#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_ACHILLES_Lineage_Results_Top_Genes	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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_ORegAnno_bin	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_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_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ATP7B	540	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	52539025	52539025	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr13:52539025T>C	ENST00000242839.4	-	5	2008	c.1852A>G	c.(1852-1854)Att>Gtt	p.I618V	ATP7B_ENST00000542656.1_Intron|ATP7B_ENST00000448424.2_Missense_Mutation_p.I618V|ATP7B_ENST00000400370.3_Intron|ATP7B_ENST00000418097.2_Missense_Mutation_p.I618V|ATP7B_ENST00000400366.3_Missense_Mutation_p.I507V|ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000344297.5_Missense_Mutation_p.I618V|ATP7B_ENST00000417240.2_5'Flank	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	618	HMA 6. {ECO:0000255|PROSITE- ProRule:PRU00280}.				cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)	p.I618V(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	ATTTTGATAATATCCCGTGGA	0.358									Wilson disease																																								1	Substitution - Missense(1)	kidney(1)											75.0	74.0	74.0					13																	52539025		1865	4096	5961	SO:0001583	missense	540	Familial Cancer Database		U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"""ATPases / P-type"""	870	protein-coding gene	gene with protein product	"""Wilson disease"", ""copper pump 2"", ""copper-transporting ATPase 2"""	606882	"""ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"""	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.1852A>G	13.37:g.52539025T>C	ENSP00000242839:p.Ile618Val		Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	37	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	T	15.11	2.736564	0.49045	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000344297;ENST00000448424;ENST00000418097	D;D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42;-2.42	5.95	4.77	0.60923	Heavy metal-associated domain, HMA (3);Heavy metal-associated domain, copper ion-binding (1);	0.132624	0.64402	N	0.000003	D	0.93187	0.7830	M	0.70275	2.135	0.80722	D	1	P;P;B;P;D;B	0.63046	0.76;0.947;0.361;0.785;0.992;0.217	P;P;B;P;D;B	0.78314	0.621;0.755;0.219;0.723;0.991;0.326	D	0.92850	0.6296	10	0.56958	D	0.05	-15.8759	12.0589	0.53550	0.0:0.067:0.0:0.933	.	618;618;618;507;618;618	E7ET55;B7ZLR4;F5H748;P35670-3;P35670-2;P35670	.;.;.;.;.;ATP7B_HUMAN	V	618;507;618;618;618	ENSP00000242839:I618V;ENSP00000383217:I507V;ENSP00000342559:I618V;ENSP00000416738:I618V;ENSP00000393343:I618V	ENSP00000242839:I618V	I	-	1	0	ATP7B	51437026	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.508000	0.45450	1.075000	0.40932	0.533000	0.62120	ATT		0.358	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1		NM_000053	
CLK2	1196	hgsc.bcm.edu;ucsc.edu	37	1	155240724	155240729	+	In_Frame_Del	DEL	CCGGCT	CCGGCT	-			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	CCGGCT	CCGGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr1:155240724_155240729delCCGGCT	ENST00000368361.4	-	2	355_360	c.40_45delAGCCGG	c.(40-45)agccggdel	p.SR14del	CLK2_ENST00000361168.5_In_Frame_Del_p.SR14del|CLK2_ENST00000536801.1_In_Frame_Del_p.SR14del|CLK2_ENST00000355560.4_In_Frame_Del_p.SR14del|CLK2_ENST00000497188.1_5'Flank			P49760	CLK2_HUMAN	CDC-like kinase 2	14					negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.R15L(1)		endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GGTAACTCCCCCGGCTGCCTCGCTCT	0.558								Other conserved DNA damage response genes																																									1	Substitution - Missense(1)	lung(1)																																								SO:0001651	inframe_deletion	1196			L29218	CCDS1107.1, CCDS72939.1	1q21	2008-05-02			ENSG00000176444	ENSG00000176444		"""CDC-like kinases"""	2069	protein-coding gene	gene with protein product		602989				7990150, 9856501	Standard	XM_005244876		Approved	clk2	uc001fjw.3	P49760	OTTHUMG00000035873	ENST00000368361.4:c.40_45delAGCCGG	1.37:g.155240724_155240729delCCGGCT	ENSP00000357345:p.Ser14_Arg15del		B1AVS9|B5MBX6|Q96CQ0	In_Frame_Del	DEL	ENST00000368361.4	37																																																																																					0.558	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1		NM_003993	
