68358647A>G	ENST00000339507.5	+	5	1024	c.194A>G	c.(193-195)aAg>aGg	p.K65R	PRMT7_ENST00000449359.3_Intron|PRMT7_ENST00000348497.4_Missense_Mutation_p.K65R|PRMT7_ENST00000564441.1_3'UTR|PRMT7_ENST00000441236.1_Intron			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	65	SAM-dependent MTase PRMT-type 1. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	[myelin basic protein]-arginine N-methyltransferase activity (GO:0016277)|histone binding (GO:0042393)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|urinary_tract(1)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		AGAGGACAGAAGGCCTTGGTT	0.517																																					p.K65R		Atlas-SNP	.											.	PRMT7	51	.	0			c.A194G						.						144.0	117.0	126.0					16																	68358647		2198	4300	6498	SO:0001583	missense	54496	exon5			GACAGAAGGCCTT	AK001502	CCDS10866.1, CCDS54033.1	16q22.1	2008-02-05			ENSG00000132600	ENSG00000132600		"""Protein arginine methyltransferases"""	25557	protein-coding gene	gene with protein product		610087				15044439	Standard	NM_001184824		Approved	FLJ10640, KIAA1933	uc002evy.2	Q9NVM4	OTTHUMG00000137556	ENST00000339507.5:c.194A>G	chr16.hg19:g.68358647A>G	ENSP00000343103:p.Lys65Arg	173.0	0.0		108.0	78.0	NM_019023	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Missense_Mutation	SNP	ENST00000339507.5	hg19	CCDS10866.1	.	.	.	.	.	.	.	.	.	.	A	12.34	1.908869	0.33721	.	.	ENSG00000132600	ENST00000348497;ENST00000339507	T;T	0.77229	-1.08;-1.04	5.46	4.3	0.51218	.	0.217571	0.47852	D	0.000212	T	0.58047	0.2095	N	0.11560	0.145	0.20403	N	0.999906	B;B	0.15141	0.009;0.012	B;B	0.20384	0.029;0.013	T	0.40021	-0.9585	10	0.16896	T	0.51	-32.3451	11.7641	0.51920	0.8432:0.1568:0.0:0.0	.	65;65	Q9NVM4;Q9NVM4-4	ANM7_HUMAN;.	R	65	ENSP00000345775:K65R;ENSP00000343103:K65R	ENSP00000343103:K65R	K	+	2	0	PRMT7	66916148	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	1.443000	0.35057	2.062000	0.61559	0.482000	0.46254	AAG	.	.		0.517	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023	
ATP2C2	9914	hgsc.bcm.edu	37	16	84476156	84476156	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr16:84476156C>T	ENST00000262429.4	+	15	1441	c.1352C>T	c.(1351-1353)gCc>gTc	p.A451V	ATP2C2_ENST00000416219.2_Missense_Mutation_p.A451V|ATP2C2_ENST00000420010.2_3'UTR	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	451					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						AGAAAGAACGCCGTGATGGGG	0.562																																					p.A451V		Atlas-SNP	.											.	ATP2C2	75	.	0			c.C1352T						.						163.0	168.0	166.0					16																	84476156		1882	4108	5990	SO:0001583	missense	9914	exon15			AGAACGCCGTGAT	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"""ATPases / P-type"""	29103	protein-coding gene	gene with protein product	"""secretory pathway calcium ATPase 2"""	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.1352C>T	chr16.hg19:g.84476156C>T	ENSP00000262429:p.Ala451Val	92.0	0.0		56.0	38.0	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Missense_Mutation	SNP	ENST00000262429.4	hg19	CCDS42207.1	.	.	.	.	.	.	.	.	.	.	C	8.505	0.865107	0.17250	.	.	ENSG00000064270	ENST00000416219;ENST00000262429;ENST00000420010	T;T	0.70631	-0.5;-0.5	4.92	4.92	0.64577	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.710792	0.13564	N	0.378527	T	0.46347	0.1388	N	0.01789	-0.72	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.09377	0.004;0.002;0.003;0.002	T	0.32666	-0.9898	10	0.34782	T	0.22	.	13.9502	0.64111	0.0:0.8354:0.1646:0.0	.	451;300;468;451	E7ES94;F8WAA5;O75185-2;O75185	.;.;.;AT2C2_HUMAN	V	451;451;300	ENSP00000397925:A451V;ENSP00000262429:A451V	ENSP00000262429:A451V	A	+	2	0	ATP2C2	83033657	0.002000	0.14202	0.007000	0.13788	0.268000	0.26511	1.748000	0.38308	2.436000	0.82500	0.491000	0.48974	GCC	.	.		0.562	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	
ZC3H18	124245	hgsc.bcm.edu	37	16	88688677	88688677	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr16:88688677G>T	ENST00000301011.5	+	9	1748	c.1548G>T	c.(1546-1548)aaG>aaT	p.K516N	ZC3H18_ENST00000452588.2_Missense_Mutation_p.K540N	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	516						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		ATGAGTGGAAGGACCCTTGGC	0.597																																					p.K516N	Ovarian(121;375 2276 20373 38669)	Atlas-SNP	.											.	ZC3H18	90	.	0			c.G1548T						.						56.0	58.0	57.0					16																	88688677		2198	4300	6498	SO:0001583	missense	124245	exon9			GTGGAAGGACCCT	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"""Zinc fingers, CCCH-type domain containing"""	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.1548G>T	chr16.hg19:g.88688677G>T	ENSP00000301011:p.Lys516Asn	210.0	1.0		131.0	108.0	NM_144604	Q96DG4|Q96MP7	Missense_Mutation	SNP	ENST00000301011.5	hg19	CCDS10967.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.123933	0.56613	.	.	ENSG00000158545	ENST00000301011;ENST00000289509;ENST00000452588	T;T	0.54279	0.58;0.58	5.83	3.88	0.44766	.	0.148768	0.64402	D	0.000013	T	0.41351	0.1155	L	0.45581	1.43	0.41213	D	0.986456	P;P	0.45474	0.859;0.859	B;B	0.39503	0.301;0.301	T	0.27706	-1.0066	10	0.14252	T	0.57	-41.2211	11.719	0.51670	0.1429:0.0:0.8571:0.0	.	540;516	E7ERS3;Q86VM9	.;ZCH18_HUMAN	N	516;484;540	ENSP00000301011:K516N;ENSP00000416951:K540N	ENSP00000289509:K484N	K	+	3	2	ZC3H18	87216178	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.147000	0.31602	1.480000	0.48289	0.655000	0.94253	AAG	.	.		0.597	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604	
