#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_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_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
MS4A3	932	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	59830060	59830060	+	Silent	SNP	G	G	A	rs376718907		TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr11:59830060G>A	ENST00000278865.3	+	3	349	c.276G>A	c.(274-276)ccG>ccA	p.P92P	MS4A3_ENST00000358152.2_Intron|MS4A3_ENST00000395032.2_Intron|MS4A3_ENST00000534744.1_Intron	NM_006138.4	NP_006129.4	Q96HJ5	MS4A3_HUMAN	membrane-spanning 4-domains, subfamily A, member 3 (hematopoietic cell-specific)	92						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(4)|kidney(2)|lung(9)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21		all_epithelial(135;0.245)				CAGGCTACCCGATTTGGGGTG	0.423																																																0								G	,,	1,4401	2.1+/-5.4	0,1,2200	159.0	147.0	151.0		,,276	-9.2	0.0	11		151	0,8590		0,0,4295	no	intron,intron,coding-synonymous	MS4A3	NM_001031666.1,NM_001031809.1,NM_006138.4	,,	0,1,6495	AA,AG,GG		0.0,0.0227,0.0077	,,	,,92/215	59830060	1,12991	2201	4295	6496	SO:0001819	synonymous_variant	932			L35848	CCDS31567.1, CCDS31568.1, CCDS41651.1	11q12-q13.1	2008-03-25				ENSG00000149516			7317	protein-coding gene	gene with protein product		606498		CD20L		7524084	Standard	NM_006138		Approved	HTM4	uc001nom.3	Q96HJ5		ENST00000278865.3:c.276G>A	11.37:g.59830060G>A			A8MTP8|Q8NHW2	Silent	SNP	ENST00000278865.3	37	CCDS31567.1																																																																																				0.423	MS4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394417.1			51	63	51	63
IL18	3606	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	112014361	112014361	+	Missense_Mutation	SNP	C	C	A			TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr11:112014361C>A	ENST00000280357.7	-	6	759	c.540G>T	c.(538-540)ttG>ttT	p.L180F	IL18_ENST00000533858.1_5'Flank|IL18_ENST00000528832.1_Missense_Mutation_p.L180F|IL18_ENST00000524595.1_Missense_Mutation_p.L176F|SDHD_ENST00000532699.1_Intron	NM_001562.3	NP_001553.1	Q14116	IL18_HUMAN	interleukin 18	180					angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|cellular response to organic cyclic compound (GO:0071407)|chemokine biosynthetic process (GO:0042033)|granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0042253)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma biosynthetic process (GO:0042095)|interleukin-13 biosynthetic process (GO:0042231)|interleukin-2 biosynthetic process (GO:0042094)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|natural killer cell activation (GO:0030101)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of tissue remodeling (GO:0034105)|regulation of cell adhesion (GO:0030155)|sleep (GO:0030431)|T-helper 1 type immune response (GO:0042088)|type 2 immune response (GO:0042092)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)						all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)		ATCTATCCCCCAATTCATCCT	0.388																																																0													50.0	47.0	48.0					11																	112014361		1818	4076	5894	SO:0001583	missense	3606			U90434	CCDS44731.1, CCDS58180.1	11q22.2-q22.3	2014-04-04	2014-04-04		ENSG00000150782	ENSG00000150782		"""Interleukins and interleukin receptors"""	5986	protein-coding gene	gene with protein product	"""interferon-gamma-inducing factor"""	600953	"""interleukin 18 (interferon-gamma-inducing factor)"""			7477296, 9693051	Standard	NM_001562		Approved	IGIF, IL1F4, IL-1g, IL-18	uc001pnb.2	Q14116	OTTHUMG00000167006	ENST00000280357.7:c.540G>T	11.37:g.112014361C>A	ENSP00000280357:p.Leu180Phe		O75599|Q6FGY3|Q6WWJ7	Missense_Mutation	SNP	ENST00000280357.7	37	CCDS44731.1	.	.	.	.	.	.	.	.	.	.	C	1.899	-0.453505	0.04540	.	.	ENSG00000150782	ENST00000280357;ENST00000524595;ENST00000528832	T;T;T	0.18810	2.19;2.19;2.19	4.85	-1.85	0.07784	.	2.565290	0.01303	N	0.010361	T	0.13457	0.0326	N	0.22421	0.69	0.09310	N	1	B;B;B	0.23735	0.072;0.072;0.09	B;B;B	0.28991	0.033;0.033;0.097	T	0.18147	-1.0346	10	0.10111	T	0.7	-30.3423	5.1803	0.15156	0.2828:0.3072:0.0:0.41	.	176;180;180	Q6WWJ7;Q14116;Q96KJ8	.;IL18_HUMAN;.	F	180;176;180	ENSP00000280357:L180F;ENSP00000434561:L176F;ENSP00000434161:L180F	ENSP00000280357:L180F	L	-	3	2	IL18	111519571	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.402000	0.07223	0.026000	0.15269	-1.432000	0.01085	TTG		0.388	IL18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392409.1	NM_001562		6	12	6	12
