#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
SESN3	143686	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	94923103	94923103	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr11:94923103G>A	ENST00000536441.1	-	4	701	c.365C>T	c.(364-366)tCt>tTt	p.S122F	SESN3_ENST00000393234.1_Missense_Mutation_p.S122F|SESN3_ENST00000278499.2_Intron|SESN3_ENST00000537480.1_5'Flank|RP11-712B9.2_ENST00000534864.1_RNA|RP11-712B9.2_ENST00000534891.1_RNA|SESN3_ENST00000416495.2_Missense_Mutation_p.S122F	NM_001271594.1|NM_144665.2	NP_001258523.1|NP_653266.2	P58005	SESN3_HUMAN	sestrin 3	122					glucose homeostasis (GO:0042593)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)|response to insulin (GO:0032868)	nucleus (GO:0005634)				endometrium(5)|large_intestine(6)|lung(3)|skin(1)|stomach(1)	16		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.234)		TATTAAGTAAGAACACTGATG	0.328																																																0													61.0	60.0	61.0					11																	94923103		2201	4297	6498	SO:0001583	missense	143686			AK096300	CCDS8303.1, CCDS60938.1	11q21	2005-09-18			ENSG00000149212	ENSG00000149212			23060	protein-coding gene	gene with protein product		607768				12607115	Standard	NM_144665		Approved	SEST3, MGC29667	uc001pfj.4	P58005	OTTHUMG00000167829	ENST00000536441.1:c.365C>T	11.37:g.94923103G>A	ENSP00000441927:p.Ser122Phe		B7Z7P9|Q96AD1	Missense_Mutation	SNP	ENST00000536441.1	37	CCDS8303.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.200809	0.79015	.	.	ENSG00000149212	ENST00000536441;ENST00000393234;ENST00000416495	T;T;T	0.26957	1.7;1.7;1.7	5.78	5.78	0.91487	.	0.131822	0.52532	D	0.000076	T	0.50274	0.1606	M	0.84433	2.695	0.58432	D	0.999994	D;P	0.61080	0.989;0.918	P;P	0.58873	0.847;0.815	T	0.54931	-0.8219	10	0.62326	D	0.03	-2.6324	13.25	0.60045	0.0724:0.0:0.9276:0.0	.	122;122	P58005-3;P58005	.;SESN3_HUMAN	F	122	ENSP00000441927:S122F;ENSP00000376926:S122F;ENSP00000407008:S122F	ENSP00000376926:S122F	S	-	2	0	SESN3	94562751	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.438000	0.80431	2.722000	0.93159	0.563000	0.77884	TCT		0.328	SESN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396475.3	NM_144665		20	61	20	61
LIMA1	51474	hgsc.bcm.edu;broad.mit.edu	37	12	50586281	50586281	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr12:50586281G>A	ENST00000341247.4	-	9	1243	c.1094C>T	c.(1093-1095)tCc>tTc	p.S365F	LIMA1_ENST00000547825.1_Missense_Mutation_p.S63F|LIMA1_ENST00000552008.1_5'UTR|RP3-405J10.3_ENST00000552061.1_RNA|LIMA1_ENST00000552491.1_Missense_Mutation_p.S63F|LIMA1_ENST00000552909.1_Missense_Mutation_p.S205F|LIMA1_ENST00000552823.1_Missense_Mutation_p.S205F|LIMA1_ENST00000552783.1_Missense_Mutation_p.S206F|LIMA1_ENST00000394943.3_Missense_Mutation_p.S366F	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	365					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						GGAGGCTCTGGAATCTGGACT	0.458																																																0													152.0	141.0	145.0					12																	50586281		2203	4300	6503	SO:0001583	missense	51474			AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"""epithelial protein lost in neoplasm beta"""	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.1094C>T	12.37:g.50586281G>A	ENSP00000340184:p.Ser365Phe		B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	G	16.22	3.060461	0.55432	.	.	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	T;T;D;D;T;D;D	0.85702	-1.25;-1.24;-1.59;-2.02;-1.29;-1.59;-1.59	5.44	5.44	0.79542	.	0.376460	0.30210	N	0.010143	T	0.80369	0.4610	N	0.19112	0.55	0.34271	D	0.681039	P;P;P	0.42123	0.771;0.472;0.654	B;B;B	0.43575	0.424;0.26;0.404	D	0.86533	0.1823	10	0.66056	D	0.02	-7.6932	17.6257	0.88093	0.0:0.0:1.0:0.0	.	375;365;205	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	F	63;63;205;366;365;206;205;284	ENSP00000448463:S63F;ENSP00000448706:S63F;ENSP00000450266:S205F;ENSP00000378400:S366F;ENSP00000340184:S365F;ENSP00000448779:S206F;ENSP00000450087:S205F	ENSP00000340184:S365F	S	-	2	0	LIMA1	48872548	1.000000	0.71417	1.000000	0.80357	0.510000	0.34073	3.885000	0.56182	2.832000	0.97577	0.655000	0.94253	TCC		0.458	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		8	107	8	107