CSMD3	114788	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	113243821	113243821	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr8:113243821C>A	ENST00000297405.5	-	69	11025	c.10781G>T	c.(10780-10782)gGa>gTa	p.G3594V	CSMD3_ENST00000343508.3_Missense_Mutation_p.G3554V|CSMD3_ENST00000455883.2_Missense_Mutation_p.G3425V|CSMD3_ENST00000352409.3_Missense_Mutation_p.G3524V	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3594						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G3594V(2)|p.G3554V(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TTGAATAAATCCTTGAAATAC	0.348										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																							3	Substitution - Missense(3)	kidney(2)|lung(1)											124.0	133.0	130.0					8																	113243821		2203	4300	6503	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.10781G>T	8.37:g.113243821C>A	ENSP00000297405:p.Gly3594Val		Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.823913	0.90873	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.34667	1.7;1.69;1.77;1.35;1.74	5.15	5.15	0.70609	.	0.000000	0.64402	D	0.000001	T	0.61627	0.2362	M	0.73217	2.22	0.80722	D	1	D;D;P	0.89917	1.0;1.0;0.911	D;D;P	0.80764	0.994;0.987;0.646	T	0.63825	-0.6549	10	0.87932	D	0	.	19.1714	0.93580	0.0:1.0:0.0:0.0	.	3425;3594;3554	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	V	3554;3594;2864;3425;3524	ENSP00000345799:G3554V;ENSP00000297405:G3594V;ENSP00000341558:G2864V;ENSP00000412263:G3425V;ENSP00000343124:G3524V	ENSP00000297405:G3594V	G	-	2	0	CSMD3	113312997	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.494000	0.81503	2.843000	0.97960	0.585000	0.79938	GGA		0.348	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1		NM_052900	
DEFB123	245936	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	30037860	30037860	+	Nonsense_Mutation	SNP	T	T	A	rs377702716		TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr20:30037860T>A	ENST00000376309.3	+	2	267	c.87T>A	c.(85-87)taT>taA	p.Y29*		NM_153324.2	NP_697019.1	Q8N688	DB123_HUMAN	defensin, beta 123	29					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)		p.Y29*(1)|p.Y29Y(1)		kidney(1)|lung(2)	3	Lung NSC(7;0.000139)|all_lung(7;0.000197)|all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			GGAATCTTTATGGCAAATGCC	0.428																																																	2	Substitution - Nonsense(1)|Substitution - coding silent(1)	lung(1)|kidney(1)											152.0	150.0	151.0					20																	30037860		2203	4300	6503	SO:0001587	stop_gained	245936			AA933749	CCDS13180.1	20q11.1	2008-07-17			ENSG00000180424	ENSG00000180424		"""Defensins, beta"""	18103	protein-coding gene	gene with protein product	"""beta defensin 23"""					11854508	Standard	NM_153324		Approved	DEFB-23	uc002wvy.3	Q8N688	OTTHUMG00000032170	ENST00000376309.3:c.87T>A	20.37:g.30037860T>A	ENSP00000365486:p.Tyr29*			Nonsense_Mutation	SNP	ENST00000376309.3	37	CCDS13180.1	.	.	.	.	.	.	.	.	.	.	T	13.82	2.350383	0.41599	.	.	ENSG00000180424	ENST00000376309	.	.	.	4.52	-1.97	0.07503	.	0.652135	0.13716	N	0.367726	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	-0.3934	3.1092	0.06352	0.3405:0.3221:0.0:0.3374	.	.	.	.	X	29	.	ENSP00000365486:Y29X	Y	+	3	2	DEFB123	29501521	0.082000	0.21442	0.589000	0.28718	0.395000	0.30598	-0.744000	0.04839	-0.368000	0.08040	0.533000	0.62120	TAT		0.428	DEFB123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078510.2		NM_153324	
GBP6	163351	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	89847441	89847441	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr1:89847441G>A	ENST00000370456.4	+	7	1153	c.1060G>A	c.(1060-1062)Gac>Aac	p.D354N	GBP6_ENST00000535065.1_Missense_Mutation_p.D224N	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	354					cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.D354N(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		GGAGCTGCTGGACATGCATGC	0.547																																																	1	Substitution - Missense(1)	kidney(1)											81.0	73.0	76.0					1																	89847441		2203	4300	6503	SO:0001583	missense	163351			BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.1060G>A	1.37:g.89847441G>A	ENSP00000359485:p.Asp354Asn		A2RRM3|Q6ZN86|Q7Z3F0	Missense_Mutation	SNP	ENST00000370456.4	37	CCDS723.1	.	.	.	.	.	.	.	.	.	.	G	9.319	1.057609	0.19907	.	.	ENSG00000183347	ENST00000544311;ENST00000370456;ENST00000535065	T;T	0.56776	0.44;0.44	4.75	2.43	0.29744	Guanylate-binding protein, C-terminal (3);	0.638563	0.15479	N	0.260217	T	0.17152	0.0412	L	0.31526	0.94	0.28781	N	0.899852	B	0.15473	0.013	B	0.20384	0.029	T	0.09618	-1.0666	10	0.42905	T	0.14	-2.3061	3.5711	0.07917	0.1056:0.1668:0.5568:0.1708	.	354	Q6ZN66	GBP6_HUMAN	N	325;354;224	ENSP00000359485:D354N;ENSP00000442530:D224N	ENSP00000359485:D354N	D	+	1	0	GBP6	89620029	0.935000	0.31712	0.818000	0.32626	0.145000	0.21501	1.156000	0.31712	0.964000	0.38108	-0.291000	0.09656	GAC		0.547	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1		NM_198460	