CADM1	23705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	115109342	115109342	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr11:115109342T>C	ENST00000452722.3	-	3	322	c.302A>G	c.(301-303)aAt>aGt	p.N101S	CADM1_ENST00000331581.6_Missense_Mutation_p.N101S|CADM1_ENST00000537058.1_Missense_Mutation_p.N101S|CADM1_ENST00000537140.1_5'UTR|CADM1_ENST00000542447.2_Missense_Mutation_p.N101S|CADM1_ENST00000536727.1_Missense_Mutation_p.N101S	NM_014333.3	NP_055148.3			cell adhesion molecule 1											cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		GCTAGAAAAATTCAGCAACTG	0.393																																																0													82.0	81.0	81.0					11																	115109342		2201	4296	6497	SO:0001583	missense	23705			AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5951	protein-coding gene	gene with protein product	"""nectin-like 2"""	605686	"""tumor suppressor in lung cancer 1"", ""immunoglobulin superfamily, member 4"""	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.302A>G	11.37:g.115109342T>C	ENSP00000395359:p.Asn101Ser			Missense_Mutation	SNP	ENST00000452722.3	37	CCDS8373.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.34|15.34	2.805699|2.805699	0.50315|0.50315	.|.	.|.	ENSG00000182985|ENSG00000182985	ENST00000543249|ENST00000542447;ENST00000452722;ENST00000537058;ENST00000536727;ENST00000404468;ENST00000331581;ENST00000545094	.|T;T;T;T;T;T	.|0.63913	.|-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	5.81|5.81	5.81|5.81	0.92471|0.92471	.|Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.69187|0.69187	0.3083|0.3083	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	D|D	1|1	.|D;D;D;B;D	.|0.76494	.|0.998;0.999;0.999;0.236;0.997	.|D;D;D;B;D	.|0.81914	.|0.987;0.995;0.994;0.18;0.983	T|T	0.63808|0.63808	-0.6553|-0.6553	5|10	.|0.06099	.|T	.|0.92	.|.	16.167|16.167	0.81768|0.81768	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|101;101;102;101;101	.|Q9BY67-2;F5H0J4;A4FVB5;Q9BY67;A0A4Z1	.|.;.;.;CADM1_HUMAN;.	V|S	85|101;101;101;101;60;101;68	.|ENSP00000439176:N101S;ENSP00000395359:N101S;ENSP00000439817:N101S;ENSP00000440322:N101S;ENSP00000329797:N101S;ENSP00000439696:N68S	.|ENSP00000329797:N101S	I|N	-|-	1|2	0|0	CADM1|CADM1	114614552|114614552	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.665000|7.665000	0.83852|0.83852	2.214000|2.214000	0.71695|0.71695	0.528000|0.528000	0.53228|0.53228	ATT|AAT		0.393	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333		28	28	28	28
KERA	11081	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	91445220	91445220	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr12:91445220T>C	ENST00000266719.3	-	3	1209	c.962A>G	c.(961-963)cAt>cGt	p.H321R		NM_007035.3	NP_008966.1	O60938	KERA_HUMAN	keratocan	321					carbohydrate metabolic process (GO:0005975)|cornea development in camera-type eye (GO:0061303)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|response to stimulus (GO:0050896)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(2)|large_intestine(8)|lung(5)|prostate(2)|skin(2)	19						GTAGCGAAGATGAGGTCCATA	0.438																																																0													123.0	103.0	110.0					12																	91445220		2203	4299	6502	SO:0001583	missense	11081			AF063301	CCDS9037.1	12q21.3-q22	2014-09-17				ENSG00000139330		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	6309	protein-coding gene	gene with protein product	"""keratocan proteoglycan"""	603288		CNA2		10565548, 10802664	Standard	NM_007035		Approved	SLRR2B	uc001tbl.3	O60938		ENST00000266719.3:c.962A>G	12.37:g.91445220T>C	ENSP00000266719:p.His321Arg			Missense_Mutation	SNP	ENST00000266719.3	37	CCDS9037.1	.	.	.	.	.	.	.	.	.	.	T	1.533	-0.543795	0.04053	.	.	ENSG00000139330	ENST00000266719	T	0.17528	2.27	5.62	1.99	0.26369	.	0.198636	0.53938	N	0.000055	T	0.07234	0.0183	N	0.16862	0.45	0.24595	N	0.993802	B	0.02656	0.0	B	0.01281	0.0	T	0.41538	-0.9503	10	0.02654	T	1	-6.5436	6.7997	0.23744	0.0:0.5814:0.0:0.4186	.	321	O60938	KERA_HUMAN	R	321	ENSP00000266719:H321R	ENSP00000266719:H321R	H	-	2	0	KERA	89969351	0.640000	0.27243	0.978000	0.43139	0.415000	0.31203	1.114000	0.31196	0.416000	0.25844	-0.256000	0.11100	CAT		0.438	KERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407149.2	NM_007035		13	32	13	32
