#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
ASTN2	23245	broad.mit.edu	37	9	119770423	119770423	+	Silent	SNP	G	G	A			TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr9:119770423G>A	ENST00000313400.4	-	7	1639	c.1539C>T	c.(1537-1539)ctC>ctT	p.L513L	ASTN2_ENST00000361209.2_Silent_p.L462L|ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Silent_p.L513L			O75129	ASTN2_HUMAN	astrotactin 2	513	EGF-like 1.				negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						TTTGTCCACAGAGGTCCCTCA	0.582																																						uc004bjt.2																			0				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						c.(1384-1386)ctC>ctT		Homo sapiens astrotactin 2 (ASTN2), transcript variant 1, mRNA.							97.0	88.0	91.0					9																	119770423		2203	4300	6503	SO:0001819	synonymous_variant	23245					integral to membrane		g.chr9:119770423G>A	AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.1539C>T	9.37:g.119770423G>A						ASTN2_uc022bml.1_Silent_p.L162L|ASTN2_uc022bmm.1_Silent_p.L162L	p.L462L	NM_014010	NP_054729	O75129	ASTN2_HUMAN			5	1487	-			513					A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Silent	SNP	ENST00000313400.4	37	c.1386C>T																																																																																					0.582	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		10	77	0	0	0	1	0	10	77				
PDZRN4	29951	broad.mit.edu	37	12	41966431	41966431	+	Missense_Mutation	SNP	T	T	C			TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr12:41966431T>C	ENST00000402685.2	+	10	1858	c.1850T>C	c.(1849-1851)aTt>aCt	p.I617T	PDZRN4_ENST00000539469.2_Missense_Mutation_p.I359T|PDZRN4_ENST00000298919.7_Missense_Mutation_p.I357T	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	617							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				TCAGACTGCATTGGCAACCCA	0.473																																						uc010skn.2																			0				breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77						c.(1849-1851)aTt>aCt		Homo sapiens PDZ domain containing ring finger 4 (PDZRN4), transcript variant 1, mRNA.							87.0	87.0	87.0					12																	41966431		2203	4300	6503	SO:0001583	missense	29951						ubiquitin-protein ligase activity|zinc ion binding	g.chr12:41966431T>C	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.1850T>C	12.37:g.41966431T>C	ENSP00000384197:p.Ile617Thr					PDZRN4_uc001rmq.4_Missense_Mutation_p.I359T|PDZRN4_uc009zjz.3_Missense_Mutation_p.I357T|PDZRN4_uc001rmr.3_Missense_Mutation_p.I244T	p.I617T	NM_001164595	NP_001158067	Q6ZMN7	PZRN4_HUMAN			9	1858	+	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)	617					Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Missense_Mutation	SNP	ENST00000402685.2	37	c.1850T>C	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	T	0.331	-0.955891	0.02267	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	T;T;T	0.71817	-0.6;3.85;3.84	4.08	-6.74	0.01743	.	1.547480	0.04225	N	0.334178	T	0.61837	0.2379	L	0.34521	1.04	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.002	T	0.50874	-0.8776	10	0.51188	T	0.08	2.7839	17.7752	0.88505	0.0:0.1025:0.0:0.8975	.	617;357;359	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	T	617;359;357	ENSP00000384197:I617T;ENSP00000439990:I359T;ENSP00000298919:I357T	ENSP00000298919:I357T	I	+	2	0	PDZRN4	40252698	0.000000	0.05858	0.001000	0.08648	0.539000	0.34962	-0.153000	0.10144	-1.548000	0.01712	-0.248000	0.11899	ATT		0.473	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		20	60	0	0	0	1	0	20	60				
CXXC4	80319	broad.mit.edu	37	4	105412390	105412390	+	Silent	SNP	C	C	T			TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr4:105412390C>T	ENST00000426831.1	-	1	77	c.63G>A	c.(61-63)ttG>ttA	p.L21L	CXXC4_ENST00000466963.1_Intron|AC004053.1_ENST00000500179.1_RNA|CXXC4_ENST00000394767.2_Silent_p.L190L|AC093628.1_ENST00000606234.1_RNA			Q9H2H0	CXXC4_HUMAN	CXXC finger protein 4	21					negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)|zygotic specification of dorsal/ventral axis (GO:0007352)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)	DNA binding (GO:0003677)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(123;3.05e-08)		TTGCCATTTGCAACGACGGCT	0.617																																						uc003hxg.3																			0				kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11						c.(61-63)ttG>ttA		Homo sapiens CXXC finger protein 4 (CXXC4), mRNA.							106.0	119.0	115.0					4																	105412390		2203	4300	6503	SO:0001819	synonymous_variant	80319				Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|zygotic specification of dorsal/ventral axis		DNA binding|PDZ domain binding|zinc ion binding	g.chr4:105412390C>T		CCDS3665.1, CCDS3665.2	4q22-q24	2014-02-18	2011-12-01		ENSG00000168772	ENSG00000168772			24593	protein-coding gene	gene with protein product	"""Dvl-binding protein IDAX (inhibition of the Dvl and Axin complex)"""	611645				11113207	Standard	NM_025212		Approved	IDAX	uc003hxf.2	Q9H2H0	OTTHUMG00000131121	ENST00000426831.1:c.63G>A	4.37:g.105412390C>T						AK094561_uc003hxh.1_Intron|CXXC4_uc010ilo.3_Intron	p.L21L	NM_025212	NP_079488	Q9H2H0	CXXC4_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;3.05e-08)	0	78	-			21						Silent	SNP	ENST00000426831.1	37	c.63G>A																																																																																					0.617	CXXC4-201	KNOWN	basic	protein_coding	protein_coding		NM_025212		16	306	0	0	0	1	0	16	306				