GOLGB1	2804	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	121415221	121415221	+	Silent	SNP	T	T	C	rs202178297		TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr3:121415221T>C	ENST00000340645.5	-	13	4259	c.4134A>G	c.(4132-4134)caA>caG	p.Q1378Q	GOLGB1_ENST00000393667.3_Silent_p.Q1383Q	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1378					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.Q1378Q(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CAATTTGTAGTTGGCTGCTTT	0.403													T|||	1	0.000199681	0.0	0.0	5008	,	,		20445	0.001		0.0	False		,,,				2504	0.0																1	Substitution - coding silent(1)	kidney(1)											158.0	164.0	162.0					3																	121415221		2203	4299	6502	SO:0001819	synonymous_variant	2804			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.4134A>G	3.37:g.121415221T>C			B2ZZ91|D3DN92|E7EP74|Q14398	Silent	SNP	ENST00000340645.5	37	CCDS3004.1																																																																																				0.403	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1		NM_004487	
GRID2	2895	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	94376877	94376877	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr4:94376877C>T	ENST00000282020.4	+	11	1868	c.1610C>T	c.(1609-1611)aCg>aTg	p.T537M	GRID2_ENST00000510992.1_Missense_Mutation_p.T442M	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	537					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)	p.T537M(2)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		GTGGACTTTACGACACGTTAC	0.433																																																	2	Substitution - Missense(2)	prostate(1)|kidney(1)											145.0	132.0	136.0					4																	94376877		2203	4300	6503	SO:0001583	missense	2895			AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.1610C>T	4.37:g.94376877C>T	ENSP00000282020:p.Thr537Met		E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	37	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.944581	0.92593	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.16457	2.34;2.34	5.97	5.97	0.96955	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.55561	0.1928	M	0.93062	3.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.64334	-0.6432	10	0.87932	D	0	.	20.4388	0.99107	0.0:1.0:0.0:0.0	.	442;537	E9PH24;O43424	.;GRID2_HUMAN	M	537;442	ENSP00000282020:T537M;ENSP00000421257:T442M	ENSP00000282020:T537M	T	+	2	0	GRID2	94595900	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	4.947000	0.63583	2.836000	0.97738	0.655000	0.94253	ACG		0.433	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			
IFNA8	3445	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	21409486	21409486	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr9:21409486T>A	ENST00000380205.1	+	1	341	c.311T>A	c.(310-312)cTt>cAt	p.L104H		NM_002170.3	NP_002161.2	P32881	IFNA8_HUMAN	interferon, alpha 8	104					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)	p.L104H(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	9				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0174)		GATGAGACCCTTCTAGATGAA	0.502																																																	1	Substitution - Missense(1)	kidney(1)											102.0	97.0	98.0					9																	21409486		2203	4300	6503	SO:0001583	missense	3445				CCDS6507.1	9p22	2010-08-24			ENSG00000120242	ENSG00000120242		"""Interferons"""	5429	protein-coding gene	gene with protein product	"""interferon alpha-B''"", ""interferon alpha type 201"""	147568				1385305	Standard	NM_002170		Approved	IFN-alphaB	uc003zpc.1	P32881	OTTHUMG00000019677	ENST00000380205.1:c.311T>A	9.37:g.21409486T>A	ENSP00000369553:p.Leu104His		P01565|P09236|Q5VWV7|Q5VYQ3	Missense_Mutation	SNP	ENST00000380205.1	37	CCDS6507.1	.	.	.	.	.	.	.	.	.	.	T	13.47	2.245875	0.39697	.	.	ENSG00000120242	ENST00000380205	T	0.05139	3.49	3.48	2.21	0.28008	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.757438	0.11887	N	0.519989	T	0.19485	0.0468	M	0.77712	2.385	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.14643	-1.0465	10	0.87932	D	0	.	2.544	0.04732	0.2325:0.1293:0.0:0.6382	.	104	P32881	IFNA8_HUMAN	H	104	ENSP00000369553:L104H	ENSP00000369553:L104H	L	+	2	0	IFNA8	21399486	0.000000	0.05858	0.030000	0.17652	0.009000	0.06853	-0.130000	0.10498	1.593000	0.50029	0.402000	0.26972	CTT		0.502	IFNA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051906.1		NM_002170	
INPPL1	3636	hgsc.bcm.edu;ucsc.edu	37	11	71939276	71939278	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr11:71939276_71939278delAGA	ENST00000298229.2	+	2	429_431	c.225_227delAGA	c.(223-228)ggagaa>gga	p.E76del	INPPL1_ENST00000538751.1_5'UTR|INPPL1_ENST00000541756.1_5'UTR	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	76	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						TGCCTGATGGAGAAGATTTCTTG	0.586																																																	0																																										SO:0001651	inframe_deletion	3636			Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"""Sterile alpha motif (SAM) domain containing"", ""SH2 domain containing"""	6080	protein-coding gene	gene with protein product	"""51C protein"""	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.225_227delAGA	11.37:g.71939279_71939281delAGA	ENSP00000298229:p.Glu76del		B2RTX5|Q13577|Q13578	In_Frame_Del	DEL	ENST00000298229.2	37	CCDS8213.1																																																																																				0.586	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1		NM_001567	