CDK10	8558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	89755723	89755723	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr16:89755723G>A	ENST00000353379.7	+	2	194	c.151G>A	c.(151-153)Ggc>Agc	p.G51S	CDK10_ENST00000514965.1_3'UTR|RP11-368I7.4_ENST00000567544.1_5'Flank|CDK10_ENST00000331006.8_Intron|CDK10_ENST00000505473.1_5'UTR	NM_001098533.2|NM_001160367.1|NM_052988.4	NP_001092003.2|NP_001153839.1|NP_443714.3	Q15131	CDK10_HUMAN	cyclin-dependent kinase 10	51	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|traversing start control point of mitotic cell cycle (GO:0007089)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			ovary(1)	1		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0276)		GGGTACCTACGGCATTGTGTG	0.582																																																0													193.0	144.0	161.0					16																	89755723		2198	4300	6498	SO:0001583	missense	8558			L33264	CCDS10984.2, CCDS32514.1, CCDS32514.2	16q24.3	2011-11-08	2007-11-21		ENSG00000185324	ENSG00000185324		"""Cyclin-dependent kinases"""	1770	protein-coding gene	gene with protein product		603464	"""cyclin-dependent kinase (CDC2-like) 10"""			8208557, 8084611	Standard	NM_052988		Approved	PISSLRE	uc010cio.3	Q15131	OTTHUMG00000138049	ENST00000353379.7:c.151G>A	16.37:g.89755723G>A	ENSP00000338673:p.Gly51Ser		A8K370|A8K8I6|A8MXU6|B3KQJ3|B7Z420|D3DX82|D3DX83|Q0VGZ7|Q15130|Q6PJC0	Missense_Mutation	SNP	ENST00000353379.7	37	CCDS10984.2	.	.	.	.	.	.	.	.	.	.	G	32	5.174737	0.94807	.	.	ENSG00000185324	ENST00000393082;ENST00000353379	T	0.64085	-0.08	4.77	4.77	0.60923	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.049590	0.85682	D	0.000000	T	0.79281	0.4419	M	0.75615	2.305	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.82246	-0.0552	10	0.66056	D	0.02	-29.4107	17.8045	0.88598	0.0:0.0:1.0:0.0	.	51	Q15131	CDK10_HUMAN	S	22;51	ENSP00000338673:G51S	ENSP00000338673:G51S	G	+	1	0	CDK10	88283224	1.000000	0.71417	0.995000	0.50966	0.934000	0.57294	8.702000	0.91338	2.202000	0.70862	0.561000	0.74099	GGC		0.582	CDK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269925.2			30	48	30	48
GNAL	2774	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	11880999	11880999	+	Silent	SNP	G	G	A			TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr18:11880999G>A	ENST00000423027.3	+	12	1332	c.1011G>A	c.(1009-1011)acG>acA	p.T337T	GNAL_ENST00000269162.5_Silent_p.T337T|GNAL_ENST00000602628.1_Silent_p.T130T|GNAL_ENST00000535121.1_Silent_p.T337T|GNAL_ENST00000334049.6_Silent_p.T414T			P38405	GNAL_HUMAN	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide, olfactory type	337					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|response to amphetamine (GO:0001975)|response to caffeine (GO:0031000)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)	12						GGATCAGCACGGCCACCGGTG	0.622																																																0													93.0	66.0	75.0					18																	11880999		2203	4300	6503	SO:0001819	synonymous_variant	2774			AF493893	CCDS11851.1, CCDS11852.1, CCDS58614.1	18p11.22-p11.21	2003-12-17			ENSG00000141404	ENSG00000141404			4388	protein-coding gene	gene with protein product		139312				1302014	Standard	NM_182978		Approved		uc002kqc.3	P38405	OTTHUMG00000131660	ENST00000423027.3:c.1011G>A	18.37:g.11880999G>A			B7ZA26|Q86XU3	Silent	SNP	ENST00000423027.3	37	CCDS11852.1																																																																																				0.622	GNAL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254561.2	NM_182978, NM_002071		31	53	31	53
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	179593263	179593263	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr2:179593263C>T	ENST00000591111.1	-	64	18663	c.18439G>A	c.(18439-18441)Gga>Aga	p.G6147R	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.G5220R|TTN_ENST00000589042.1_Missense_Mutation_p.G6464R|TTN_ENST00000460472.2_Intron|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	12931	Ig-like 42.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTACTGCTTCCGAAGTCATTT	0.398																																																0													63.0	56.0	59.0					2																	179593263		1898	4132	6030	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.18439G>A	2.37:g.179593263C>T	ENSP00000465570:p.Gly6147Arg		A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	11.94	1.789115	0.31685	.	.	ENSG00000155657	ENST00000342992	T	0.74737	-0.87	5.63	5.63	0.86233	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.91885	0.7431	H	0.98089	4.145	0.80722	D	1	D	0.89917	1.0	D	0.70016	0.967	D	0.94220	0.7466	9	0.87932	D	0	.	20.0572	0.97657	0.0:1.0:0.0:0.0	.	6147	Q8WZ42	TITIN_HUMAN	R	5220	ENSP00000343764:G5220R	ENSP00000343764:G5220R	G	-	1	0	TTN	179301508	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.507000	0.60434	2.826000	0.97356	0.655000	0.94253	GGA		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		5	15	5	15