TMEM132D	121256	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	130185090	130185090	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr12:130185090C>T	ENST00000422113.2	-	2	559	c.233G>A	c.(232-234)cGg>cAg	p.R78Q	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	78					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TGACTCCACCCGGGACTGCAG	0.547																																																0													60.0	56.0	58.0					12																	130185090		2203	4300	6503	SO:0001583	missense	121256			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.233G>A	12.37:g.130185090C>T	ENSP00000408581:p.Arg78Gln		Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.919068	0.92249	.	.	ENSG00000151952	ENST00000422113	T	0.16897	2.31	5.33	5.33	0.75918	.	0.000000	0.56097	D	0.000030	T	0.44498	0.1296	M	0.75884	2.315	0.36095	D	0.84371	D	0.89917	1.0	D	0.77557	0.99	T	0.52026	-0.8630	9	.	.	.	-42.2379	19.0288	0.92946	0.0:1.0:0.0:0.0	.	78	Q14C87	T132D_HUMAN	Q	78	ENSP00000408581:R78Q	.	R	-	2	0	TMEM132D	128751043	0.999000	0.42202	0.931000	0.37212	0.983000	0.72400	5.910000	0.69931	2.472000	0.83506	0.555000	0.69702	CGG		0.547	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		27	64	27	64
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	rs28934576		TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr17:7577120C>T	ENST00000269305.4	-	8	1007	c.818G>A	c.(817-819)cGt>cAt	p.R273H	TP53_ENST00000359597.4_Missense_Mutation_p.R273H|TP53_ENST00000455263.2_Missense_Mutation_p.R273H|TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.R273H|TP53_ENST00000445888.2_Missense_Mutation_p.R273H	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	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		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.R273H(521)|p.R273L(93)|p.R273P(32)|p.0?(8)|p.?(2)|p.R273fs*32(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273S(1)|p.E258fs*71(1)|p.R273fs*72(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.R273fs*33(1)|p.E271_R273delEVR(1)|p.V272_K292del21(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)	GGCACAAACACGCACCTCAAA	0.542	R273H(EN_ENDOMETRIUM)|R273H(HEC59_ENDOMETRIUM)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(MDAMB468_BREAST)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(NCIH1155_LUNG)|R273H(NCIH1793_LUNG)|R273H(NCIH1975_LUNG)|R273H(NCIH2405_LUNG)|R273H(NCIH508_LARGE_INTESTINE)|R273H(OC314_OVARY)|R273H(PANC1_PANCREAS)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SKMEL30_SKIN)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SUIT2_PANCREAS)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(SW480_LARGE_INTESTINE)|R273H(SW620_LARGE_INTESTINE)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)	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)			C|||	1	0.000199681	0.0	0.0	5008	,	,		18620	0.0		0.001	False		,,,				2504	0.0				Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	669	Substitution - Missense(647)|Whole gene deletion(8)|Deletion - Frameshift(6)|Deletion - In frame(5)|Unknown(2)|Insertion - Frameshift(1)	large_intestine(136)|lung(99)|breast(74)|ovary(59)|upper_aerodigestive_tract(55)|central_nervous_system(46)|oesophagus(35)|haematopoietic_and_lymphoid_tissue(30)|stomach(26)|urinary_tract(25)|pancreas(15)|endometrium(13)|liver(12)|skin(11)|bone(9)|biliary_tract(7)|penis(4)|cervix(2)|genital_tract(2)|NS(2)|soft_tissue(2)|vulva(1)|thyroid(1)|fallopian_tube(1)|prostate(1)|thymus(1)	