DLC1	10395	broad.mit.edu	37	8	12948874	12948874	+	Missense_Mutation	SNP	T	T	A			TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr8:12948874T>A	ENST00000276297.4	-	14	4217	c.3808A>T	c.(3808-3810)Act>Tct	p.T1270S	DLC1_ENST00000358919.2_Missense_Mutation_p.T833S|DLC1_ENST00000510318.1_5'UTR|DLC1_ENST00000520226.1_Missense_Mutation_p.T759S|DLC1_ENST00000512044.2_Missense_Mutation_p.T867S	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	1270	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						AGCCCTTGAGTGGCAGCTAGG	0.423																																						uc003wwm.2																			0				NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						c.(3808-3810)Act>Tct		Homo sapiens deleted in liver cancer 1 (DLC1), transcript variant 1, mRNA.							107.0	114.0	112.0					8																	12948874		2203	4300	6503	SO:0001583	missense	10395				actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of Rho protein signal transduction|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding	g.chr8:12948874T>A	AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.3808A>T	8.37:g.12948874T>A	ENSP00000276297:p.Thr1270Ser					DLC1_uc003wwk.1_Missense_Mutation_p.T833S|DLC1_uc003wwl.1_Missense_Mutation_p.T867S|DLC1_uc011kxx.1_Missense_Mutation_p.T759S	p.T1270S	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN			13	4252	-			1270			Rho-GAP.		B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	c.3808A>T	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.815265	0.90790	.	.	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000510318;ENST00000512044;ENST00000520226	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	4.66	4.66	0.58398	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.62159	0.2405	M	0.71581	2.175	0.80722	D	1	B;P;D	0.63046	0.277;0.897;0.992	B;P;D	0.71184	0.327;0.488;0.972	T	0.64812	-0.6319	10	0.51188	T	0.08	.	14.6308	0.68655	0.0:0.0:0.0:1.0	.	1270;867;833	Q96QB1;E9PDZ8;Q96QB1-1	RHG07_HUMAN;.;.	S	1270;833;209;867;759	ENSP00000276297:T1270S;ENSP00000351797:T833S;ENSP00000422595:T867S;ENSP00000428028:T759S	ENSP00000276297:T1270S	T	-	1	0	DLC1	12993245	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.131000	0.71670	2.113000	0.64589	0.529000	0.55759	ACT		0.423	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		30	81	0	0	0	1	0	30	81				
TOMM40	10452	broad.mit.edu	37	19	45397111	45397111	+	Silent	SNP	C	C	T	rs536598319		TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr19:45397111C>T	ENST00000426677.2	+	4	690	c.510C>T	c.(508-510)ccC>ccT	p.P170P	TOMM40_ENST00000405636.2_Silent_p.P170P|TOMM40_ENST00000592434.1_Silent_p.P170P|TOMM40_ENST00000252487.5_Silent_p.P170P|CTB-129P6.4_ENST00000585408.1_RNA	NM_001128917.1	NP_001122389.1	O96008	TOM40_HUMAN	translocase of outer mitochondrial membrane 40 homolog (yeast)	170					cellular protein metabolic process (GO:0044267)|ion transport (GO:0006811)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial outer membrane translocase complex (GO:0005742)|pore complex (GO:0046930)	porin activity (GO:0015288)|protein transmembrane transporter activity (GO:0008320)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(1)	5	Lung NSC(12;0.0018)|all_lung(12;0.00481)			OV - Ovarian serous cystadenocarcinoma(262;0.0033)|Epithelial(262;0.176)		AGCTGGGCCCCGGTCTCAGGT	0.647													C|||	1	0.000199681	0.0	0.0	5008	,	,		18936	0.001		0.0	False		,,,				2504	0.0					uc002paa.4																			0				breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(1)	5						c.(508-510)ccC>ccT		Homo sapiens translocase of outer mitochondrial membrane 40 homolog (yeast) (TOMM40), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.							56.0	49.0	51.0					19																	45397111		2203	4300	6503	SO:0001819	synonymous_variant	10452				protein targeting to mitochondrion	integral to membrane of membrane fraction|integral to mitochondrial outer membrane|mitochondrial outer membrane translocase complex|pore complex	porin activity|protein transmembrane transporter activity|voltage-gated anion channel activity	g.chr19:45397111C>T	AF043250	CCDS12646.1	19q13	2008-07-04				ENSG00000130204			18001	protein-coding gene	gene with protein product		608061				10980201, 15644312	Standard	NM_006114		Approved	PEREC1, D19S1177E, C19orf1, TOM40, PER-EC1	uc002paa.4	O96008		ENST00000426677.2:c.510C>T	19.37:g.45397111C>T						TOMM40_uc002ozz.3_Silent_p.P170P|TOMM40_uc002ozx.4_Silent_p.P170P|TOMM40_uc002ozy.4_Silent_p.P170P	p.P170P	NM_001128917	NP_006105	O96008	TOM40_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.0033)|Epithelial(262;0.176)	3	706	+	Lung NSC(12;0.0018)|all_lung(12;0.00481)		170					Q86VW4|Q8WY09|Q8WY10|Q8WY11|Q9BR95	Silent	SNP	ENST00000426677.2	37	c.510C>T	CCDS12646.1																																																																																				0.647	TOMM40-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453241.1			20	42	0	0	0	1	0	20	42				