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			35	54	35	54
EIF4A2	1974	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	186501406	186501406	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr3:186501406G>T	ENST00000323963.5	+	1	71	c.7G>T	c.(7-9)Ggt>Tgt	p.G3C	EIF4A2_ENST00000356531.5_5'UTR|RP11-573D15.9_ENST00000577781.1_RNA|SNORA63_ENST00000363548.1_RNA|SNORD2_ENST00000459163.1_RNA|EIF4A2_ENST00000440191.2_Missense_Mutation_p.G3C			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	3					cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|urinary_tract(1)	28	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)		GATCATGTCTGGTGGCTCCGC	0.572			T	BCL6	NHL																																		Dom	yes		3	3q27.3	1974	"""eukaryotic translation initiation factor 4A, isoform 2"""		L	0													141.0	143.0	143.0					3																	186501406		2203	4300	6503	SO:0001583	missense	1974			D30655	CCDS3282.1	3q28	2012-02-23	2010-02-10		ENSG00000156976	ENSG00000156976	3.6.1.1	"""DEAD-boxes"""	3284	protein-coding gene	gene with protein product		601102	"""eukaryotic translation initiation factor 4A, isoform 2"""	EIF4F		8521730	Standard	NM_001967		Approved	DDX2B, EIF4A, BM-010	uc003fqs.3	Q14240	OTTHUMG00000156564	ENST00000323963.5:c.7G>T	3.37:g.186501406G>T	ENSP00000326381:p.Gly3Cys		D3DNU9|Q53XJ6|Q96B90|Q96EA8	Missense_Mutation	SNP	ENST00000323963.5	37	CCDS3282.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.406533	0.62399	.	.	ENSG00000156976	ENST00000441007;ENST00000445596;ENST00000323963;ENST00000440191	T;T;T	0.32988	1.43;1.61;1.61	4.48	4.48	0.54585	.	0.632453	0.16522	N	0.210774	T	0.23014	0.0556	L	0.29908	0.895	0.80722	D	1	B;P	0.45348	0.329;0.856	B;B	0.36418	0.224;0.219	T	0.13361	-1.0512	10	0.72032	D	0.01	-22.682	15.0416	0.71796	0.0:0.0:1.0:0.0	.	3;3	Q14240-2;Q14240	.;IF4A2_HUMAN	C	3	ENSP00000415878:G3C;ENSP00000326381:G3C;ENSP00000398370:G3C	ENSP00000326381:G3C	G	+	1	0	EIF4A2	187984100	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.578000	0.74032	2.475000	0.83589	0.563000	0.77884	GGT		0.572	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967		59	100	59	100
BBS7	55212	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	122756377	122756377	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr4:122756377G>T	ENST00000264499.4	-	14	1616	c.1433C>A	c.(1432-1434)cCc>cAc	p.P478H	BBS7_ENST00000506636.1_Missense_Mutation_p.P478H	NM_176824.2	NP_789794.1	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7	478					brain development (GO:0007420)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|digestive tract morphogenesis (GO:0048546)|eye development (GO:0001654)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|limb development (GO:0060173)|melanosome transport (GO:0032402)|nonmotile primary cilium assembly (GO:0035058)|palate development (GO:0060021)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|visual perception (GO:0007601)	axoneme (GO:0005930)|BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						ACAGGTTTTGGGTTGAATTCT	0.393									Bardet-Biedl syndrome																																							0													224.0	205.0	211.0					4																	122756377		2203	4300	6503	SO:0001583	missense	55212	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AF521644	CCDS3724.1, CCDS54799.1	4q27	2013-01-08			ENSG00000138686	ENSG00000138686			18758	protein-coding gene	gene with protein product		607590					Standard	NM_176824		Approved	FLJ10715, BBS2L1	uc003ied.3	Q8IWZ6	OTTHUMG00000133076	ENST00000264499.4:c.1433C>A	4.37:g.122756377G>T	ENSP00000264499:p.Pro478His		Q4W5P8|Q8N581|Q9NVI4	Missense_Mutation	SNP	ENST00000264499.4	37	CCDS3724.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.808853	0.90707	.	.	ENSG00000138686	ENST00000264499;ENST00000506636	D;D	0.97016	-4.21;-4.18	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.98457	0.9486	M	0.89287	3.02	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99383	1.0923	10	0.87932	D	0	-8.5228	19.2795	0.94046	0.0:0.0:1.0:0.0	.	478	Q8IWZ6	BBS7_HUMAN	H	478	ENSP00000264499:P478H;ENSP00000423626:P478H	ENSP00000264499:P478H	P	-	2	0	BBS7	122975827	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	9.748000	0.98867	2.549000	0.85964	0.650000	0.86243	CCC		0.393	BBS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256716.1			18	47	18	47