GRCh37	CM004342|CM010472|CM920677	TP53	M	rs28934576						67.0	58.0	61.0					17																	7577120		2203	4300	6503	SO:0001583	missense	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.818G>A	17.37:g.7577120C>T	ENSP00000269305:p.Arg273His		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	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.03	3.532510	0.64972	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99868	-7.32;-7.32;-7.32;-7.32;-7.32;-7.32	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.79475	2.455	0.80722	A	1	P;D;P;P	0.89917	0.631;1.0;0.831;0.48	B;D;P;B	0.77004	0.274;0.989;0.516;0.242	D	0.96531	0.9393	9	0.72032	D	0.01	-11.9995	15.662	0.77193	0.0:1.0:0.0:0.0	rs28934576	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	H	273;273;273;273;273;262;141	ENSP00000352610:R273H;ENSP00000269305:R273H;ENSP00000398846:R273H;ENSP00000391127:R273H;ENSP00000391478:R273H;ENSP00000425104:R141H	ENSP00000269305:R273H	R	-	2	0	TP53	7517845	1.000000	0.71417	0.068000	0.19968	0.665000	0.39181	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		35	11	35	11
PPP1R12C	54776	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	55607493	55607493	+	Missense_Mutation	SNP	G	G	C			TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr19:55607493G>C	ENST00000263433.3	-	8	1094	c.1079C>G	c.(1078-1080)tCc>tGc	p.S360C	PPP1R12C_ENST00000435544.2_Missense_Mutation_p.S286C|PPP1R12C_ENST00000376393.2_Missense_Mutation_p.S360C	NM_001271618.1|NM_017607.2	NP_001258547.1|NP_060077.1			protein phosphatase 1, regulatory subunit 12C											central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	22			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		GCGCTCCTTGGACAAGTCCTG	0.657																																																0													46.0	56.0	52.0					19																	55607493		2203	4300	6503	SO:0001583	missense	54776			AF312028	CCDS12916.1	19q13.42	2013-01-10	2011-10-04		ENSG00000125503	ENSG00000125503		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14947	protein-coding gene	gene with protein product	"""myosin-binding subunit 85"""	613245	"""leukocyte receptor cluster (LRC) member 3"", ""protein phosphatase 1, regulatory (inhibitor) subunit 12C"""	LENG3		11399775	Standard	NM_017607		Approved	DKFZP434D0412, p84, MBS85, p85	uc002qix.4	Q9BZL4		ENST00000263433.3:c.1079C>G	19.37:g.55607493G>C	ENSP00000263433:p.Ser360Cys			Missense_Mutation	SNP	ENST00000263433.3	37	CCDS12916.1	.	.	.	.	.	.	.	.	.	.	G	18.78	3.696495	0.68386	.	.	ENSG00000125503	ENST00000263433;ENST00000376393;ENST00000435544	T;T;T	0.70045	-0.26;-0.28;-0.45	4.59	4.59	0.56863	.	0.165523	0.40469	N	0.001092	T	0.78387	0.4275	L	0.58101	1.795	0.42093	D	0.991307	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.80764	0.987;0.994;0.987	T	0.80569	-0.1324	10	0.59425	D	0.04	.	15.2754	0.73737	0.0:0.0:1.0:0.0	.	286;360;360	B4DME2;Q9BZL4-3;Q9BZL4	.;.;PP12C_HUMAN	C	360;360;286	ENSP00000263433:S360C;ENSP00000365573:S360C;ENSP00000387833:S286C	ENSP00000263433:S360C	S	-	2	0	PPP1R12C	60299305	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.479000	0.45197	2.261000	0.74972	0.655000	0.94253	TCC		0.657	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607		14	83	14	83