ADAMTS18	170692	broad.mit.edu	37	16	77401462	77401462	+	Silent	SNP	G	G	A	rs113746494		TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr16:77401462G>A	ENST00000282849.5	-	4	1072	c.654C>T	c.(652-654)ccC>ccT	p.P218P	ADAMTS18_ENST00000567121.1_5'UTR	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	218					eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.G216_G219del(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						GGCCAGAGCCGGGGTAGCCAC	0.552																																						uc002ffc.4																			1	Deletion - In frame(1)	p.G216_G219del(2)	ovary(1)	NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						c.(652-654)ccC>ccT		Homo sapiens ADAM metallopeptidase with thrombospondin type 1 motif, 18 (ADAMTS18), mRNA.							83.0	75.0	78.0					16																	77401462		2198	4300	6498	SO:0001819	synonymous_variant	170692				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding	g.chr16:77401462G>A	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.654C>T	16.37:g.77401462G>A						ADAMTS18_uc002ffe.1_5'UTR|ADAMTS18_uc010vni.1_Non-coding_Transcript	p.P218P	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN			3	1073	-			218					Q6P4R5|Q6ZWJ9	Silent	SNP	ENST00000282849.5	37	c.654C>T	CCDS10926.1																																																																																				0.552	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			5	107	0	0	0	1	0	5	107				
ZNF254	9534	broad.mit.edu	37	19	24310503	24310503	+	Missense_Mutation	SNP	T	T	G			TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr19:24310503T>G	ENST00000357002.4	+	4	1816	c.1701T>G	c.(1699-1701)atT>atG	p.I567M	ZNF254_ENST00000342944.6_Missense_Mutation_p.I482M	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	567					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				ATAAGAGAATTCATACTGGAG	0.333																																						uc002nru.3																			0											c.(1699-1701)atT>atG		Homo sapiens zinc finger protein 254 (ZNF254), mRNA.							31.0	34.0	33.0					19																	24310503		2190	4284	6474	SO:0001583	missense	9534				negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:24310503T>G	AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"""Zinc fingers, C2H2-type"", ""-"""	13047	protein-coding gene	gene with protein product		604768	"""zinc finger protein 539"""	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.1701T>G	19.37:g.24310503T>G	ENSP00000349494:p.Ile567Met					ZNF254_uc010xrk.2_Missense_Mutation_p.I482M	p.I567M	NM_203282	NP_975011	O75437	ZN254_HUMAN			3	1835	+		all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)	567					A4QPC0|Q86XL7	Missense_Mutation	SNP	ENST00000357002.4	37	c.1701T>G	CCDS32983.1	.	.	.	.	.	.	.	.	.	.	T	11.08	1.534829	0.27475	.	.	ENSG00000213096	ENST00000342944;ENST00000357002	T;T	0.01025	5.43;5.43	0.525	0.525	0.17072	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01454	0.0047	N	0.12502	0.225	0.26153	N	0.98012	D	0.76494	0.999	D	0.66847	0.947	T	0.55988	-0.8053	9	0.62326	D	0.03	.	5.2926	0.15735	0.0:1.0E-4:0.0:0.9999	.	567	O75437	ZN254_HUMAN	M	482;567	ENSP00000445527:I482M;ENSP00000349494:I567M	ENSP00000445527:I482M	I	+	3	3	ZNF254	24102343	0.001000	0.12720	0.242000	0.24170	0.930000	0.56654	-0.558000	0.05978	0.446000	0.26666	0.254000	0.18369	ATT		0.333	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876		13	33	0	0	0	1	0	13	33				
FAM155A	728215	broad.mit.edu	37	13	108518546	108518546	+	Silent	SNP	G	G	C			TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr13:108518546G>C	ENST00000375915.2	-	1	537	c.399C>G	c.(397-399)ccC>ccG	p.P133P		NM_001080396.2	NP_001073865.1	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	133						integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						CTCCCGGGGAGGGGGGCAGGG	0.721																																						uc001vql.3																			0				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						c.(397-399)ccC>ccG		Homo sapiens family with sequence similarity 155, member A (FAM155A), mRNA.							6.0	9.0	8.0					13																	108518546		1508	3409	4917	SO:0001819	synonymous_variant	728215					integral to membrane	binding	g.chr13:108518546G>C	L10374	CCDS32006.1	13q33.3	2008-04-15			ENSG00000204442	ENSG00000204442			33877	protein-coding gene	gene with protein product							Standard	NM_001080396		Approved		uc001vql.3	B1AL88	OTTHUMG00000017326	ENST00000375915.2:c.399C>G	13.37:g.108518546G>C							p.P133P	NM_001080396	NP_001073865	B1AL88	F155A_HUMAN			0	915	-			133					B2RUV1|B7Z334	Silent	SNP	ENST00000375915.2	37	c.399C>G	CCDS32006.1																																																																																				0.721	FAM155A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045736.2	NM_001080396		8	20	0	0	0	1	0	8	20				