TP53	7157	hgsc.bcm.edu	37	17	7578555	7578555	+	Splice_Site	SNP	C	C	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr17:7578555C>T	ENST00000269305.4	-	5	565		c.e5-1		TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000445888.2_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(39)|p.0?(8)|p.V73fs*9(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CAGGGGAGTACTGTAGGAAGA	0.552		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											.	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000545858,NS,carcinoma,0,58	TP53	33396	.	51	Unknown(39)|Whole gene deletion(8)|Deletion - Frameshift(3)|Insertion - In frame(1)	ovary(9)|pancreas(6)|bone(5)|upper_aerodigestive_tract(4)|liver(4)|lung(4)|breast(4)|large_intestine(3)|central_nervous_system(3)|oesophagus(3)|haematopoietic_and_lymphoid_tissue(2)|stomach(1)|endometrium(1)|urinary_tract(1)|autonomic_ganglia(1)	c.376-1G>A						.						42.0	42.0	42.0					17																	7578555		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGAGTACTGTAGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.376-1G>A	chr17.hg19:g.7578555C>T		72.0	0.0		45.0	36.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.431133	0.62844	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591	.	.	.	4.87	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4246	0.50003	0.0:0.9094:0.0:0.0906	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7519280	1.000000	0.71417	0.999000	0.59377	0.918000	0.54935	7.639000	0.83342	1.359000	0.45940	0.655000	0.94253	.	.	.		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron
SREBF1	6720	hgsc.bcm.edu	37	17	17719813	17719813	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr17:17719813C>T	ENST00000261646.5	-	10	2189	c.2005G>A	c.(2005-2007)Gca>Aca	p.A669T	SREBF1_ENST00000583732.1_5'Flank|SREBF1_ENST00000355815.4_Missense_Mutation_p.A699T|MIR33B_ENST00000385104.1_RNA|SREBF1_ENST00000395757.1_Missense_Mutation_p.A415T|SREBF1_ENST00000338854.5_Missense_Mutation_p.A669T	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	669					aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|negative regulation of insulin secretion (GO:0046676)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of fatty acid metabolic process (GO:0019217)|regulation of heart rate by chemical signal (GO:0003062)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucagon (GO:0033762)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sterol response element binding (GO:0032810)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	14						ACCAGGGCTGCGTCTCGGGCG	0.697																																					p.A699T		Atlas-SNP	.											.	SREBF1	47	.	0			c.G2095A						.						11.0	11.0	11.0					17																	17719813		2174	4272	6446	SO:0001583	missense	6720	exon11			GGGCTGCGTCTCG	BC057388	CCDS11189.1, CCDS32583.1	17p11.2	2013-05-21			ENSG00000072310	ENSG00000072310		"""Basic helix-loop-helix proteins"""	11289	protein-coding gene	gene with protein product		184756				8402897, 7759101	Standard	NM_001005291		Approved	SREBP1, bHLHd1, SREBP-1c	uc002grt.2	P36956	OTTHUMG00000059313	ENST00000261646.5:c.2005G>A	chr17.hg19:g.17719813C>T	ENSP00000261646:p.Ala669Thr	56.0	0.0		72.0	39.0	NM_001005291	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Missense_Mutation	SNP	ENST00000261646.5	hg19	CCDS11189.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.73|18.73	3.687461|3.687461	0.68157|0.68157	.|.	.|.	ENSG00000072310|ENSG00000072310	ENST00000338854;ENST00000355815;ENST00000261646;ENST00000395757;ENST00000395756;ENST00000418712;ENST00000423161|ENST00000395751	T;T;T;T|.	0.12984|.	2.63;2.63;2.63;2.63|.	5.4|5.4	3.35|3.35	0.38373|0.38373	.|.	0.060400|.	0.64402|.	D|.	0.000004|.	T|T	0.69079|0.69079	0.3071|0.3071	L|L	0.61036|0.61036	1.89|1.89	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.988;0.995;0.999|.	T|T	0.66775|0.66775	-0.5838|-0.5838	10|5	0.51188|.	T|.	0.08|.	-18.258|-18.258	14.2833|14.2833	0.66228|0.66228	0.2707:0.7293:0.0:0.0|0.2707:0.7293:0.0:0.0	.|.	669;699;288|.	P36956;P36956-4;A8MTU8|.	SRBP1_HUMAN;.;.|.	T|H	669;699;669;415;288;506;595|676	ENSP00000345822:A669T;ENSP00000348069:A699T;ENSP00000261646:A669T;ENSP00000379106:A415T|.	ENSP00000261646:A669T|.	A|R	-|-	1|2	0|0	SREBF1|SREBF1	17660538|17660538	1.000000|1.000000	0.71417|0.71417	0.008000|0.008000	0.14137|0.14137	0.161000|0.161000	0.22273|0.22273	5.975000|5.975000	0.70475|0.70475	0.609000|0.609000	0.30018|0.30018	0.561000|0.561000	0.74099|0.74099	GCA|CGC	.	.		0.697	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176	