ITGB3	3690	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	45377874	45377874	+	Silent	SNP	G	G	C			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr17:45377874G>C	ENST00000559488.1	+	12	1960	c.1944G>C	c.(1942-1944)cgG>cgC	p.R648R	RP11-290H9.4_ENST00000575039.1_RNA|ITGB3_ENST00000435993.2_Silent_p.R601R|RP11-290H9.4_ENST00000576345.1_RNA|ITGB3_ENST00000560629.1_Missense_Mutation_p.G637R	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	648					activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)	p.R601R(1)|p.R648R(1)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	AGTTTGACCGGGGAGCCCTAC	0.483																																																	2	Substitution - coding silent(2)	kidney(2)											142.0	117.0	126.0					17																	45377874		2203	4300	6503	SO:0001819	synonymous_variant	3690				CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"""CD molecules"", ""Integrins"""	6156	protein-coding gene	gene with protein product	"""platelet glycoprotein IIIa"""	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.1944G>C	17.37:g.45377874G>C			A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Silent	SNP	ENST00000559488.1	37	CCDS11511.1																																																																																				0.483	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3		NM_000212	
JAK1	3716	hgsc.bcm.edu;ucsc.edu	37	1	65310524	65310524	+	Frame_Shift_Del	DEL	G	G	-			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr1:65310524delG	ENST00000342505.4	-	16	2412	c.2164delC	c.(2164-2166)ctgfs	p.L722fs	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	722	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TCACGGGCCAGGAGGAGGTTT	0.527			Mis		ALL																																			Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	0													96.0	109.0	105.0					1																	65310524		2064	4199	6263	SO:0001589	frameshift_variant	3716			M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2164delC	1.37:g.65310524delG	ENSP00000343204:p.Leu722fs		Q59GQ2|Q9UD26	Frame_Shift_Del	DEL	ENST00000342505.4	37	CCDS41346.1																																																																																				0.527	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1		NM_002227	
MED12	9968	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	70342188	70342188	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chrX:70342188A>G	ENST00000374080.3	+	8	1272	c.1240A>G	c.(1240-1242)Act>Gct	p.T414A	MED12_ENST00000333646.6_Missense_Mutation_p.T414A|MED12_ENST00000374102.1_Missense_Mutation_p.T414A			Q93074	MED12_HUMAN	mediator complex subunit 12	414					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.T414A(2)		breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					CAGTGCCTTCACTCAGCAGGT	0.483			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																																	Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	2	Substitution - Missense(2)	kidney(2)											111.0	98.0	102.0					X																	70342188		2018	4164	6182	SO:0001583	missense	9968			U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.1240A>G	X.37:g.70342188A>G	ENSP00000363193:p.Thr414Ala		O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	37	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	.	17.81	3.480955	0.63849	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.04	5.04	0.67666	Mediator complex, subunit Med12, LCEWAV-domain (1);	0.052768	0.85682	D	0.000000	T	0.36054	0.0953	L	0.38175	1.15	0.53688	D	0.999979	B;P;P;B	0.38280	0.336;0.625;0.532;0.387	B;B;P;P	0.48089	0.356;0.315;0.535;0.566	T	0.12293	-1.0553	10	0.44086	T	0.13	-11.8934	13.9873	0.64343	1.0:0.0:0.0:0.0	.	414;261;414;414	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	A	414;414;414;414;382	ENSP00000333125:T414A;ENSP00000363215:T414A;ENSP00000363193:T414A;ENSP00000414203:T382A	ENSP00000333125:T414A	T	+	1	0	MED12	70258913	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.497000	0.90488	1.877000	0.54381	0.478000	0.44815	ACT		0.483	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1		NM_005120	
NOC4L	79050	broad.mit.edu	37	12	132633361	132633361	+	Silent	SNP	G	G	T			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr12:132633361G>T	ENST00000330579.1	+	9	863	c.822G>T	c.(820-822)ctG>ctT	p.L274L	NOC4L_ENST00000535343.1_3'UTR|NOC4L_ENST00000538784.1_5'Flank	NM_024078.1	NP_076983.1	Q9BVI4	NOC4L_HUMAN	nucleolar complex associated 4 homolog (S. cerevisiae)	274					rRNA processing (GO:0006364)	integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.L274L(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|skin(2)	14	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.2e-08)|Epithelial(86;3.34e-07)|all cancers(50;1.97e-05)		AGGTGCTGCTGATTGTGCATG	0.726																																																	1	Substitution - coding silent(1)	kidney(1)											26.0	22.0	23.0					12																	132633361		2189	4292	6481	SO:0001819	synonymous_variant	79050				CCDS9277.1	12q24.33	2011-08-12			ENSG00000184967	ENSG00000184967			28461	protein-coding gene	gene with protein product		612819				12446671	Standard	NM_024078		Approved	MGC3162, NET49, UTP19	uc001ujz.1	Q9BVI4	OTTHUMG00000168260	ENST00000330579.1:c.822G>T	12.37:g.132633361G>T			Q8N2S5|Q96I14	Silent	SNP	ENST00000330579.1	37	CCDS9277.1																																																																																				0.726	NOC4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398999.1		NM_024078	