SLC30A2	7780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	26371659	26371659	+	Missense_Mutation	SNP	G	G	C			TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr1:26371659G>C	ENST00000374278.3	-	2	316	c.100C>G	c.(100-102)Ccc>Gcc	p.P34A	SLC30A2_ENST00000498060.1_5'UTR|SLC30A2_ENST00000374276.3_Missense_Mutation_p.P34A	NM_032513.3	NP_115902.1	Q9BRI3	ZNT2_HUMAN	solute carrier family 30 (zinc transporter), member 2	34					positive regulation of sequestering of zinc ion (GO:0061090)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)	cation transmembrane transporter activity (GO:0008324)			cervix(1)|endometrium(2)|kidney(1)|lung(8)|stomach(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.09e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00614)|READ - Rectum adenocarcinoma(331;0.0649)		CCAGGTCGGGGCAGAGGAATC	0.597																																																0													60.0	59.0	59.0					1																	26371659		2203	4300	6503	SO:0001583	missense	7780			AK023491	CCDS272.1, CCDS30644.1	1p35.3	2013-05-22			ENSG00000158014	ENSG00000158014		"""Solute carriers"""	11013	protein-coding gene	gene with protein product		609617		ZNT2			Standard	NM_001004434		Approved		uc001blg.1	Q9BRI3	OTTHUMG00000007508	ENST00000374278.3:c.100C>G	1.37:g.26371659G>C	ENSP00000363396:p.Pro34Ala		Q71RC8	Missense_Mutation	SNP	ENST00000374278.3	37	CCDS272.1	.	.	.	.	.	.	.	.	.	.	G	11.89	1.772996	0.31411	.	.	ENSG00000158014	ENST00000374278;ENST00000374276	T;T	0.65364	0.49;-0.15	5.73	-0.762	0.11034	.	0.998365	0.08109	N	0.996527	T	0.47432	0.1445	L	0.44542	1.39	0.09310	N	1	B;B	0.15719	0.007;0.014	B;B	0.15052	0.005;0.012	T	0.28235	-1.0050	10	0.12766	T	0.61	-0.7149	6.0839	0.19956	0.4871:0.1374:0.3754:0.0	.	34;34	Q9BRI3;Q9BRI3-2	ZNT2_HUMAN;.	A	34	ENSP00000363396:P34A;ENSP00000363394:P34A	ENSP00000363394:P34A	P	-	1	0	SLC30A2	26244246	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.118000	0.15605	-0.433000	0.07286	-0.812000	0.03155	CCC		0.597	SLC30A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019742.1	NM_032513		24	50	24	50
ROR1	4919	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	64515592	64515592	+	Silent	SNP	C	C	T	rs148616064		TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr1:64515592C>T	ENST00000371079.1	+	3	768	c.393C>T	c.(391-393)tgC>tgT	p.C131C	ROR1_ENST00000371080.1_Silent_p.C131C|ROR1_ENST00000482426.1_3'UTR	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	131	Ig-like C2-type.				peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						ACTTCCAGTGCGTGGCAACAA	0.567																																																0								C	,	0,4406		0,0,2203	101.0	106.0	104.0		393,393	-5.4	1.0	1	dbSNP_134	104	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous	ROR1	NM_001083592.1,NM_005012.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	131/394,131/938	64515592	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4919			M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"""Immunoglobulin superfamily / I-set domain containing"""	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.393C>T	1.37:g.64515592C>T			Q5VVX6|Q66K77|Q92776	Silent	SNP	ENST00000371079.1	37	CCDS626.1																																																																																				0.567	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012		44	81	44	81
HFM1	164045	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	91818120	91818120	+	Silent	SNP	A	A	G			TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr1:91818120A>G	ENST00000370425.3	-	16	2018	c.1920T>C	c.(1918-1920)ttT>ttC	p.F640F	HFM1_ENST00000294696.5_5'UTR|HFM1_ENST00000370424.3_Silent_p.F319F|HFM1_ENST00000462405.1_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	640	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TGTACTCTTCAAACAGTCCTC	0.358																																																0													90.0	84.0	86.0					1																	91818120		1843	4097	5940	SO:0001819	synonymous_variant	164045			AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.1920T>C	1.37:g.91818120A>G			B1B0B6|Q8N9Q0	Silent	SNP	ENST00000370425.3	37	CCDS30769.2																																																																																				0.358	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		19	99	19	99