RAB34	83871	hgsc.bcm.edu	37	17	27044336	27044336	+	5'UTR	SNP	C	C	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr17:27044336C>T	ENST00000395245.3	-	0	575				RPL23A_ENST00000422514.2_5'Flank|RAB34_ENST00000395243.3_5'UTR|RAB34_ENST00000415040.2_5'UTR|RAB34_ENST00000450529.1_Intron|RAB34_ENST00000301043.6_5'UTR|RAB34_ENST00000453384.3_Intron|RAB34_ENST00000447716.1_Intron|RAB34_ENST00000395242.2_5'UTR|RPL23A_ENST00000394938.4_5'Flank|RPL23A_ENST00000496182.1_5'Flank|RAB34_ENST00000436730.3_Intron	NM_001256281.1|NM_031934.5	NP_001243210.1|NP_114140.4	Q9BZG1	RAB34_HUMAN	RAB34, member RAS oncogene family						antigen processing and presentation (GO:0019882)|Golgi to plasma membrane protein transport (GO:0043001)|lysosome localization (GO:0032418)|phagosome maturation (GO:0090382)|phagosome-lysosome fusion (GO:0090385)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|vesicle (GO:0031982)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|skin(2)	14	Lung NSC(42;0.00431)					GCCGGATCCGCGTCAGCGACC	0.726																																					p.A131T	Pancreas(175;216 2049 29940 32498 41589)	Atlas-SNP	.											.	.	.	.	0			c.G391A						.						4.0	7.0	6.0					17																	27044336		1237	2196	3433	SO:0001623	5_prime_UTR_variant	0	exon1			GATCCGCGTCAGC	AF322067	CCDS11240.1, CCDS45636.1, CCDS54101.1, CCDS58536.1	17q11.2	2008-07-18			ENSG00000109113	ENSG00000109113		"""RAB, member RAS oncogene"""	16519	protein-coding gene	gene with protein product		610917				12446704	Standard	NM_031934		Approved	RAB39, RAH	uc010was.1	P0DI83	OTTHUMG00000132680	ENST00000395245.3:c.-52G>A	chr17.hg19:g.27044336C>T		52.0	0.0		79.0	46.0	NM_001256281	B4E3A0|E9PEJ9|Q5BJE6|Q8NCJ8|Q96AR4	Missense_Mutation	SNP	ENST00000395245.3	hg19	CCDS11240.1																																																																																			.	.		0.726	RAB34-018	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345906.1	NM_031934	
ATAD5	79915	hgsc.bcm.edu	37	17	29219640	29219640	+	Missense_Mutation	SNP	A	A	T	rs77256126	byFrequency	TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr17:29219640A>T	ENST00000321990.4	+	20	4652	c.4274A>T	c.(4273-4275)aAt>aTt	p.N1425I		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1425					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				AATAGCAGAAATGTACAACTA	0.313																																					p.N1425I		Atlas-SNP	.											.	ATAD5	150	.	0			c.A4274T						.						79.0	80.0	80.0					17																	29219640		2203	4300	6503	SO:0001583	missense	79915	exon20			GCAGAAATGTACA		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.4274A>T	chr17.hg19:g.29219640A>T	ENSP00000313171:p.Asn1425Ile	245.0	0.0		296.0	126.0	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	hg19	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.558722	0.86231	.	.	ENSG00000176208	ENST00000321990	T	0.17054	2.3	4.84	4.84	0.62591	.	1.035660	0.07725	U	0.944257	T	0.40145	0.1105	M	0.64997	1.995	0.36743	D	0.882342	D	0.69078	0.997	D	0.65773	0.938	T	0.10268	-1.0637	10	0.72032	D	0.01	.	12.1036	0.53798	1.0:0.0:0.0:0.0	.	1425	Q96QE3	ATAD5_HUMAN	I	1425	ENSP00000313171:N1425I	ENSP00000313171:N1425I	N	+	2	0	ATAD5	26243766	0.107000	0.21998	0.686000	0.30086	0.776000	0.43924	1.855000	0.39378	1.939000	0.56221	0.260000	0.18958	AAT	.	.		0.313	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
TBX2	6909	hgsc.bcm.edu	37	17	59485703	59485703	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr17:59485703C>G	ENST00000240328.3	+	7	2256	c.1975C>G	c.(1975-1977)Ctg>Gtg	p.L659V	RP11-332H18.4_ENST00000592009.1_RNA	NM_005994.3	NP_005985.3	Q13207	TBX2_HUMAN	T-box 2	659					aorta morphogenesis (GO:0035909)|atrioventricular canal development (GO:0036302)|cardiac muscle tissue development (GO:0048738)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|developmental growth involved in morphogenesis (GO:0060560)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|endocardial cushion morphogenesis (GO:0003203)|mammary placode formation (GO:0060596)|muscle cell fate determination (GO:0007521)|negative regulation of cardiac chamber formation (GO:1901211)|negative regulation of heart looping (GO:1901208)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|palate development (GO:0060021)|pharynx development (GO:0060465)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(7)|ovary(1)	9						GCCTAGCCCCCTGCCCGAGCT	0.687																																					p.L659V	GBM(3;187 253 11467 14965 23079)	Atlas-SNP	.											