SHROOM3	57619	broad.mit.edu	37	4	77637504	77637504	+	Intron	SNP	T	T	C			TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr4:77637504T>C	ENST00000296043.6	+	3	1408				SHROOM3_ENST00000473602.1_Intron	NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3						actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			ATTCCACGACTGAATATGACA	0.453																																						uc003hkf.1																			0				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60						c.(19-21)acT>acC		Homo sapiens shroom family member 3 (SHROOM3), mRNA.							380.0	342.0	353.0					4																	77637504		876	1991	2867	SO:0001627	intron_variant	57619				apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding	g.chr4:77637504T>C	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.455+6064T>C	4.37:g.77637504T>C						SHROOM3_uc011cbx.2_Intron|SHROOM3_uc011cbz.1_Intron	p.T7T	NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	Lung(101;0.0903)		0	351	+			0					Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	37	c.21T>C	CCDS3579.2																																																																																				0.453	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		4	314	0	0	0	1	0	4	314				
GGA2	23062	broad.mit.edu	37	16	23498084	23498084	+	Missense_Mutation	SNP	G	G	T			TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr16:23498084G>T	ENST00000309859.4	-	7	689	c.607C>A	c.(607-609)Cac>Aac	p.H203N	GGA2_ENST00000567468.1_Missense_Mutation_p.H203N	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	203	GAT. {ECO:0000255|PROSITE- ProRule:PRU00373}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)		TCCTCGGGGTGGTTGCTCTTT	0.507																																						uc002dlq.3																			0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21						c.(607-609)Cac>Aac		Homo sapiens golgi-associated, gamma adaptin ear containing, ARF binding protein 2 (GGA2), mRNA.							226.0	216.0	219.0					16																	23498084		2197	4300	6497	SO:0001583	missense	23062				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|clathrin-coated vesicle|endosome membrane|trans-Golgi network	ADP-ribosylation factor binding	g.chr16:23498084G>T	AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365			16064	protein-coding gene	gene with protein product		606005				10747088, 10749927	Standard	NM_015044		Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.607C>A	16.37:g.23498084G>T	ENSP00000311962:p.His203Asn					GGA2_uc010bxo.2_Non-coding_Transcript	p.H203N	NM_015044	NP_055859	Q9UJY4	GGA2_HUMAN		GBM - Glioblastoma multiforme(48;0.0386)	6	690	-			203			GAT.		D3DWF0|O14564|Q9NYN2|Q9UPS2	Missense_Mutation	SNP	ENST00000309859.4	37	c.607C>A	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	G	10.21	1.288193	0.23478	.	.	ENSG00000103365	ENST00000309859	T	0.40225	1.04	6.07	6.07	0.98685	GAT (1);	0.102488	0.64402	D	0.000002	T	0.39172	0.1068	L	0.33624	1.015	0.36566	D	0.872697	D	0.55605	0.972	P	0.53360	0.724	T	0.24225	-1.0166	10	0.02654	T	1	-25.1868	13.0052	0.58701	0.0:0.0:0.8389:0.1611	.	203	Q9UJY4	GGA2_HUMAN	N	203	ENSP00000311962:H203N	ENSP00000311962:H203N	H	-	1	0	GGA2	23405585	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.055000	0.57441	2.890000	0.99128	0.650000	0.86243	CAC		0.507	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1			68	214	0	0	0	1	0	68	214				
FAM207A	85395	broad.mit.edu	37	21	46363721	46363721	+	Silent	SNP	G	G	A	rs200952167		TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr21:46363721G>A	ENST00000291634.6	+	2	300	c.252G>A	c.(250-252)tcG>tcA	p.S84S	FAM207A_ENST00000397826.3_Intron	NM_058190.2	NP_478070.1	Q9NSI2	F207A_HUMAN	family with sequence similarity 207, member A	84																	AGGCAGGCTCGAGTGCACGGA	0.602													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18989	0.0		0.0	False		,,,				2504	0.0					uc002zgl.3																			0											c.(250-252)tcG>tcA		Homo sapiens family with sequence similarity 207, member A (FAM207A), mRNA.		G		1,4405	2.1+/-5.4	0,1,2202	90.0	69.0	76.0		252	-0.6	0.0	21		76	0,8600		0,0,4300	no	coding-synonymous	FAM207A	NM_058190.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		84/231	46363721	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	85395							g.chr21:46363721G>A		CCDS13718.1	21q22.3	2011-08-15	2011-08-15	2011-08-15	ENSG00000160256	ENSG00000160256			15811	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 70"""	C21orf70			Standard	NM_058190		Approved	PRED56	uc002zgl.3	Q9NSI2	OTTHUMG00000090293	ENST00000291634.6:c.252G>A	21.37:g.46363721G>A						FAM207A_uc002zgm.3_Intron	p.S84S	NM_058190	NP_478070	Q9NSI2	CU070_HUMAN			1	270	+			84						Silent	SNP	ENST00000291634.6	37	c.252G>A	CCDS13718.1																																																																																				0.602	FAM207A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206639.1	NM_058190		18	53	0	0	0	1	0	18	53				