PGLYRP4	57115	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	153313006	153313006	+	Missense_Mutation	SNP	G	G	C			TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr1:153313006G>C	ENST00000359650.5	-	7	739	c.675C>G	c.(673-675)caC>caG	p.H225Q	PGLYRP4_ENST00000368739.3_Missense_Mutation_p.H221Q	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	225					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			TCCTGGGACAGTGGGTCTCCC	0.602																																																0													64.0	60.0	61.0					1																	153313006		2203	4300	6503	SO:0001583	missense	57115			AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein I beta precursor"""	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.675C>G	1.37:g.153313006G>C	ENSP00000352672:p.His225Gln		A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Missense_Mutation	SNP	ENST00000359650.5	37	CCDS30871.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.996442	0.35226	.	.	ENSG00000163218	ENST00000368739;ENST00000359650	T;T	0.16597	2.33;2.33	3.64	2.71	0.32032	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (3);	0.571592	0.16387	N	0.216626	T	0.10723	0.0262	M	0.76838	2.35	0.28652	N	0.90661	P;P	0.44139	0.6;0.827	B;P	0.46253	0.375;0.509	T	0.13764	-1.0497	10	0.19590	T	0.45	-19.5214	7.3499	0.26684	0.1256:0.0:0.8744:0.0	.	221;225	Q96LB8-2;Q96LB8	.;PGRP4_HUMAN	Q	221;225	ENSP00000357728:H221Q;ENSP00000352672:H225Q	ENSP00000352672:H225Q	H	-	3	2	PGLYRP4	151579630	1.000000	0.71417	0.987000	0.45799	0.702000	0.40608	1.296000	0.33389	0.830000	0.34757	0.655000	0.94253	CAC		0.602	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393		8	88	8	88
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	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			28	72	28	72
RUFY1	80230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	179016595	179016595	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr5:179016595C>T	ENST00000319449.4	+	9	1087	c.1075C>T	c.(1075-1077)Cag>Tag	p.Q359*	RUFY1_ENST00000393438.2_Nonsense_Mutation_p.Q251*|RUFY1_ENST00000377001.2_Missense_Mutation_p.A407V|RUFY1_ENST00000437570.2_Nonsense_Mutation_p.Q251*	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	359					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGAACAGCAGCAGTTAAGAGA	0.353										HNSCC(44;0.11)																																						0													107.0	106.0	106.0					5																	179016595		2203	4300	6503	SO:0001587	stop_gained	80230			AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"""Zinc fingers, FYVE domain containing"""	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.1075C>T	5.37:g.179016595C>T	ENSP00000325594:p.Gln359*		Q59FF3|Q71S93|Q9H6I3	Nonsense_Mutation	SNP	ENST00000319449.4	37	CCDS4445.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.674536|5.674536	0.96764|0.96764	.|.	.|.	ENSG00000176783|ENSG00000176783	ENST00000377001|ENST00000319449;ENST00000437570;ENST00000393438	T|.	0.26810|.	1.71|.	5.09|5.09	5.09|5.09	0.68999|0.68999	.|.	.|0.101111	.|0.64402	.|D	.|0.000001	T|.	0.49355|.	0.1552|.	.|.	.|.	.|.	0.21719|0.21719	N|N	0.999572|0.999572	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.42832|.	-0.9428|.	6|.	0.87932|0.32370	D|T	0|0.25	-22.7344|-22.7344	15.1702|15.1702	0.72865|0.72865	0.0:0.8588:0.1411:0.0|0.0:0.8588:0.1411:0.0	.|.	.|.	.|.	.|.	V|X	407|359;251;251	ENSP00000366200:A407V|.	ENSP00000366200:A407V|ENSP00000325594:Q359X	A|Q	+|+	2|1	0|0	RUFY1|RUFY1	178949201|178949201	1.000000|1.000000	0.71417|0.71417	0.943000|0.943000	0.38184|0.38184	0.891000|0.891000	0.51852|0.51852	3.211000|3.211000	0.51137|0.51137	2.658000|2.658000	0.90341|0.90341	0.549000|0.549000	0.68633|0.68633	GCA|CAG		0.353	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451		25	48	25	48