ROPN1L	83853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	10461352	10461352	+	Silent	SNP	C	C	T	rs539286998		TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr5:10461352C>T	ENST00000503804.1	+	5	995	c.474C>T	c.(472-474)ggC>ggT	p.G158G	ROPN1L_ENST00000274134.4_Silent_p.G158G|ROPN1L_ENST00000510520.1_3'UTR			Q96C74	ROP1L_HUMAN	rhophilin associated tail protein 1-like	158					epithelial cilium movement (GO:0003351)|regulation of protein phosphorylation (GO:0001932)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)	14						ATCCGGAGGGCGGGCCCGCTC	0.567													C|||	1	0.000199681	0.0	0.0	5008	,	,		17318	0.0		0.0	False		,,,				2504	0.001															0													104.0	93.0	96.0					5																	10461352		2203	4300	6503	SO:0001819	synonymous_variant	83853			AF239723	CCDS3879.1	5p15	2011-01-20	2011-01-20		ENSG00000145491	ENSG00000145491			24060	protein-coding gene	gene with protein product	"""radial spoke head 11 homolog (Chlamydomonas)"""	611756	"""ropporin 1-like"""			11278869	Standard	NM_031916		Approved	ASP, FLJ25776, RSPH11	uc021xwo.1	Q96C74	OTTHUMG00000090507	ENST00000503804.1:c.474C>T	5.37:g.10461352C>T			D3DTC9|Q9BZX0	Silent	SNP	ENST00000503804.1	37	CCDS3879.1																																																																																				0.567	ROPN1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367033.1	NM_031916		60	99	60	99
SIM1	6492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	100911318	100911318	+	Silent	SNP	C	C	T			TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr6:100911318C>T	ENST00000369208.3	-	2	809	c.27G>A	c.(25-27)gcG>gcA	p.A9A	SIM1_ENST00000262901.4_Silent_p.A9A			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	9	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		TCCTAGTCCGCGCAGCATTTT	0.423																																																0													232.0	239.0	237.0					6																	100911318		2203	4300	6503	SO:0001819	synonymous_variant	6492			U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"""Basic helix-loop-helix proteins"""	10882	protein-coding gene	gene with protein product		603128	"""single-minded (Drosophila) homolog 1"", ""single-minded homolog 1 (Drosophila)"""			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.27G>A	6.37:g.100911318C>T			Q5TDP7	Silent	SNP	ENST00000369208.3	37	CCDS5045.1																																																																																				0.423	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068		32	162	32	162
OPHN1	4983	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	67414334	67414334	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chrX:67414334G>C	ENST00000355520.5	-	13	1752	c.1111C>G	c.(1111-1113)Cac>Gac	p.H371D	OPHN1_ENST00000540071.1_Missense_Mutation_p.H371D	NM_002547.2	NP_002538.1	O60890	OPHN1_HUMAN	oligophrenin 1	371					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|negative regulation of proteasomal protein catabolic process (GO:1901799)|nervous system development (GO:0007399)|regulation of endocytosis (GO:0030100)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of synaptic transmission, glutamatergic (GO:0051966)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|substrate-dependent cell migration, cell extension (GO:0006930)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|terminal bouton (GO:0043195)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|skin(2)	31						ATAGGGCTGTGGTAGATCTAC	0.348																																																0													142.0	121.0	128.0					X																	67414334		2203	4300	6503	SO:0001583	missense	4983			AJ001189	CCDS14388.1	Xq12	2011-07-04			ENSG00000079482	ENSG00000079482		"""Rho GTPase activating proteins"""	8148	protein-coding gene	gene with protein product		300127	"""mental retardation, X-linked 60"""	MRX60		9195162, 9582072	Standard	NM_002547		Approved	OPN1, ARHGAP41	uc004dww.4	O60890	OTTHUMG00000021744	ENST00000355520.5:c.1111C>G	X.37:g.67414334G>C	ENSP00000347710:p.His371Asp		B9EIP8|Q5JQ81|Q6PCC1|Q8WX47	Missense_Mutation	SNP	ENST00000355520.5	37	CCDS14388.