IL23R	149233	broad.mit.edu	37	1	67705965	67705965	+	Splice_Site	SNP	G	G	A			TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr1:67705965G>A	ENST00000347310.5	+	9	1319		c.e9+1		IL23R_ENST00000473881.1_Intron|IL23R_ENST00000395227.1_Splice_Site|AL109843.1_ENST00000408806.1_RNA|IL23R_ENST00000371002.1_Intron	NM_144701.2	NP_653302.2	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor						defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|interleukin-23-mediated signaling pathway (GO:0038155)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)	interleukin-23 receptor complex (GO:0072536)|receptor complex (GO:0043235)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	21						TCCGAACTGGGTAGGTTTTTG	0.323																																						uc001ddo.3																			0				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	21						c.e9+1		Homo sapiens interleukin 23 receptor (IL23R), mRNA.							149.0	132.0	138.0					1																	67705965		2203	4299	6502	SO:0001630	splice_region_variant	149233				inflammatory response|negative regulation of interleukin-10 production|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of interleukin-12 production|positive regulation of memory T cell differentiation|response to interferon-gamma|response to lipopolysaccharide	interleukin-23 receptor complex	receptor activity	g.chr1:67705965G>A	AF461422	CCDS637.1	1p31.2	2008-02-05			ENSG00000162594	ENSG00000162594			19100	protein-coding gene	gene with protein product		607562				12023369	Standard	NM_144701		Approved	IL-23R	uc001ddo.3	Q5VWK5	OTTHUMG00000009092	ENST00000347310.5:c.1148+1G>A	1.37:g.67705965G>A						IL23R_uc009waz.3_Splice_Site_p.G180_splice|IL23R_uc001ddp.2_Intron|IL23R_uc010opi.2_Intron|IL23R_uc010opj.2_Intron|IL23R_uc010opk.2_Intron|IL23R_uc010opl.2_Intron|IL23R_uc010opm.2_Splice_Site|IL23R_uc001ddq.3_Splice_Site_p.G129_splice|IL23R_uc010opn.2_Splice_Site_p.G228_splice|IL23R_uc001ddr.3_Intron|IL23R_uc010opo.1_Splice_Site_p.G242_splice|IL23R_uc010opp.1_Intron|IL23R_uc010opq.1_Splice_Site_p.G212_splice|IL23R_uc010opr.1_Splice_Site|IL23R_uc010oqh.2_Splice_Site_p.G24_splice|IL23R_uc010oqf.2_Splice_Site|IL23R_uc010ops.2_Splice_Site_p.G180_splice|IL23R_uc010opt.2_Splice_Site_p.G24_splice|IL23R_uc010opu.2_Splice_Site_p.G79_splice|IL23R_uc010opv.2_Splice_Site_p.G141_splice|IL23R_uc010opw.2_Intron|IL23R_uc010opx.2_Splice_Site_p.G24_splice|IL23R_uc010opy.2_Splice_Site_p.G150_splice|IL23R_uc010opz.2_Splice_Site_p.G24_splice|IL23R_uc010oqa.2_Splice_Site_p.G24_splice|IL23R_uc010oqb.2_Splice_Site_p.G212_splice|IL23R_uc010oqc.2_Splice_Site_p.G99_splice|IL23R_uc010oqd.2_Intron|IL23R_uc010oqe.2_Intron|IL23R_uc010oqg.2_Intron|IL23R_uc001dds.3_Splice_Site_p.G128_splice|IL23R_uc001ddt.3_Intron	p.G383_splice	NM_144701	NP_653302	Q5VWK5	IL23R_HUMAN			9	1233	+			383					C9JGX4|Q4VGP1|Q4VGP2|Q4VGP3|Q4VGP4|Q4VGP5|Q4VGP6|Q5VWK7|Q8IW84|Q8NFQ9|Q96AS1	Splice_Site	SNP	ENST00000347310.5	37	c.1148_splice	CCDS637.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.202836	0.58234	.	.	ENSG00000162594	ENST00000347310;ENST00000431791;ENST00000441823;ENST00000425614;ENST00000395227	.	.	.	5.19	5.19	0.71726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4119	0.67119	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IL23R	67478553	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	4.175000	0.58263	2.865000	0.98341	0.655000	0.94253	.		0.323	IL23R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025199.2	NM_144701	Intron	4	38	0	0	0	1	0	4	38				
PZP	5858	broad.mit.edu	37	12	9355129	9355129	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr12:9355129C>T	ENST00000261336.2	-	3	447	c.419G>A	c.(418-420)gGa>gAa	p.G140E	PZP_ENST00000381997.2_5'Flank	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	140					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						ACCTGTCTGTCCTGGTTTATA	0.498																																					Melanoma(125;1402 1695 4685 34487 38571)	uc001qvl.3																			0				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						c.(418-420)gGa>gAa		Homo sapiens pregnancy-zone protein (PZP), mRNA.							146.0	141.0	143.0					12																	9355129		2203	4300	6503	SO:0001583	missense	5858							g.chr12:9355129C>T	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.419G>A	12.37:g.9355129C>T	ENSP00000261336:p.Gly140Glu					PZP_uc009zgl.3_5'UTR	p.G140E	NM_002864	NP_002855					2	448	-								A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	c.419G>A	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	C	3.367	-0.129275	0.06753	.	.	ENSG00000126838	ENST00000261336	D	0.81821	-1.54	2.3	0.357	0.16079	Alpha-2-macroglobulin, N-terminal (1);	0.386473	0.20643	N	0.088377	D	0.83308	0.5226	M	0.83223	2.63	0.45076	D	0.99809	P	0.35944	0.529	P	0.46585	0.521	T	0.79401	-0.1819	10	0.66056	D	0.02	.	7.176	0.25744	0.0:0.7217:0.0:0.2783	.	140	P20742	PZP_HUMAN	E	140	ENSP00000261336:G140E	ENSP00000261336:G140E	G	-	2	0	PZP	9246396	0.976000	0.34144	0.737000	0.30932	0.036000	0.12997	0.147000	0.16202	-0.172000	0.10779	-1.842000	0.00583	GGA		0.498	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		7	163	0	0	0	1	0	7	163				