ARMC2	84071	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	109294621	109294621	+	Silent	SNP	T	T	C	rs534134058		TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr6:109294621T>C	ENST00000392644.4	+	18	2676	c.2508T>C	c.(2506-2508)caT>caC	p.H836H	ARMC2_ENST00000368972.3_Silent_p.H671H	NM_032131.4	NP_115507.4	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	836										endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)	24		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)		ACAAACTCCATTGGGAAACAG	0.393													T|||	0	0.0	0.0	0.0	5008	,	,		17382	0.0		0.0	False		,,,				2504	0.0															0													125.0	124.0	124.0					6																	109294621		2203	4300	6503	SO:0001819	synonymous_variant	84071			BC030603	CCDS5069.2, CCDS69168.1	6q21	2013-02-14			ENSG00000118690	ENSG00000118690		"""Armadillo repeat containing"""	23045	protein-coding gene	gene with protein product							Standard	XM_005267154		Approved	DKFZp434P0714, bA787I22.1	uc003pss.4	Q8NEN0	OTTHUMG00000015335	ENST00000392644.4:c.2508T>C	6.37:g.109294621T>C			A8K8Y4|B4DGF5|G5E993|Q5VVY8|Q9H0K9	Silent	SNP	ENST00000392644.4	37	CCDS5069.2																																																																																				0.393	ARMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041732.2	NM_032131		50	70	50	70
ADAM32	203102	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	39091490	39091490	+	Silent	SNP	G	G	C			TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr8:39091490G>C	ENST00000379907.4	+	16	1834	c.1707G>C	c.(1705-1707)gtG>gtC	p.V569V	ADAM32_ENST00000437682.2_Silent_p.V470V|ADAM32_ENST00000519315.1_Silent_p.V463V	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	569						integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			ATGGTGATGTGATTTATGCTT	0.368																																																0													78.0	69.0	72.0					8																	39091490		1843	4091	5934	SO:0001819	synonymous_variant	203102			BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1707G>C	8.37:g.39091490G>C			Q8TC42	Silent	SNP	ENST00000379907.4	37	CCDS47846.1																																																																																				0.368	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004		8	16	8	16
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	76939964	76939964	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chrX:76939964G>A	ENST00000373344.5	-	9	998	c.784C>T	c.(784-786)Caa>Taa	p.Q262*	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Nonsense_Mutation_p.Q224*	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	262	ADD. {ECO:0000255|PROSITE- ProRule:PRU00865}.				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						CAATACCATTGGTTGTTTTCA	0.393			"""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)											157.0	145.0	149.0					X																	76939964		2203	4296	6499	SO:0001587	stop_gained	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.784C>T	X.37:g.76939964G>A	ENSP00000362441:p.Gln262*		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Nonsense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	G	37	6.395981	0.97533	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	.	.	.	5.52	5.52	0.82312	.	0.066755	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-10.4362	13.4188	0.60985	0.0:0.0:0.8432:0.1568	.	.	.	.	X	262;224;218	.	ENSP00000362441:Q262X	Q	-	1	0	ATRX	76826620	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.876000	0.75556	2.298000	0.77334	0.513000	0.50165	CAA		0.393	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		146	59	146	59