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.591471	0.46214	.	.	ENSG00000079482	ENST00000355520;ENST00000540071	T;T	0.05855	3.38;3.39	4.98	4.98	0.66077	Rho GTPase-activating protein domain (1);	0.048272	0.85682	D	0.000000	T	0.10294	0.0252	L	0.40543	1.245	0.49389	D	0.999788	P;D	0.61080	0.718;0.989	B;P	0.50970	0.201;0.655	T	0.31280	-0.9949	10	0.21014	T	0.42	.	14.8163	0.70036	0.0:0.0:1.0:0.0	.	371;371	F5H2E3;O60890	.;OPHN1_HUMAN	D	371	ENSP00000347710:H371D;ENSP00000438617:H371D	ENSP00000347710:H371D	H	-	1	0	OPHN1	67331059	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.307000	0.72815	2.471000	0.83476	0.597000	0.82753	CAC		0.348	OPHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057011.1	NM_002547		19	28	19	28
IRS4	8471	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	107979043	107979043	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chrX:107979043C>G	ENST00000372129.2	-	1	608	c.532G>C	c.(532-534)Gcg>Ccg	p.A178P	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	178	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GCCACCATCGCGAAGTATTCG	0.612																																																0													68.0	56.0	60.0					X																	107979043		2203	4300	6503	SO:0001583	missense	8471			AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.532G>C	X.37:g.107979043C>G	ENSP00000361202:p.Ala178Pro			Missense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	C	17.68	3.448546	0.63178	.	.	ENSG00000133124	ENST00000372129	T	0.72282	-0.64	4.16	4.16	0.48862	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.071102	0.53938	D	0.000043	D	0.83834	0.5340	M	0.78049	2.395	0.54753	D	0.999986	D	0.89917	1.0	D	0.97110	1.0	D	0.86711	0.1936	10	0.72032	D	0.01	-10.7364	15.9303	0.79654	0.0:1.0:0.0:0.0	.	178	O14654	IRS4_HUMAN	P	178	ENSP00000361202:A178P	ENSP00000361202:A178P	A	-	1	0	IRS4	107865699	1.000000	0.71417	0.975000	0.42487	0.988000	0.76386	7.525000	0.81892	1.920000	0.55613	0.600000	0.82982	GCG		0.612	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		30	75	30	75
TENM1	10178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	123518058	123518058	+	Silent	SNP	C	C	T	rs201176122		TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chrX:123518058C>T	ENST00000371130.3	-	29	6765	c.6702G>A	c.(6700-6702)ctG>ctA	p.L2234L	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Silent_p.L2241L	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2234					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										AGGCTTTCTGCAGCAGGCCAT	0.458													C|||	4	0.0010596	0.0	0.0	3775	,	,		15694	0.004		0.0	False		,,,				2504	0.0															0													52.0	50.0	51.0					X																	123518058		2203	4300	6503	SO:0001819	synonymous_variant	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.6702G>A	X.37:g.123518058C>T			B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																				0.458	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		47	67	47	67
RENBP	5973	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	153208518	153208518	+	Missense_Mutation	SNP	T	T	G			TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chrX:153208518T>G	ENST00000393700.3	-	6	556	c.476A>C	c.(475-477)gAg>gCg	p.E159A	RENBP_ENST00000462086.1_5'UTR|RENBP_ENST00000412763.1_Missense_Mutation_p.E159A|RENBP_ENST00000369997.3_Missense_Mutation_p.E145A	NM_002910.5	NP_002901.2	P51606	RENBP_HUMAN	renin binding protein	159					N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)|regulation of blood pressure (GO:0008217)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|endopeptidase inhibitor activity (GO:0004866)|N-acylglucosamine 2-epimerase activity (GO:0050121)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				N-Acetyl-D-glucosamine(DB00141)	ATCCATCATCTCCACCGCTTC	0.711																																																0													15.0	12.0	13.0					X																	153208518		2190	4281	6471	SO:0001583	missense	5973				CCDS14738.2	Xq28	2013-09-23	2001-11-28		ENSG00000102032	ENSG00000102032			9959	protein-coding gene	gene with protein product	"""N-acylglucosamine 2-epimerase"", ""GlcNAc 2-epimerase"", ""N-acetyl-D-glucosamine 2-epimerase"""	312420	"""renin-binding protein"""			1618798	Standard	NM_002910		Approved	RNBP, RBP	uc004fjo.2	P51606	OTTHUMG00000024224	ENST00000393700.3:c.476A>C	X.37:g.153208518T>G	ENSP00000377303:p.Glu159Ala		B4DNZ3|Q96BI6	Missense_Mutation	SNP	ENST00000393700.3	37	CCDS14738.2	.	