.	TBX2	30	.	0			c.C1975G						.						12.0	10.0	11.0					17																	59485703		2190	4280	6470	SO:0001583	missense	6909	exon7			AGCCCCCTGCCCG	AB209378	CCDS11627.2	17q23.2	2012-01-23			ENSG00000121068	ENSG00000121068		"""T-boxes"""	11597	protein-coding gene	gene with protein product		600747				8530034	Standard	NM_005994		Approved		uc010wox.2	Q13207	OTTHUMG00000156986	ENST00000240328.3:c.1975C>G	chr17.hg19:g.59485703C>G	ENSP00000240328:p.Leu659Val	123.0	0.0		171.0	60.0	NM_005994	Q16424|Q7Z647	Missense_Mutation	SNP	ENST00000240328.3	hg19	CCDS11627.2	.	.	.	.	.	.	.	.	.	.	C	1.958	-0.439654	0.04636	.	.	ENSG00000121068	ENST00000240328	D	0.85556	-2.0	4.99	4.99	0.66335	.	1.082090	0.07085	N	0.837652	T	0.70272	0.3205	N	0.08118	0	0.37207	D	0.904656	B	0.12013	0.005	B	0.08055	0.003	T	0.54735	-0.8249	10	0.02654	T	1	.	12.144	0.54014	0.1713:0.8287:0.0:0.0	.	659	Q13207	TBX2_HUMAN	V	659	ENSP00000240328:L659V	ENSP00000240328:L659V	L	+	1	2	TBX2	56840485	0.974000	0.33945	0.960000	0.40013	0.811000	0.45836	2.241000	0.43097	2.610000	0.88304	0.561000	0.74099	CTG	.	.		0.687	TBX2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346977.2	NM_005994	
ABHD3	171586	hgsc.bcm.edu	37	18	19263881	19263881	+	Splice_Site	SNP	C	C	T	rs562863991		TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr18:19263881C>T	ENST00000289119.2	-	4	694	c.555G>A	c.(553-555)ttG>ttA	p.L185L	RP11-13N13.6_ENST00000578583.1_RNA|ABHD3_ENST00000579875.1_Intron|ABHD3_ENST00000580981.1_Intron|ABHD3_ENST00000578270.1_5'UTR|MIR320C1_ENST00000408566.1_RNA	NM_138340.4	NP_612213.2	Q8WU67	ABHD3_HUMAN	abhydrolase domain containing 3	185						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(2)	10						ATTTACTTACCAAGAGATTCT	0.284													C|||	1	0.000199681	0.0	0.0	5008	,	,		10951	0.001		0.0	False		,,,				2504	0.0				p.L185L		Atlas-SNP	.											.	ABHD3	32	.	0			c.G555A						.						58.0	64.0	62.0					18																	19263881		2203	4295	6498	SO:0001630	splice_region_variant	171586	exon4			ACTTACCAAGAGA	AK024880	CCDS32802.1	18q11.1	2011-02-16			ENSG00000158201	ENSG00000158201		"""Abhydrolase domain containing"""	18718	protein-coding gene	gene with protein product		612197					Standard	NM_138340		Approved	LABH3	uc002ktl.2	Q8WU67		ENST00000289119.2:c.555+1G>A	chr18.hg19:g.19263881C>T		443.0	1.0		430.0	161.0	NM_138340	B0YIV0|B7Z5C2|O43411	Silent	SNP	ENST00000289119.2	hg19	CCDS32802.1																																																																																			.	.		0.284	ABHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444757.1		Silent
SLC39A6	25800	hgsc.bcm.edu	37	18	33703524	33703524	+	Silent	SNP	C	C	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr18:33703524C>A	ENST00000590986.1	-	4	1363	c.1074G>T	c.(1072-1074)ctG>ctT	p.L358L	SLC39A6_ENST00000269187.5_Silent_p.L358L|SLC39A6_ENST00000440549.2_Silent_p.L83L			Q13433	S39A6_HUMAN	solute carrier family 39 (zinc transporter), member 6	358					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|lamellipodium membrane (GO:0031258)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	41						CAAGGAAACTCAGGAGAAATT	0.428																																					p.L358L		Atlas-SNP	.											.	SLC39A6	81	.	0			c.G1074T						.						185.0	185.0	185.0					18																	33703524		1873	4114	5987	SO:0001819	synonymous_variant	25800	exon4			GAAACTCAGGAGA	U41060	CCDS42428.1, CCDS45854.1	18q12.2	2013-05-22				ENSG00000141424		"""Solute carriers"""	18607	protein-coding gene	gene with protein product		608731	"""solute carrier family 39 (metal ion transporter), member 6"""			12659941, 12839489	Standard	NM_012319		Approved	LIV-1	uc010dmy.3	Q13433		ENST00000590986.1:c.1074G>T	chr18.hg19:g.33703524C>A		148.0	0.0		208.0	106.0	NM_012319	B4DR49|B4E224|Q8IXR3|Q96HP5	Silent	SNP	ENST00000590986.1	hg19	CCDS42428.1																																																																																			.	.		0.428	SLC39A6-004	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000444136.1		
ZSWIM4	65249	hgsc.bcm.edu	37	19	13919681	13919681	+	Silent	SNP	C	C	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr19:13919681C>A	ENST00000254323.2	+	4	933	c.744C>A	c.(742-744)atC>atA	p.I248I	ZSWIM4_ENST00000440752.2_5'UTR	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	248							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			GCGCAGGAATCGAGGACGCCA	0.662																																					p.I248I		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.C744A						.						18.0	19.0	19.0					19																	13919681		2193	4295	6488	SO:0001819	synonymous_variant	65249	exon4			AGGAATCGAGGAC	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"""Zinc fingers, SWIM-type"""	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.744C>A	chr19.hg19:g.13919681C>A		136.0	0.0		145.0	65.0	NM_023072		Silent	SNP	ENST00000254323.2	hg19	CCDS32924.1																																																																																			.	.		0.662	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342	