PLEK	5341	broad.mit.edu	37	2	68608012	68608012	+	Missense_Mutation	SNP	G	G	A	rs144599110		TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr2:68608012G>A	ENST00000234313.7	+	3	535	c.356G>A	c.(355-357)cGa>cAa	p.R119Q		NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	119					actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		AGGTCCATTCGACTGCCAGAA	0.458																																						uc002sen.4																			0				autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24						c.(355-357)cGa>cAa		Homo sapiens pleckstrin (PLEK), mRNA.		G	GLN/ARG	0,4406		0,0,2203	138.0	130.0	133.0		356	5.8	1.0	2	dbSNP_134	133	1,8599	1.2+/-3.3	0,1,4299	no	missense	PLEK	NM_002664.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	119/351	68608012	1,13005	2203	4300	6503	SO:0001583	missense	5341				actin cytoskeleton reorganization|cortical actin cytoskeleton organization|hemopoietic progenitor cell differentiation|inhibition of phospholipase C activity involved in G-protein coupled receptor signaling pathway|integrin-mediated signaling pathway|negative regulation of calcium-mediated signaling|negative regulation of inositol phosphate biosynthetic process|phosphatidylinositol metabolic process|platelet aggregation|positive regulation of actin filament bundle assembly|positive regulation of actin filament depolymerization|positive regulation of inositol-polyphosphate 5-phosphatase activity|positive regulation of integrin activation|positive regulation of platelet activation|protein kinase C signaling cascade|protein secretion by platelet|regulation of cell diameter|ruffle organization|thrombin receptor signaling pathway|vesicle docking involved in exocytosis	cytosol|extracellular region|membrane fraction|ruffle membrane|soluble fraction	phosphatidylinositol-3,4-bisphosphate binding|protein homodimerization activity|protein kinase C binding	g.chr2:68608012G>A	X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"""Pleckstrin homology (PH) domain containing"""	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.356G>A	2.37:g.68608012G>A	ENSP00000234313:p.Arg119Gln					PLEK_uc010fde.3_Missense_Mutation_p.R119Q	p.R119Q	NM_002664	NP_002655	P08567	PLEK_HUMAN		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)	2	518	+		Ovarian(717;0.0129)	119					B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Missense_Mutation	SNP	ENST00000234313.7	37	c.356G>A	CCDS1887.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.799472	0.70567	0.0	1.16E-4	ENSG00000115956	ENST00000234313	T	0.20332	2.08	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.22322	0.0538	L	0.59436	1.845	0.80722	D	1	D;D	0.56287	0.975;0.975	B;B	0.40506	0.331;0.331	T	0.01748	-1.1282	10	0.31617	T	0.26	.	14.2444	0.65978	0.071:0.0:0.929:0.0	.	137;119	Q59GZ2;P08567	.;PLEK_HUMAN	Q	119	ENSP00000234313:R119Q	ENSP00000234313:R119Q	R	+	2	0	PLEK	68461516	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.462000	0.66707	2.750000	0.94351	0.655000	0.94253	CGA		0.458	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664		6	237	0	0	0	1	0	6	237				
TSHR	7253	broad.mit.edu	37	14	81609760	81609760	+	Missense_Mutation	SNP	T	T	C	rs121908864		TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr14:81609760T>C	ENST00000541158.2	+	11	1680	c.1358T>C	c.(1357-1359)aTg>aCg	p.M453T	TSHR_ENST00000298171.2_Missense_Mutation_p.M453T|RP11-114N19.3_ENST00000557775.1_RNA			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	453			M -> T (in HTNA; sporadic; found in toxic thyroid nodules and hyperfunctioning thyroid adenomas). {ECO:0000269|PubMed:11434721, ECO:0000269|PubMed:12213664, ECO:0000269|PubMed:8964822, ECO:0000269|PubMed:9253356}.		adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)	p.M453T(28)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	CGCTTTCTCATGTGCAACCTG	0.527			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																															uc001xvd.1			yes	Dom	yes		14	14q31	7253	Mis	thyroid stimulating hormone receptor	yes	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism	E		thyroid  adenoma	toxic thyroid adenoma		28	Substitution - Missense(28)	p.M453T(62)	thyroid(28)	breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337	GRCh37	CM981962	TSHR	M	rs121908864	c.(1357-1359)aTg>aCg		Homo sapiens thyroid stimulating hormone receptor (TSHR), transcript variant 1, mRNA.	