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52712580	52712580	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr3:52712580G>A	ENST00000296302.7	-	2	173	c.172C>T	c.(172-174)Cga>Tga	p.R58*	PBRM1_ENST00000337303.4_Nonsense_Mutation_p.R58*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.R58*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.R58*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.R58*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.R58*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.R58*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.R58*			Q86U86	PB1_HUMAN	polybromo 1	58					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R58*(7)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTATAGTCTCGGATGGTATTA	0.433			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	7	Substitution - Nonsense(7)	kidney(6)|large_intestine(1)											130.0	118.0	122.0					3																	52712580		2203	4300	6503	SO:0001587	stop_gained	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.172C>T	3.37:g.52712580G>A	ENSP00000296302:p.Arg58*		A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	G	36	5.705422	0.96812	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103;ENST00000431678;ENST00000420148;ENST00000449505;ENST00000450271	.	.	.	5.2	3.17	0.36434	.	0.056365	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	2.9834	8.9802	0.35961	0.0:0.1109:0.6405:0.2486	.	.	.	.	X	58;58;58;58;58;58;58;58;58;2;58;58;58;58	.	ENSP00000296302:R58X	R	-	1	2	PBRM1	52687620	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	3.452000	0.52971	1.160000	0.42584	0.460000	0.39030	CGA		0.433	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PI4KA	5297	broad.mit.edu;hgsc.bcm.edu	37	22	21104191	21104191	+	Splice_Site	SNP	A	A	G			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr22:21104191A>G	ENST00000572273.1	-	28	3300		c.e28+1		PI4KA_ENST00000255882.6_Splice_Site			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha						phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.?(2)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			GGTTTCAAGTACCTGCAGGTG	0.483																																					GBM(136;1332 1831 3115 23601 50806)												2	Unknown(2)	kidney(2)											98.0	84.0	88.0					22																	21104191		2203	4300	6503	SO:0001630	splice_region_variant	5297			L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.3069+1T>C	22.37:g.21104191A>G			Q7Z625|Q9UPG2	Splice_Site	SNP	ENST00000572273.1	37		.	.	.	.	.	.	.	.	.	.	A	22.9	4.344991	0.82022	.	.	ENSG00000241973	ENST00000255882	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8319	0.70153	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PI4KA	19434191	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	9.134000	0.94467	2.102000	0.63906	0.533000	0.62120	.		0.483	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_058004	Intron
PKD1L1	168507	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	47897277	47897277	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr7:47897277G>C	ENST00000289672.2	-	28	4566	c.4516C>G	c.(4516-4518)Cag>Gag	p.Q1506E		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1506	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.Q1506E(1)	BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CATGGGCTCTGTGTCTCCGCC	0.547																																																	1	Substitution - Missense(1)	kidney(1)											81.0	80.0	81.0					7																	47897277		2203	4300	6503	SO:0001583	missense	168507			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.4516C>G	7.37:g.47897277G>C	ENSP00000289672:p.Gln1506Glu		Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	G	10.81	1.455045	0.26161	.	.	ENSG00000158683	ENST00000289672	T	0.18174	2.23	5.1	3.22	0.36961	Egg jelly receptor, REJ-like (1);	0.783877	0.11412	N	0.566676	T	0.16854	0.0405	L	0.60455	1.87	0.09310	N	1	D	0.54207	0.965	B	0.43950	0.437	T	0.16988	-1.0384	10	0.32370	T	0.25	-12.4309	3.1998	0.06646	0.0955:0.1769:0.5447:0.1828	.	1506	Q8TDX9	PK1L1_HUMAN	E	1506	ENSP00000289672:Q1506E	ENSP00000289672:Q1506E	Q	-	1	0	PKD1L1	47863802	0.001000	0.12720	0.005000	0.12908	0.041000	0.13682	0.699000	0.25586	1.084000	0.41184	0.563000	0.77884	CAG		0.547	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1		NM_138295	