MAP1S	55201	hgsc.bcm.edu	37	19	17837678	17837678	+	Silent	SNP	C	C	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr19:17837678C>T	ENST00000324096.4	+	5	1636	c.1485C>T	c.(1483-1485)ggC>ggT	p.G495G	CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000597681.1_Intron|MAP1S_ENST00000544059.2_Silent_p.G469G	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	495	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CTAGACCTGGCCAGGAGCGCC	0.682																																					p.G495G		Atlas-SNP	.											.	MAP1S	74	.	0			c.C1485T						.						3.0	4.0	4.0					19																	17837678		1936	3852	5788	SO:0001819	synonymous_variant	55201	exon5			ACCTGGCCAGGAG	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"""chromosome 19 open reading frame 5"", ""VCY2 interacting protein 1"", ""BPY2 interacting protein 1"""	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.1485C>T	chr19.hg19:g.17837678C>T		110.0	0.0		150.0	69.0	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Silent	SNP	ENST00000324096.4	hg19	CCDS32954.1																																																																																			.	.		0.682	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174	
KMT2B	9757	hgsc.bcm.edu	37	19	36214101	36214101	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr19:36214101A>G	ENST00000222270.7	+	6	2927	c.2927A>G	c.(2926-2928)cAg>cGg	p.Q976R	KMT2B_ENST00000420124.1_Missense_Mutation_p.Q976R|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	976					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CTACGTGTGCAGGACTGTGGG	0.617																																					p.Q976R		Atlas-SNP	.											.	MLL4	229	.	0			c.A2927G						.						46.0	53.0	51.0					19																	36214101		2148	4251	6399	SO:0001583	missense	8085	exon6			GTGTGCAGGACTG	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.2927A>G	chr19.hg19:g.36214101A>G	ENSP00000222270:p.Gln976Arg	64.0	0.0		71.0	29.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	A	11.93	1.786108	0.31593	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.83250	-1.7;-1.7	5.3	5.3	0.74995	Zinc finger, CXXC-type (2);	0.000000	0.42548	D	0.000690	T	0.82047	0.4952	N	0.19112	0.55	0.33580	D	0.599713	D	0.59357	0.985	P	0.57468	0.821	D	0.87656	0.2531	10	0.66056	D	0.02	.	14.3572	0.66745	1.0:0.0:0.0:0.0	.	976	Q9UMN6	MLL4_HUMAN	R	976	ENSP00000222270:Q976R;ENSP00000398837:Q976R	ENSP00000222270:Q976R	Q	+	2	0	AD000671.1	40905941	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.873000	0.75541	2.225000	0.72522	0.533000	0.62120	CAG	.	.		0.617	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
ZNF813	126017	hgsc.bcm.edu	37	19	53994274	53994274	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr19:53994274G>T	ENST00000396403.4	+	4	916	c.788G>T	c.(787-789)aGa>aTa	p.R263I	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	263					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		TGCCATCGTAGATGTCACACT	0.413																																					p.R263I		Atlas-SNP	.											.	ZNF813	81	.	0			c.G788T						.						76.0	78.0	78.0					19																	53994274		2201	4298	6499	SO:0001583	missense	126017	exon4			ATCGTAGATGTCA	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.788G>T	chr19.hg19:g.53994274G>T	ENSP00000379684:p.Arg263Ile	143.0	0.0		181.0	80.0	NM_001004301		Missense_Mutation	SNP	ENST00000396403.4	hg19	CCDS46172.1	.	.	.	.	.	.	.	.	.	.	g	12.28	1.890420	0.33348	.	.	ENSG00000198346	ENST00000396403	T	0.02446	4.29	1.15	1.15	0.20763	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11067	0.0270	M	0.74467	2.265	0.19575	N	0.999967	D	0.76494	0.999	D	0.66084	0.941	T	0.08371	-1.0725	9	0.51188	T	0.08	.	8.7303	0.34494	0.0:0.0:1.0:0.0	.	263	Q6ZN06	ZN813_HUMAN	I	263	ENSP00000379684:R263I	ENSP00000379684:R263I	R	+	2	0	ZNF813	58686086	0.000000	0.05858	0.080000	0.20451	0.109000	0.19521	-3.818000	0.00358	0.194000	0.20326	0.197000	0.17608	AGA	.	.		0.413	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