Thyrotropin Alfa(DB00024)						734.0	582.0	633.0					14																	81609760		2203	4300	6503	SO:0001583	missense	7253				cell-cell signaling|positive regulation of cell proliferation	integral to plasma membrane	protein binding|thyroid-stimulating hormone receptor activity	g.chr14:81609760T>C	AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"""GPCR / Class A : Gonadotropin and TSH receptors"""	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.1358T>C	14.37:g.81609760T>C	ENSP00000441235:p.Met453Thr						p.M453T	NM_000369	NP_000360	P16473	TSHR_HUMAN		BRCA - Breast invasive adenocarcinoma(234;0.0402)	9	1514	+			453		M -> T (in HTNA; sporadic; found in toxic thyroid nodules and hyperfunctioning thyroid adenomas).			A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Missense_Mutation	SNP	ENST00000541158.2	37	c.1358T>C	CCDS9872.1	.	.	.	.	.	.	.	.	.	.	T	18.61	3.661392	0.67700	.	.	ENSG00000165409	ENST00000541158;ENST00000412429;ENST00000298171	T;T	0.39406	1.08;1.08	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.76528	0.4000	H	0.96604	3.85	0.80722	A	1	D	0.76494	0.999	D	0.81914	0.995	D	0.85108	0.0961	9	0.87932	D	0	.	16.0365	0.80635	0.0:0.0:0.0:1.0	.	453	F5GYU5	.	T	453;100;453	ENSP00000441235:M453T;ENSP00000298171:M453T	ENSP00000298171:M453T	M	+	2	0	TSHR	80679513	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.040000	0.89188	2.196000	0.70406	0.459000	0.35465	ATG		0.527	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369		52	105	0	0	0	1	0	52	105				
IGSF1	3547	broad.mit.edu	37	X	130411859	130411859	+	Missense_Mutation	SNP	G	G	C			TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chrX:130411859G>C	ENST00000361420.3	-	13	2370	c.2291C>G	c.(2290-2292)cCc>cGc	p.P764R	IGSF1_ENST00000370903.3_Missense_Mutation_p.P769R|IGSF1_ENST00000467244.1_5'Flank|IGSF1_ENST00000370910.1_Missense_Mutation_p.P755R|IGSF1_ENST00000370904.1_Missense_Mutation_p.P755R			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	764					regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						CGGCTCACTGGGCTCAGACCA	0.527																																						uc004ewe.4																			0				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						c.(2305-2307)cCc>cGc		Homo sapiens immunoglobulin superfamily, member 1 (IGSF1), transcript variant 3, mRNA.							109.0	100.0	103.0					X																	130411859		2203	4300	6503	SO:0001583	missense	3547				regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding	g.chrX:130411859G>C	AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.2291C>G	X.37:g.130411859G>C	ENSP00000355010:p.Pro764Arg					IGSF1_uc004ewd.3_Missense_Mutation_p.P764R|IGSF1_uc022cdv.1_Missense_Mutation_p.P755R|IGSF1_uc004ewf.2_Missense_Mutation_p.P744R	p.P769R	NM_001170961	NP_001164432	Q8N6C5	IGSF1_HUMAN			12	2589	-			764					B5MEG2|H9KV64|O15070|Q9NTC8	Missense_Mutation	SNP	ENST00000361420.3	37	c.2306C>G	CCDS14629.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.698398	0.48307	.	.	ENSG00000147255	ENST00000370910;ENST00000361420;ENST00000370904;ENST00000370903	T;T;T;T	0.12569	2.67;2.67;2.67;2.67	4.88	4.88	0.63580	Immunoglobulin-like fold (1);	0.372467	0.20026	N	0.100814	T	0.28300	0.0699	L	0.39467	1.215	0.38553	D	0.949516	P;D;D	0.89917	0.829;1.0;1.0	P;D;D	0.91635	0.733;0.999;0.999	T	0.03403	-1.1040	10	0.87932	D	0	.	12.9346	0.58307	0.0:0.0:1.0:0.0	.	755;208;764	Q8N6C5-2;C9JP68;Q8N6C5	.;.;IGSF1_HUMAN	R	755;764;755;769	ENSP00000359947:P755R;ENSP00000355010:P764R;ENSP00000359941:P755R;ENSP00000359940:P769R	ENSP00000355010:P764R	P	-	2	0	IGSF1	130239540	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	1.711000	0.37930	2.354000	0.79902	0.594000	0.82650	CCC		0.527	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1			7	112	0	0	0	1	0	7	112				
PEX1	5189	broad.mit.edu	37	7	92120650	92120650	+	Missense_Mutation	SNP	A	A	G			TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr7:92120650A>G	ENST00000248633.4	-	21	3469	c.3374T>C	c.(3373-3375)aTg>aCg	p.M1125T	PEX1_ENST00000438045.1_Missense_Mutation_p.M803T|PEX1_ENST00000428214.1_Missense_Mutation_p.M1068T|AC007566.10_ENST00000427458.1_RNA|AC007566.10_ENST00000441539.1_RNA	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	1125					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			GAGCCGGTACATATTGAATTT	0.408																																						uc003uly.3																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						c.(3373-3375)aTg>aCg		Homo sapiens peroxisomal biogenesis factor 1 (PEX1), mRNA.							133.0	136.0	135.0					7																	92120650		2203	4300	6503	SO:0001583	missense	5189				microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding	g.chr7:92120650A>G	AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"""ATPases / AAA-type"""	8850	protein-coding gene	gene with protein product		602136	"""peroxisome biogenesis factor 1"", ""Zellweger syndrome 1"", ""Zellweger syndrome"""	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.3374T>C	7.37:g.92120650A>G	ENSP00000248633:p.Met1125Thr					PEX1_uc011khr.2_Missense_Mutation_p.M917T|PEX1_uc010ley.3_Missense_Mutation_p.M1068T|PEX1_uc011khs.2_Missense_Mutation_p.M803T	p.M1125T	NM_000466	NP_000457	O43933	PEX1_HUMAN	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)		20	3470	-	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	1125					A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Missense_Mutation	SNP	ENST00000248633.4	37	c.3374T>C	CCDS5627.