PPARGC1A	10891	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	23833232	23833232	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr4:23833232G>T	ENST00000264867.2	-	3	496	c.377C>A	c.(376-378)tCc>tAc	p.S126Y	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	126					androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|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 stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.S126Y(1)		central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				AGGCATGGAGGAAGGACTAGC	0.542																																					Esophageal Squamous(29;694 744 13796 34866 44181)												1	Substitution - Missense(1)	kidney(1)											339.0	268.0	292.0					4																	23833232		2203	4300	6503	SO:0001583	missense	10891			AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"""RNA binding motif (RRM) containing"""	9237	protein-coding gene	gene with protein product		604517	"""peroxisome proliferative activated receptor, gamma, coactivator 1"", ""peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"""	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.377C>A	4.37:g.23833232G>T	ENSP00000264867:p.Ser126Tyr		B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Missense_Mutation	SNP	ENST00000264867.2	37	CCDS3429.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.986703	0.93106	.	.	ENSG00000109819	ENST00000264867	T	0.24908	1.83	6.03	6.03	0.97812	.	0.048703	0.85682	D	0.000000	T	0.51075	0.1653	L	0.57536	1.79	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.40232	-0.9574	10	0.62326	D	0.03	-6.9495	20.5568	0.99304	0.0:0.0:1.0:0.0	.	126	Q9UBK2	PRGC1_HUMAN	Y	126	ENSP00000264867:S126Y	ENSP00000264867:S126Y	S	-	2	0	PPARGC1A	23442330	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.637000	0.83313	2.861000	0.98227	0.655000	0.94253	TCC		0.542	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1		NM_013261	
PPP2R2B	5521	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	146077636	146077636	+	Silent	SNP	G	G	A			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr5:146077636G>A	ENST00000394413.3	-	3	810	c.240C>T	c.(238-240)ttC>ttT	p.F80F	PPP2R2B_ENST00000530902.1_5'UTR|PPP2R2B_ENST00000453001.1_Silent_p.F80F|PPP2R2B_ENST00000394411.4_Silent_p.F80F|PPP2R2B_ENST00000356826.3_Silent_p.F80F|PPP2R2B_ENST00000394409.3_Silent_p.F138F|PPP2R2B_ENST00000508545.2_Silent_p.F69F|PPP2R2B_ENST00000504198.1_Silent_p.F86F|PPP2R2B_ENST00000394414.1_Silent_p.F146F|PPP2R2B_ENST00000336640.6_Silent_p.F83F|PPP2R2B_ENST00000394410.2_Silent_p.F69F			Q00005	2ABB_HUMAN	protein phosphatase 2, regulatory subunit B, beta	80					apoptotic process (GO:0006915)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)	p.F69F(1)|p.F80F(1)|p.F83F(1)|p.F138F(1)		endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(9)|ovary(1)|prostate(4)|skin(3)	32			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCAGGTAATCGAACTCGGGTT	0.383																																																	4	Substitution - coding silent(4)	kidney(4)											128.0	135.0	132.0					5																	146077636		2203	4300	6503	SO:0001819	synonymous_variant	5521			M64930	CCDS4283.1, CCDS4284.1, CCDS43380.1, CCDS4284.2, CCDS64282.1	5q32	2013-01-10	2010-04-14		ENSG00000156475	ENSG00000156475	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9305	protein-coding gene	gene with protein product	"""PP2A subunit B isoform beta"""	604325	"""spinocerebellar ataxia 12"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, beta isoform"""	SCA12		1849734, 10581021	Standard	NM_181674		Approved	PR55-BETA, PR52B	uc003log.5	Q00005	OTTHUMG00000163381	ENST00000394413.3:c.240C>T	5.37:g.146077636G>A			A6NEJ2|A8K102|B3KPD0|B7Z2F2|B7Z304|D3DQF7|D3DQF8|G3V149	Silent	SNP	ENST00000394413.3	37	CCDS4284.1																																																																																				0.383	PPP2R2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251893.2		NM_181678	
RIC8B	55188	hgsc.bcm.edu;ucsc.edu	37	12	107254049	107254053	+	Frame_Shift_Del	DEL	ATAGT	ATAGT	-			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	ATAGT	ATAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr12:107254049_107254053delATAGT	ENST00000392839.2	+	8	1416_1420	c.1310_1314delATAGT	c.(1309-1314)gatagtfs	p.DS437fs	RIC8B_ENST00000392837.4_Frame_Shift_Del_p.DS437fs|RIC8B_ENST00000549643.1_5'UTR|RIC8B_ENST00000355478.2_Frame_Shift_Del_p.DS397fs	NM_018157.2	NP_060627.2	Q9NVN3	RIC8B_HUMAN	RIC8 guanine nucleotide exchange factor B	437					regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	G-protein alpha-subunit binding (GO:0001965)|guanyl-nucleotide exchange factor activity (GO:0005085)			kidney(2)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	19						TTTGCAGTGGATAGTCTGCTGAAAT	0.473																																																	0																																										SO:0001589	frameshift_variant	55188			AK128102	CCDS9109.2	12q23.3	2013-08-05	2013-08-05		ENSG00000111785	ENSG00000111785			25555	protein-coding gene	gene with protein product		609147	"""resistance to inhibitors of cholinesterase 8 homolog B (C. elegans)"""				Standard	XM_005268998		Approved	FLJ10620, hSyn, RIC8	uc001tlx.3	Q9NVN3	OTTHUMG00000144188	ENST00000392839.2:c.1310_1314delATAGT	12.37:g.107254049_107254053delATAGT	ENSP00000376583:p.Asp437fs		A2RTZ0|Q4G103|Q6ZRN4|Q86WD3	Frame_Shift_Del	DEL	ENST00000392839.2	37	CCDS9109.2																																																																																				0.473	RIC8B-006	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000291398.2		NM_018157	