.	.	.	.	.	.	.	.	.	T	7.451	0.642716	0.14451	.	.	ENSG00000102032	ENST00000393700;ENST00000412763;ENST00000369997	T;T;T	0.32988	1.51;1.43;1.51	3.92	1.35	0.21983	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	0.473921	0.22547	U	0.058655	T	0.24586	0.0596	L	0.58669	1.825	0.25995	N	0.982192	B;B	0.23990	0.051;0.095	B;B	0.23574	0.023;0.047	T	0.17319	-1.0373	10	0.33141	T	0.24	-8.1491	4.9509	0.14013	0.0:0.1069:0.3541:0.539	.	159;159	P51606-2;P51606	.;RENBP_HUMAN	A	159;159;145	ENSP00000377303:E159A;ENSP00000387811:E159A;ENSP00000359014:E145A	ENSP00000359014:E145A	E	-	2	0	RENBP	152861712	0.972000	0.33761	0.195000	0.23364	0.190000	0.23558	1.204000	0.32296	0.002000	0.14630	0.153000	0.16174	GAG		0.711	RENBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061103.3	NM_002910		21	20	21	20
SYNE1	23345	broad.mit.edu;ucsc.edu	37	6	152485384	152485384	+	Missense_Mutation	SNP	C	C	T	rs372990463		TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr6:152485384C>T	ENST00000367255.5	-	131	24305	c.23704G>A	c.(23704-23706)Gct>Act	p.A7902T	SYNE1_ENST00000356820.4_Missense_Mutation_p.A2426T|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000448038.1_Missense_Mutation_p.A7831T|SYNE1_ENST00000354674.4_Missense_Mutation_p.A57T|SYNE1_ENST00000341594.5_Missense_Mutation_p.A7514T|SYNE1_ENST00000539504.1_Missense_Mutation_p.A57T|SYNE1_ENST00000265368.4_Missense_Mutation_p.A7902T|SYNE1_ENST00000423061.1_Missense_Mutation_p.A7831T	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7902					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCGATGTGAGCGAGCCAGGTC	0.502										HNSCC(10;0.0054)																																						0								C	THR/ALA,THR/ALA	0,4406		0,0,2203	103.0	92.0	96.0		23491,23704	3.4	1.0	6		96	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	SYNE1	NM_033071.3,NM_182961.3	58,58	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging	7831/8750,7902/8798	152485384	2,13004	2203	4300	6503	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.23704G>A	6.37:g.152485384C>T	ENSP00000356224:p.Ala7902Thr		E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	20.5	3.998983	0.74818	0.0	2.33E-4	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79;0.79	5.26	3.37	0.38596	.	0.252994	0.27549	N	0.018862	T	0.36744	0.0978	N	0.22421	0.69	0.42346	D	0.992356	D;D;D;D;P	0.71674	0.985;0.998;0.998;0.998;0.896	P;D;P;D;B	0.64321	0.821;0.924;0.876;0.924;0.378	T	0.34976	-0.9807	10	0.56958	D	0.05	.	9.5516	0.39313	0.142:0.7837:0.0:0.0743	.	7902;7902;7831;7831;104	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	T	7902;57;548;7831;7902;7831;7514;2426;64;59;824;57	ENSP00000356224:A7902T;ENSP00000441052:A57T;ENSP00000356226:A548T;ENSP00000396024:A7831T;ENSP00000265368:A7902T;ENSP00000390975:A7831T;ENSP00000341887:A7514T;ENSP00000349276:A2426T;ENSP00000356220:A824T;ENSP00000346701:A57T	ENSP00000265368:A7902T	A	-	1	0	SYNE1	152527077	0.775000	0.28604	0.965000	0.40720	0.856000	0.48823	1.510000	0.35790	1.219000	0.43474	-0.225000	0.12378	GCT		0.502	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		57	25	57	25
IL36B	27177	broad.mit.edu;ucsc.edu	37	2	113788702	113788702	+	Missense_Mutation	SNP	C	C	T	rs199927949		TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr2:113788702C>T	ENST00000259213.4	-	3	151	c.44G>A	c.(43-45)cGt>cAt	p.R15H	IL36B_ENST00000327407.2_Missense_Mutation_p.R15H	NM_014438.3	NP_055253.2	Q9NZH7	IL36B_HUMAN	interleukin 36, beta	15					immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-1 receptor binding (GO:0005149)			kidney(1)|ovary(1)|pancreas(1)	3						TCGAGAATCACGAATAGCATA	0.478																																																0													110.0	99.0	102.0					2																	113788702		2203	4300	6503	SO:0001583	missense	27177			AF201833	CCDS2109.1, CCDS2110.1	2q14	2011-07-14	2011-06-06	2011-06-06	ENSG00000136696	ENSG00000136696		"""Interleukins and interleukin receptors"""	15564	protein-coding gene	gene with protein product		605508	"""interleukin 1 family, member 8 (eta)"""	IL1F8		10625660, 10512743, 16646978	Standard	NM_173178		Approved	FIL1, IL-1H2, IL-1F8, FILI-(ETA), IL1-ETA, IL1H2, MGC126880, MGC126882	uc002tiq.1	Q9NZH7	OTTHUMG00000131338	ENST00000259213.4:c.44G>A	2.37:g.113788702C>T	ENSP00000259213:p.Arg15His		Q3MIH0|Q53SR6|Q7RTZ7|Q9UHA5	Missense_Mutation	SNP	ENST00000259213.4	37	CCDS2109.1	.	