SLC12A5	57468	hgsc.bcm.edu	37	20	44669254	44669254	+	Splice_Site	SNP	G	G	C	rs142641765		TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr20:44669254G>C	ENST00000454036.2	+	7	972		c.e7+1		SLC12A5_ENST00000372315.1_Silent_p.P285P|SLC12A5_ENST00000243964.3_Splice_Site	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5						cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	CCAACTTCCCGTGAGTGCTGC	0.567																																					.		Atlas-SNP	.											SLC12A5,NS,lymphoid_neoplasm,0,1	SLC12A5	181	.	0			c.923+1G>C						.						183.0	151.0	162.0					20																	44669254		2203	4300	6503	SO:0001630	splice_region_variant	57468	exon7			CTTCCCGTGAGTG	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"""Solute carriers"""	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.923+1G>C	chr20.hg19:g.44669254G>C		52.0	0.0		76.0	31.0	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Splice_Site	SNP	ENST00000454036.2	hg19	CCDS46610.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.573137	0.86542	.	.	ENSG00000124140	ENST00000454036;ENST00000243964	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.3986	0.87453	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC12A5	44102661	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.657000	0.98554	2.572000	0.86782	0.655000	0.94253	.	.	G|1.000;A|0.000		0.567	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		Intron
NHP2L1	4809	hgsc.bcm.edu	37	22	42071125	42071125	+	Silent	SNP	G	G	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr22:42071125G>A	ENST00000401959.1	-	4	515	c.199C>T	c.(199-201)Ctg>Ttg	p.L67L	NHP2L1_ENST00000355257.3_Silent_p.L67L|NHP2L1_ENST00000215956.5_Silent_p.L67L|NHP2L1_ENST00000402458.1_Silent_p.L71L|NHP2L1_ENST00000463675.1_5'UTR	NM_005008.3	NP_004999.1	P55769	NH2L1_HUMAN	NHP2 non-histone chromosome protein 2-like 1 (S. cerevisiae)	67					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ribosome biogenesis (GO:0042254)|RNA splicing (GO:0008380)	box C/D snoRNP complex (GO:0031428)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|lung(1)|prostate(1)	4						GGCAGGTGCAGAATGATCTCC	0.582																																					p.L67L		Atlas-SNP	.											.	NHP2L1	13	.	0			c.C199T						.						64.0	62.0	62.0					22																	42071125		2203	4300	6503	SO:0001819	synonymous_variant	4809	exon3			GGTGCAGAATGAT		CCDS14022.1, CCDS33653.1	22q13	2009-01-06	2001-11-28		ENSG00000100138	ENSG00000100138			7819	protein-coding gene	gene with protein product	"""small nuclear ribonucleoprotein 15.5kDa (U4/U6.U5)"""	601304	"""non-histone chromosome protein 2 (S. cerevisiae)-like 1"", ""sperm specific antigen 1"""	SSFA1		8978773	Standard	NM_005008		Approved	SNU13, FA-1, SPAG12, SNRNP15-5, 15.5K	uc003bav.3	P55769	OTTHUMG00000151189	ENST00000401959.1:c.199C>T	chr22.hg19:g.42071125G>A		69.0	0.0		108.0	69.0	NM_001003796		Silent	SNP	ENST00000401959.1	hg19	CCDS14022.1																																																																																			.	.		0.582	NHP2L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321682.1	NM_001003796	
TLR8	51311	hgsc.bcm.edu	37	X	12939763	12939763	+	Silent	SNP	A	A	G			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chrX:12939763A>G	ENST00000218032.6	+	2	2691	c.2604A>G	c.(2602-2604)aaA>aaG	p.K868K	TLR8_ENST00000311912.5_Silent_p.K886K	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	868					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CTAAGGTAAAAGGCTACAGGT	0.408																																					p.K868K		Atlas-SNP	.											.	TLR8	134	.	0			c.A2604G						.						152.0	144.0	146.0					X																	12939763		2203	4300	6503	SO:0001819	synonymous_variant	51311	exon2			GGTAAAAGGCTAC	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.2604A>G	chrX.hg19:g.12939763A>G		65.0	0.0		98.0	5.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Silent	SNP	ENST00000218032.6	hg19	CCDS14152.1																																																																																			.	.		0.408	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
IQSEC2	23096	hgsc.bcm.edu	37	X	53263732	53263732	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chrX:53263732G>A	ENST00000375368.5	-	14	4306	c.4106C>T	c.(4105-4107)cCa>cTa	p.P1369L	IQSEC2_ENST00000396435.3_Missense_Mutation_p.P1379L|IQSEC2_ENST00000375365.2_3'UTR			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	1369	Pro-rich.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						TTTGTGGGCTGGAGGGTGCTG	0.677																																					p.P1379L		Atlas-SNP	.											.	IQSEC2	195	.	0			c.C4136T						.						8.0	7.0	8.0					X																	53263732		687	1576	2263	SO:0001583	missense	23096	exon15			TGGGCTGGAGGGT	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"""mental retardation, X-linked 1 (non-dysmorphic)"""	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.4106C>T	chrX.hg19:g.53263732G>A	ENSP00000364517:p.Pro1369Leu	70.0	0.0		65.0	52.0	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	hg19		.	.	.	.	.	.	.	.	.	.	g	15.13	2.741957	0.49151	.	.	ENSG00000124313	ENST00000396435;ENST00000375368	T;T	0.11063	2.81;2.81	2.69	2.69	0.31865	.	0.701726	0.11901	U	0.518576	T	0.06234	0.0161	N	0.08118	0	0.46356	D	0.999009	B	0.14012	0.009	B	0.16289	0.015	T	0.27673	-1.0067	10	0.42905	T	0.14	.	10.6206	0.45478	0.0:0.0:1.0:0.0	.	1379	Q5JU85-2	.	L	1379;1369	ENSP00000379712:P1379L;ENSP00000364517:P1369L	ENSP00000364517:P1369L	P	-	2	0	IQSEC2	53280457	0.874000	0.30092	1.000000	0.80357	0.906000	0.53458	1.273000	0.33121	1.619000	0.50296	0.411000	0.27672	CCA	.	.		0.677	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345	