GPR45	11250	broad.mit.edu;ucsc.edu	37	2	105858978	105858978	+	Silent	SNP	G	G	A	rs141451236		TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr2:105858978G>A	ENST00000258456.1	+	1	779	c.663G>A	c.(661-663)acG>acA	p.T221T		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	221						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	28						TCCTCAACACGGTCCGCAAGA	0.677																																																0								G		0,4406		0,0,2203	61.0	60.0	60.0		663	-5.5	0.7	2	dbSNP_134	60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GPR45	NM_007227.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		221/373	105858978	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	11250			AF118266	CCDS2066.1	2q11.1-q12	2012-08-21			ENSG00000135973	ENSG00000135973		"""GPCR / Class A : Orphans"""	4503	protein-coding gene	gene with protein product		604838				10036181	Standard	NM_007227		Approved	PSP24, PSP24A	uc002tco.1	Q9Y5Y3	OTTHUMG00000130805	ENST00000258456.1:c.663G>A	2.37:g.105858978G>A			Q6NWS4|Q6NXU6	Silent	SNP	ENST00000258456.1	37	CCDS2066.1																																																																																				0.677	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253348.1	NM_007227		23	58	23	58
NEB	4703	broad.mit.edu;ucsc.edu	37	2	152406213	152406213	+	Silent	SNP	A	A	G			TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr2:152406213A>G	ENST00000172853.10	-	102	15030	c.14883T>C	c.(14881-14883)taT>taC	p.Y4961Y	NEB_ENST00000427231.2_Silent_p.Y6662Y|NEB_ENST00000604864.1_Silent_p.Y6662Y|NEB_ENST00000397345.3_Silent_p.Y6662Y|NEB_ENST00000409198.1_Silent_p.Y4961Y|NEB_ENST00000603639.1_Silent_p.Y6662Y			P20929	NEBU_HUMAN	nebulin	4961					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CTGGAAGTCTATATCCAGTGG	0.488																																																0													126.0	125.0	125.0					2																	152406213		1969	4167	6136	SO:0001819	synonymous_variant	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.14883T>C	2.37:g.152406213A>G			F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																					0.488	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		4	22	4	22
SNED1	25992	broad.mit.edu;ucsc.edu	37	2	241969887	241969887	+	Missense_Mutation	SNP	G	G	A	rs185349960	byFrequency	TCGA-DB-5273-01A-01D-1468-08	TCGA-DB-5273-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	938f1aec-2069-4c76-8110-7f086b59e86b	54997159-244a-485c-a81f-e546b76046e8	g.chr2:241969887G>A	ENST00000310397.8	+	2	400	c.400G>A	c.(400-402)Gtc>Atc	p.V134I	SNED1_ENST00000342631.6_Missense_Mutation_p.V134I|SNED1_ENST00000405547.3_Missense_Mutation_p.V134I|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000401884.1_Missense_Mutation_p.V134I	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	134	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		CACGGAGGACGTCAGGCACTA	0.627													G|||	3	0.000599042	0.0008	0.0	5008	,	,		19500	0.002		0.0	False		,,,				2504	0.0															0								G	ILE/VAL	6,4220		0,6,2107	56.0	65.0	62.0		400	0.2	0.1	2		62	0,8446		0,0,4223	yes	missense	SNED1	NM_001080437.1	29	0,6,6330	AA,AG,GG		0.0,0.142,0.0473	benign	134/1414	241969887	6,12666	2113	4223	6336	SO:0001583	missense	25992			AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.400G>A	2.37:g.241969887G>A	ENSP00000308893:p.Val134Ile		B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Missense_Mutation	SNP	ENST00000310397.8	37	CCDS46562.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	G	3.011	-0.203900	0.06180	0.00142	0.0	ENSG00000162804	ENST00000401884;ENST00000405547;ENST00000310397;ENST00000342631	D;D;D;D	0.82711	-1.56;-1.64;-1.59;-1.62	5.44	0.183	0.15082	Nidogen, extracellular domain (2);	.	.	.	.	T	0.53400	0.1794	N	0.01522	-0.82	0.09310	N	1	B	0.14805	0.011	B	0.12837	0.008	T	0.47100	-0.9143	9	0.02654	T	1	.	9.0641	0.36453	0.7002:0.0:0.2998:0.0	.	134	Q8TER0	SNED1_HUMAN	I	134	ENSP00000384871:V134I;ENSP00000386007:V134I;ENSP00000308893:V134I;ENSP00000342992:V134I	ENSP00000308893:V134I	V	+	1	0	SNED1	241618560	0.249000	0.23941	0.051000	0.19133	0.456000	0.32438	0.573000	0.23699	0.113000	0.18004	0.655000	0.94253	GTC		0.627	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482		6	23	6	23