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.094503	0.56075	.	.	ENSG00000127980	ENST00000438045;ENST00000248633;ENST00000428214	D;D;D	0.94497	-3.38;-3.44;-3.43	5.4	5.4	0.78164	.	0.233626	0.52532	D	0.000068	D	0.90848	0.7125	L	0.43152	1.355	0.80722	D	1	P;B;B	0.36465	0.554;0.181;0.181	B;B;B	0.30029	0.11;0.075;0.075	D	0.90574	0.4524	10	0.44086	T	0.13	-9.0938	15.7033	0.77558	1.0:0.0:0.0:0.0	.	803;917;1125	E9PE75;B4DER6;O43933	.;.;PEX1_HUMAN	T	803;1125;1068	ENSP00000410438:M803T;ENSP00000248633:M1125T;ENSP00000394413:M1068T	ENSP00000248633:M1125T	M	-	2	0	PEX1	91958586	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.678000	0.91211	2.182000	0.69389	0.402000	0.26972	ATG		0.408	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		3	116	0	0	0	1	0	3	116				
STAT4	6775	broad.mit.edu	37	2	191900911	191900911	+	Missense_Mutation	SNP	T	T	A			TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr2:191900911T>A	ENST00000392320.2	-	17	1863	c.1549A>T	c.(1549-1551)Atg>Ttg	p.M517L	STAT4_ENST00000358470.4_Missense_Mutation_p.M517L|STAT4_ENST00000470708.1_5'UTR	NM_003151.3	NP_003142.1	Q14765	STAT4_HUMAN	signal transducer and activator of transcription 4	517					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(4)|endometrium(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			TCTGCCAGCATATGGAGTTGA	0.458																																						uc002usm.2																			0				breast(4)|endometrium(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	42						c.(1549-1551)Atg>Ttg		Homo sapiens signal transducer and activator of transcription 4 (STAT4), transcript variant 1, mRNA.							106.0	93.0	98.0					2																	191900911		2203	4300	6503	SO:0001583	missense	6775				JAK-STAT cascade	cytoplasm|nucleus	calcium ion binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity	g.chr2:191900911T>A		CCDS2310.1	2q32.2-q32.3	2013-02-14			ENSG00000138378	ENSG00000138378		"""SH2 domain containing"""	11365	protein-coding gene	gene with protein product		600558				8007943, 8700208	Standard	NM_003151		Approved		uc002usn.2	Q14765	OTTHUMG00000132700	ENST00000392320.2:c.1549A>T	2.37:g.191900911T>A	ENSP00000376134:p.Met517Leu					STAT4_uc002usn.2_Missense_Mutation_p.M517L|STAT4_uc010zgk.1_Missense_Mutation_p.M362L|STAT4_uc002uso.2_Missense_Mutation_p.M517L	p.M517L	NM_003151	NP_003142	Q14765	STAT4_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)		16	1864	-			517					Q96NZ6	Missense_Mutation	SNP	ENST00000392320.2	37	c.1549A>T	CCDS2310.1	.	.	.	.	.	.	.	.	.	.	T	34	5.327029	0.95708	.	.	ENSG00000138378	ENST00000358470;ENST00000392320	D;D	0.86865	-2.18;-2.18	5.83	5.83	0.93111	STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);EF-hand-like domain (1);	0.036537	0.85682	D	0.000000	D	0.90079	0.6901	M	0.79805	2.47	0.80722	D	1	P;P;P	0.46020	0.871;0.871;0.871	B;B;P	0.46275	0.423;0.423;0.51	D	0.91386	0.5131	10	0.72032	D	0.01	-23.62	16.2005	0.82071	0.0:0.0:0.0:1.0	.	426;517;517	Q53S87;B4DV04;Q14765	.;.;STAT4_HUMAN	L	517	ENSP00000351255:M517L;ENSP00000376134:M517L	ENSP00000351255:M517L	M	-	1	0	STAT4	191609156	1.000000	0.71417	0.978000	0.43139	0.984000	0.73092	8.040000	0.89188	2.227000	0.72691	0.528000	0.53228	ATG		0.458	STAT4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335586.1	NM_003151		6	81	0	0	0	1	0	6	81				
OR4C11	219429	broad.mit.edu	37	11	55371142	55371142	+	Silent	SNP	G	G	A	rs146621611	byFrequency	TCGA-EM-A2OW-01A-11D-A202-08	TCGA-EM-A2OW-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17a66d24-de77-4f2a-a8ad-d2c6a69e7671	a4765371-2387-4002-9887-2615e5136f7b	g.chr11:55371142G>A	ENST00000302231.4	-	1	732	c.708C>T	c.(706-708)tcC>tcT	p.S236S		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						ACGTGCAAGCGGAGAGAGCCT	0.413													-|||	19	0.00379393	0.0144	0.0	5008	,	,		14931	0.0		0.0	False		,,,				2504	0.0					uc010rii.2																			0				endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						c.(706-708)tcC>tcT		Homo sapiens olfactory receptor, family 4, subfamily C, member 11 (OR4C11), mRNA.		-		60,4296		4,52,2122	74.0	64.0	67.0		708	-7.2	0.0	11	dbSNP_134	67	0,8006		0,0,4003	no	coding-synonymous	OR4C11	NM_001004700.2		4,52,6125	AA,AG,GG		0.0,1.3774,0.4854		236/311	55371142	60,12302	2178	4003	6181	SO:0001819	synonymous_variant	219429				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55371142G>A	AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"""GPCR / Class A : Olfactory receptors"""	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.708C>T	11.37:g.55371142G>A							p.S236S	NM_001004700	NP_001004700	Q6IEV9	OR4CB_HUMAN			0	733	-			236					B9EIL4|Q8NGL8	Silent	SNP	ENST00000302231.4	37	c.708C>T	CCDS31503.1																																																																																				0.413	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700		4	113	0	0	0	1	0	4	113				