P2RY10	27334	hgsc.bcm.edu	37	X	78216621	78216621	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chrX:78216621G>T	ENST00000171757.2	+	4	884	c.604G>T	c.(604-606)Gct>Tct	p.A202S	P2RY10_ENST00000544091.1_Missense_Mutation_p.A202S	NM_014499.2	NP_055314.1	O00398	P2Y10_HUMAN	purinergic receptor P2Y, G-protein coupled, 10	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(22)|ovary(3)|skin(2)	42						GATTACAGTTGCTGAGCTTGC	0.453																																					p.A202S		Atlas-SNP	.											.	P2RY10	99	.	0			c.G604T						.						177.0	130.0	146.0					X																	78216621		2203	4300	6503	SO:0001583	missense	27334	exon2			ACAGTTGCTGAGC	AF000545	CCDS14442.1	Xq21.1	2012-08-23			ENSG00000078589	ENSG00000078589		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	19906	protein-coding gene	gene with protein product		300529				11004484, 9755289	Standard	NM_014499		Approved	P2Y10	uc004edf.3	O00398	OTTHUMG00000021896	ENST00000171757.2:c.604G>T	chrX.hg19:g.78216621G>T	ENSP00000171757:p.Ala202Ser	50.0	0.0		69.0	60.0	NM_198333	D3DTE5|Q4VBN7|Q86V16	Missense_Mutation	SNP	ENST00000171757.2	hg19	CCDS14442.1	.	.	.	.	.	.	.	.	.	.	G	17.37	3.371981	0.61624	.	.	ENSG00000078589	ENST00000544091;ENST00000171757	T;T	0.69806	-0.43;-0.43	4.82	4.82	0.62117	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.71467	0.3343	L	0.45352	1.415	0.45607	D	0.998542	P	0.50943	0.94	P	0.62014	0.897	T	0.65401	-0.6177	10	0.11182	T	0.66	.	15.5411	0.76048	0.0:0.0:1.0:0.0	.	202	O00398	P2Y10_HUMAN	S	202	ENSP00000443138:A202S;ENSP00000171757:A202S	ENSP00000171757:A202S	A	+	1	0	P2RY10	78103277	0.994000	0.37717	0.998000	0.56505	0.988000	0.76386	3.523000	0.53488	2.231000	0.72958	0.540000	0.68198	GCT	.	.		0.453	P2RY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057323.1		
GPR112	139378	hgsc.bcm.edu	37	X	135428111	135428111	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chrX:135428111C>A	ENST00000394143.1	+	6	2537	c.2246C>A	c.(2245-2247)aCc>aAc	p.T749N	GPR112_ENST00000394141.1_Missense_Mutation_p.T544N|GPR112_ENST00000370652.1_Missense_Mutation_p.T749N|GPR112_ENST00000287534.4_Missense_Mutation_p.T686N|GPR112_ENST00000412101.1_Missense_Mutation_p.T544N	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	749					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					ACATCCATAACCAATATGCCT	0.378																																					p.T749N		Atlas-SNP	.											.	GPR112	459	.	0			c.C2246A						.						78.0	64.0	69.0					X																	135428111		2203	4300	6503	SO:0001583	missense	139378	exon6			CCATAACCAATAT	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.2246C>A	chrX.hg19:g.135428111C>A	ENSP00000377699:p.Thr749Asn	234.0	0.0		252.0	231.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	hg19	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	c	11.55	1.673419	0.29693	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.33865	1.43;1.43;1.39;1.52;1.39	2.86	0.923	0.19413	.	.	.	.	.	T	0.30603	0.0770	L	0.27053	0.805	0.09310	N	1	B;B;D	0.64830	0.087;0.045;0.994	B;B;P	0.53266	0.047;0.015;0.722	T	0.12941	-1.0528	9	0.62326	D	0.03	.	2.4185	0.04442	0.3023:0.5201:0.0:0.1776	.	686;544;749	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	N	749;749;544;686;544	ENSP00000377699:T749N;ENSP00000359686:T749N;ENSP00000416526:T544N;ENSP00000287534:T686N;ENSP00000377697:T544N	ENSP00000287534:T686N	T	+	2	0	GPR112	135255777	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	0.638000	0.24674	0.362000	0.24319	0.279000	0.19357	ACC	.	.		0.378	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
SLITRK2	84631	hgsc.bcm.edu	37	X	144905309	144905309	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chrX:144905309T>A	ENST00000370490.1	+	1	5621	c.1366T>A	c.(1366-1368)Tat>Aat	p.Y456N	SLITRK2_ENST00000413937.2_Missense_Mutation_p.Y456N|SLITRK2_ENST00000434188.2_Missense_Mutation_p.Y456N|SLITRK2_ENST00000447897.2_Missense_Mutation_p.Y456N|SLITRK2_ENST00000428560.2_Missense_Mutation_p.Y456N			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	456					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					CTATTTAGAGTATAATGTCAT	0.388																																					p.Y456N		Atlas-SNP	.											.	SLITRK2	221	.	0			c.T1366A						.						133.0	140.0	138.0					X																	144905309		2203	4300	6503	SO:0001583	missense	84631	exon5			TTAGAGTATAATG	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"""slit-like 1 (Drosophila)"""	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.1366T>A	chrX.hg19:g.144905309T>A	ENSP00000359521:p.Tyr456Asn	80.0	0.0		95.0	84.0	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	hg19	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.618482	0.46736	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.55930	0.49;0.49;0.49;0.49;0.49;0.49	5.69	4.52	0.55395	.	