.	.	.	.	.	.	.	.	.	c	3.068	-0.191760	0.06299	.	.	ENSG00000136696	ENST00000259213;ENST00000327407	T;T	0.18174	2.23;2.23	3.21	-0.271	0.12922	.	0.697553	0.13089	N	0.414654	T	0.06962	0.0177	N	0.21194	0.64	0.09310	N	1	B;B	0.32051	0.009;0.354	B;B	0.26770	0.012;0.073	T	0.32955	-0.9887	10	0.11794	T	0.64	.	2.1127	0.03707	0.2502:0.4051:0.0:0.3447	.	15;15	Q9NZH7-2;Q9NZH7	.;IL36B_HUMAN	H	15	ENSP00000259213:R15H;ENSP00000328420:R15H	ENSP00000259213:R15H	R	-	2	0	IL36B	113505173	0.000000	0.05858	0.066000	0.19879	0.076000	0.17211	-0.726000	0.04936	0.156000	0.19299	0.506000	0.49869	CGT		0.478	IL36B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254110.1	NM_014438		17	43	17	43
TP53	7157	broad.mit.edu;hgsc.bcm.edu	37	17	7578471	7578471	+	Frame_Shift_Del	DEL	G	G	-	rs137852790|rs137852791|rs72661116		TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chr17:7578471delG	ENST00000269305.4	-	5	648	c.459delC	c.(457-459)cccfs	p.P153fs	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Frame_Shift_Del_p.P153fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.P153fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.P153fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.P153fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.P153fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	153	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		P -> A (in sporadic cancers; somatic mutation).|P -> F (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|P -> H (in a sporadic cancer; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> R (in a sporadic cancer; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.P153P(7)|p.T150fs*16(6)|p.?(5)|p.P152fs*14(5)|p.P153fs*26(2)|p.G154fs*27(2)|p.P153fs*22(2)|p.D148_T155delDSTPPPGT(1)|p.Q144_G154del11(1)|p.P151_V173del23(1)|p.P153_G154insX(1)|p.D148fs*23(1)|p.T150_P153delTPPP(1)|p.T18fs*16(1)|p.Q144fs*16(1)|p.S149fs*72(1)|p.T57fs*16(1)|p.P152fs*27(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CGCGGGTGCCGGGCGGGGGTG	0.612		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	48	Deletion - Frameshift(21)|Whole gene deletion(8)|Substitution - coding silent(7)|Unknown(5)|Deletion - In frame(4)|Insertion - Frameshift(2)|Insertion - In frame(1)	skin(8)|ovary(7)|upper_aerodigestive_tract(5)|stomach(4)|breast(4)|bone(4)|central_nervous_system(3)|urinary_tract(3)|oesophagus(3)|haematopoietic_and_lymphoid_tissue(2)|lung(2)|large_intestine(1)|soft_tissue(1)|liver(1)											50.0	51.0	51.0					17																	7578471		2203	4300	6503	SO:0001589	frameshift_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.459delC	17.37:g.7578471delG	ENSP00000269305:p.Pro153fs		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	37	CCDS11118.1																																																																																				0.612	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		70	28	70	28
ATRX	546	broad.mit.edu;hgsc.bcm.edu	37	X	76813062	76813063	+	Frame_Shift_Ins	INS	-	-	AG			TCGA-HT-8108-01A-11D-2395-08	TCGA-HT-8108-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83398327-b05a-4e54-ae4b-1cffc6bde4da	657f8664-082c-411b-92f1-2e5e82ad5bd5	g.chrX:76813062_76813063insAG	ENST00000373344.5	-	30	6772_6773	c.6558_6559insCT	c.(6556-6561)tcttttfs	p.F2187fs	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Ins_p.F2149fs	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2187	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Interaction with MECP2.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						ACAACTCGAAAAGACAGTGACT	0.347			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)																																								SO:0001589	frameshift_variant	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.6557_6558dupCT	X.37:g.76813063_76813064dupAG	ENSP00000362441:p.Phe2187fs		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Ins	INS	ENST00000373344.5	37	CCDS14434.1																																																																																				0.347	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		65	101	65	101