RPGRIP1	57096	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	21771589	21771589	+	Silent	SNP	C	C	T			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr14:21771589C>T	ENST00000400017.2	+	5	687	c.687C>T	c.(685-687)agC>agT	p.S229S	RPGRIP1_ENST00000206660.6_Silent_p.S229S|RPGRIP1_ENST00000556336.1_Silent_p.S202S|RPGRIP1_ENST00000557771.1_Silent_p.S202S	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	229					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)		p.S229S(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		TCATGGCCAGCAATACCATGC	0.443																																																	1	Substitution - coding silent(1)	kidney(1)											69.0	67.0	67.0					14																	21771589		1928	4152	6080	SO:0001819	synonymous_variant	57096			AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.687C>T	14.37:g.21771589C>T			Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Silent	SNP	ENST00000400017.2	37	CCDS45080.1																																																																																				0.443	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1		NM_020366	
RYR1	6261	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	38985140	38985140	+	Silent	SNP	G	G	A			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr19:38985140G>A	ENST00000359596.3	+	39	6423	c.6423G>A	c.(6421-6423)gcG>gcA	p.A2141A	RYR1_ENST00000355481.4_Silent_p.A2141A|RYR1_ENST00000360985.3_Silent_p.A2141A			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2141	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.A2141A(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TGCCGCGGGCGTACACCATCT	0.677																																																	1	Substitution - coding silent(1)	kidney(1)											58.0	53.0	55.0					19																	38985140		2203	4300	6503	SO:0001819	synonymous_variant	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.6423G>A	19.37:g.38985140G>A			Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																				0.677	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			
SHROOM4	57477	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	50376678	50376678	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chrX:50376678T>A	ENST00000289292.7	-	4	2678	c.2395A>T	c.(2395-2397)Act>Tct	p.T799S	SHROOM4_ENST00000376020.2_Missense_Mutation_p.T799S|SHROOM4_ENST00000460112.3_Missense_Mutation_p.T683S			Q9ULL8	SHRM4_HUMAN	shroom family member 4	799					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)	p.T799S(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					TGGGTAAAAGTCTTGTTGCTA	0.433																																																	1	Substitution - Missense(1)	kidney(1)											112.0	106.0	108.0					X																	50376678		2203	4300	6503	SO:0001583	missense	57477			AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.2395A>T	X.37:g.50376678T>A	ENSP00000289292:p.Thr799Ser		A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	37	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	T	10.50	1.367939	0.24771	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	D;D;D	0.87650	-2.28;-2.28;-2.28	5.92	0.712	0.18167	.	0.607699	0.16818	N	0.198262	T	0.71728	0.3374	N	0.24115	0.695	0.19575	N	0.999961	B	0.30406	0.278	B	0.25140	0.058	T	0.56685	-0.7938	10	0.10111	T	0.7	.	7.2264	0.26018	0.0:0.1641:0.4391:0.3968	.	799	Q9ULL8	SHRM4_HUMAN	S	799;799;683	ENSP00000289292:T799S;ENSP00000365188:T799S;ENSP00000421450:T683S	ENSP00000289292:T799S	T	-	1	0	SHROOM4	50393418	0.970000	0.33590	0.984000	0.44739	0.968000	0.65278	0.780000	0.26760	-0.001000	0.14495	-0.360000	0.07572	ACT		0.433	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4		NM_020717	
SPAST	6683	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	32323916	32323916	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr2:32323916A>G	ENST00000315285.3	+	4	763	c.638A>G	c.(637-639)aAt>aGt	p.N213S	SPAST_ENST00000345662.1_Intron	NM_014946.3	NP_055761.2			spastin									p.N213S(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GACGTCTATAATGACAGTACT	0.363																																																	1	Substitution - Missense(1)	kidney(1)											85.0	80.0	82.0					2																	32323916		2203	4300	6503	SO:0001583	missense	6683			AJ246001	CCDS1778.1, CCDS1779.1	2p24-p21	2014-09-17	2005-03-15	2005-03-17	ENSG00000021574	ENSG00000021574		"""ATPases / AAA-type"""	11233	protein-coding gene	gene with protein product		604277	"""spastic paraplegia 4 (autosomal dominant; spastin)"""	SPG4		10493830, 10610178	Standard	NM_014946		Approved	FSP2, ADPSP, KIAA1083	uc002roc.3	Q9UBP0	OTTHUMG00000128455	ENST00000315285.3:c.638A>G	2.37:g.32323916A>G	ENSP00000320885:p.Asn213Ser			Missense_Mutation	SNP	ENST00000315285.3	37	CCDS1778.1	.	