0.000000	0.85682	D	0.000000	T	0.35682	0.0940	N	0.02721	-0.515	0.52501	D	0.999957	P	0.45827	0.867	P	0.51701	0.677	T	0.18116	-1.0347	10	0.23302	T	0.38	-6.5822	8.8304	0.35080	0.0:0.0897:0.0:0.9103	.	456	Q9H156	SLIK2_HUMAN	N	456	ENSP00000334374:Y456N;ENSP00000411681:Y456N;ENSP00000359521:Y456N;ENSP00000397015:Y456N;ENSP00000407347:Y456N;ENSP00000412010:Y456N	ENSP00000334374:Y456N	Y	+	1	0	SLITRK2	144713001	1.000000	0.71417	0.998000	0.56505	0.502000	0.33828	8.040000	0.89188	0.770000	0.33336	-0.314000	0.08810	TAT	.	.		0.388	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539	
COL22A1	169044	hgsc.bcm.edu	37	8	139824123	139824124	+	Frame_Shift_Ins	INS	-	-	G	rs377477852	byFrequency	TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr8:139824123_139824124insG	ENST00000303045.6	-	9	1813_1814	c.1367_1368insC	c.(1366-1368)ccafs	p.P456fs	COL22A1_ENST00000435777.1_Frame_Shift_Ins_p.P456fs	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	456	Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GCCGCTGGGGTGGGGGTGGAGG	0.604										HNSCC(7;0.00092)																											p.P456fs		Atlas-INDEL	.											.	COL22A1	390	.	0			c.1368_1369insC						.																																			SO:0001589	frameshift_variant	169044	exon9			.	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.1368dupC	chr8.hg19:g.139824128_139824128dupG	ENSP00000303153:p.Pro456fs	114.0	0.0		211.0	13.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Frame_Shift_Ins	INS	ENST00000303045.6	hg19	CCDS6376.1																																																																																			.	.		0.604	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
PLCH1	23007	hgsc.bcm.edu	37	3	155311807	155311807	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chr3:155311807delC	ENST00000340059.7	-	3	356	c.357delG	c.(355-357)tggfs	p.W119fs	PLCH1_ENST00000460012.1_Frame_Shift_Del_p.W101fs|PLCH1_ENST00000447496.2_Frame_Shift_Del_p.W119fs|PLCH1_ENST00000414191.1_Frame_Shift_Del_p.W101fs|PLCH1_ENST00000334686.6_Frame_Shift_Del_p.W101fs|PLCH1_ENST00000494598.1_Frame_Shift_Del_p.W119fs	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	119	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			GGCCTGTGATCCAGGTGCGGG	0.542																																					p.I120fs		Atlas-INDEL	.											.	PLCH1	406	.	0			c.358delA						.						80.0	75.0	77.0					3																	155311807		2203	4300	6503	SO:0001589	frameshift_variant	23007	exon3			.	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.357delG	chr3.hg19:g.155311807delC	ENSP00000345988:p.Trp119fs	104.0	0.0		138.0	63.0	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Frame_Shift_Del	DEL	ENST00000340059.7	hg19	CCDS46939.1																																																																																			.	.		0.542	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996	
AWAT2	158835	hgsc.bcm.edu	37	X	69264286	69264286	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-AAED-01A-12D-A40R-10	TCGA-DD-AAED-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4c060df4-2a85-49c8-ac6e-3f11f3513b51	bf60ba6e-38fa-4254-b22a-31bf89f3a555	g.chrX:69264286delA	ENST00000276101.3	-	2	117	c.112delT	c.(112-114)tacfs	p.Y38fs		NM_001002254.1	NP_001002254.1	Q6E213	AWAT2_HUMAN	acyl-CoA wax alcohol acyltransferase 2	38					wax biosynthetic process (GO:0010025)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	long-chain-alcohol O-fatty-acyltransferase activity (GO:0047196)|retinol O-fatty-acyltransferase activity (GO:0050252)			endometrium(3)|large_intestine(3)|lung(2)|ovary(1)	9						ACCACCAGGTAGAGGTTGACA	0.522																																					p.Y38fs	NSCLC(80;1334 1436 9350 24214 26427)	Atlas-INDEL	.											.	AWAT2	36	.	0			c.113delA						.						126.0	93.0	104.0					X																	69264286		2203	4300	6503	SO:0001589	frameshift_variant	158835	exon2			.	BC063698	CCDS35320.1	Xq13.1	2009-02-23	2009-02-23	2009-02-23	ENSG00000147160	ENSG00000147160			23251	protein-coding gene	gene with protein product	"""multifunctional O-acyltransferase"""	300925	"""diacylglycerol O-acyltransferase 2-like 4"""	DGAT2L4		14970677, 16106050, 15671038	Standard	NM_001002254		Approved	MFAT	uc004dxt.1	Q6E213	OTTHUMG00000021763	ENST00000276101.3:c.112delT	chrX.hg19:g.69264286delA	ENSP00000421172:p.Tyr38fs	221.0	0.0		256.0	211.0	NM_001002254	Q6IEE3|Q6P437	Frame_Shift_Del	DEL	ENST00000276101.3	hg19	CCDS35320.1																																																																																			.	.		0.522	AWAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358738.1	NM_001002254	