.	.	.	.	.	.	.	.	.	A	7.988	0.752659	0.15778	.	.	ENSG00000021574	ENST00000315285	D	0.92752	-3.1	5.56	5.56	0.83823	.	0.916639	0.09575	N	0.783662	T	0.81245	0.4782	N	0.08118	0	0.37191	D	0.903957	B	0.02656	0.0	B	0.04013	0.001	T	0.72301	-0.4334	10	0.07813	T	0.8	-38.2973	7.992	0.30246	0.8454:0.0:0.1546:0.0	.	213	Q9UBP0	SPAST_HUMAN	S	213	ENSP00000320885:N213S	ENSP00000320885:N213S	N	+	2	0	SPAST	32177420	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	3.894000	0.56250	2.113000	0.64589	0.477000	0.44152	AAT		0.363	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1		NM_199436	
STAP2	55620	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	4325497	4325497	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr19:4325497G>T	ENST00000594605.1	-	10	998	c.875C>A	c.(874-876)tCt>tAt	p.S292Y	STAP2_ENST00000600324.1_Missense_Mutation_p.S292Y|STAP2_ENST00000597593.1_5'UTR	NM_001013841.1	NP_001013863.1	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	292	Pro-rich.					cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.S292Y(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		GTCCTGGCTAGACGCAGGTGA	0.587																																																	1	Substitution - Missense(1)	kidney(1)											87.0	93.0	91.0					19																	4325497		2203	4300	6503	SO:0001583	missense	55620			AJ245719	CCDS12128.1, CCDS45926.1	19p13.3	2011-05-03	2007-08-09		ENSG00000178078	ENSG00000178078			30430	protein-coding gene	gene with protein product		607881				10980601, 11441184	Standard	XM_005259592		Approved	STAP-2, BKS	uc002mac.3	Q9UGK3		ENST00000594605.1:c.875C>A	19.37:g.4325497G>T	ENSP00000471052:p.Ser292Tyr		A6NKK3|Q9NXI2	Missense_Mutation	SNP	ENST00000594605.1	37	CCDS45926.1	.	.	.	.	.	.	.	.	.	.	G	9.601	1.128731	0.21041	.	.	ENSG00000178078	ENST00000314714;ENST00000424810	.	.	.	3.02	3.02	0.34903	.	2.073350	0.02964	U	0.143494	T	0.43211	0.1237	L	0.36672	1.1	0.09310	N	1	D;P	0.54207	0.965;0.924	P;P	0.51135	0.563;0.66	T	0.41645	-0.9497	9	0.87932	D	0	-17.7188	9.8099	0.40817	0.0:0.0:1.0:0.0	.	292;292	Q9UGK3-2;Q9UGK3	.;STAP2_HUMAN	Y	292	.	ENSP00000317912:S292Y	S	-	2	0	STAP2	4276497	0.519000	0.26242	0.004000	0.12327	0.050000	0.14768	2.641000	0.46587	2.013000	0.59113	0.479000	0.44913	TCT		0.587	STAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458114.2		NM_001013841	
SYNE2	23224	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	64447732	64447732	+	Silent	SNP	G	G	A			TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr14:64447732G>A	ENST00000344113.4	+	16	1889	c.1677G>A	c.(1675-1677)caG>caA	p.Q559Q	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000358025.3_Silent_p.Q559Q|SYNE2_ENST00000554584.1_Silent_p.Q559Q	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	559					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.Q559Q(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TTAATAAACAGTATATGATGG	0.264																																																	1	Substitution - coding silent(1)	kidney(1)											81.0	85.0	84.0					14																	64447732		1788	4059	5847	SO:0001819	synonymous_variant	23224			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.1677G>A	14.37:g.64447732G>A			Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																				0.264	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2		NM_182914	
ZNF880	400713	hgsc.bcm.edu	37	19	52888050	52888050	+	Missense_Mutation	SNP	A	A	G	rs76053634	byFrequency	TCGA-BP-4987-01A-01D-1462-08	TCGA-BP-4987-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7924f8ff-8e78-4910-9dc5-db14d5ee7011	10d7ba85-b3b5-4a53-a686-70be8848a041	g.chr19:52888050A>G	ENST00000422689.2	+	4	1232	c.1217A>G	c.(1216-1218)cAa>cGa	p.Q406R		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	406					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						ACGGGAGAGCAACCTTACAAA	0.398																																																	0													70.0	64.0	66.0					19																	52888050		1568	3582	5150	SO:0001583	missense	400713			BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1217A>G	19.37:g.52888050A>G	ENSP00000406318:p.Gln406Arg		B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	A	4.567	0.105370	0.08731	.	.	ENSG00000221923	ENST00000422689	T	0.15718	2.4	1.84	1.84	0.25277	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04182	0.0116	N	0.00392	-1.555	0.19775	N	0.999952	B	0.17667	0.023	B	0.23150	0.044	T	0.43360	-0.9396	8	.	.	.	.	8.4442	0.32833	1.0:0.0:0.0:0.0	.	406	Q6PDB4	ZN880_HUMAN	R	406	ENSP00000406318:Q406R	.	Q	+	2	0	ZNF880	57579862	0.002000	0.14202	0.418000	0.26571	0.177000	0.22998	0.149000	0.16243	0.834000	0.34852	0.450000	0.29827	CAA		0.398	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1		NM_001145434	
