#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs142470496	byFrequency	TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr22:29091840T>C	ENST00000405598.1	-	12	1308	c.1117A>G	c.(1117-1119)Aag>Gag	p.K373E	CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000544772.1_Missense_Mutation_p.K152E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000464581.1_5'Flank			O96017	CHK2_HUMAN	checkpoint kinase 2	373	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.K373E(9)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCCAAAATCTTGGAGTGCCCA	0.418			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			9	Substitution - Missense(9)	p.K373E(9)	kidney(4)|prostate(2)|endometrium(1)|stomach(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(454-456)Aag>Gag	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2																																				SO:0001583	missense	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091840T>C	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1117A>G	22.37:g.29091840T>C	ENSP00000386087:p.Lys373Glu					CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000405598.1_Missense_Mutation_p.K373E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E	p.K152E	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1890	-			373			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	37	c.454A>G	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	T	19.06	3.754336	0.69648	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000544772;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731	T;T;T;T;T;T;T;T;T	0.54071	0.9;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.9	5.89	5.89	0.94794	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043710	0.85682	D	0.000000	T	0.56292	0.1975	N	0.11756	0.17	0.80722	D	1	D;D;D;D;D;D	0.76494	0.996;0.999;0.998;0.998;0.993;0.991	P;D;D;D;D;P	0.74674	0.905;0.984;0.943;0.969;0.923;0.896	T	0.64769	-0.6329	10	0.87932	D	0	-1.7726	15.4726	0.75453	0.0:0.0:0.0:1.0	.	282;152;373;344;373;416	O96017-4;Q9HBS5;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	E	344;282;152;373;373;373;416;282;344	ENSP00000329012:K344E;ENSP00000372021:K282E;ENSP00000442458:K152E;ENSP00000329178:K373E;ENSP00000385747:K373E;ENSP00000386087:K373E;ENSP00000372023:K416E;ENSP00000384919:K282E;ENSP00000384835:K344E	ENSP00000329178:K373E	K	-	1	0	CHEK2	27421840	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	4.270000	0.58896	2.248000	0.74166	0.528000	0.53228	AAG		0.418	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		4	22	0	0	0	1	0	4	22				
HMGA2	8091	broad.mit.edu	37	12	66221789	66221789	+	Silent	SNP	C	C	T	rs552619480		TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr12:66221789C>T	ENST00000403681.2	+	2	1260	c.120C>T	c.(118-120)acC>acT	p.T40T	RPSAP52_ENST00000489520.2_RNA|HMGA2_ENST00000393578.3_Silent_p.T40T|HMGA2_ENST00000393577.3_Silent_p.T40T|HMGA2_ENST00000541363.1_Silent_p.T40T|HMGA2_ENST00000536545.1_Silent_p.T40T|HMGA2_ENST00000354636.3_Silent_p.T40T|HMGA2_ENST00000425208.2_Silent_p.T40T	NM_003483.4	NP_003474.1	P52926	HMGA2_HUMAN	high mobility group AT-hook 2	40					adrenal gland development (GO:0030325)|base-excision repair (GO:0006284)|cell proliferation in forebrain (GO:0021846)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|chromatin organization (GO:0006325)|chromosome breakage (GO:0031052)|chromosome condensation (GO:0030261)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA damage response, detection of DNA damage (GO:0042769)|endodermal cell differentiation (GO:0035987)|epithelial to mesenchymal transition (GO:0001837)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|heterochromatin assembly (GO:0031507)|histone H2A-S139 phosphorylation (GO:0035978)|male gonad development (GO:0008584)|mesenchymal cell differentiation (GO:0048762)|mesodermal cell differentiation (GO:0048333)|mesodermal-endodermal cell signaling (GO:0003131)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|multicellular organismal development (GO:0007275)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of DNA binding (GO:0043392)|negative regulation of double-strand break repair via nonhomologous end joining (GO:2001033)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|oncogene-induced cell senescence (GO:0090402)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of cellular response to X-ray (GO:2000685)|positive regulation of cellular senescence (GO:2000774)|positive regulation of gene expression (GO:0010628)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle process (GO:0010564)|regulation of cellular response to drug (GO:2001038)|regulation of growth hormone secretion (GO:0060123)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|senescence-associated heterochromatin focus assembly (GO:0035986)|signal transduction (GO:0007165)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|senescence-associated heterochromatin focus (GO:0035985)|SMAD protein complex (GO:0071141)	5'-deoxyribose-5-phosphate lyase activity (GO:0051575)|AT DNA binding (GO:0003680)|C2H2 zinc finger domain binding (GO:0070742)|cAMP response element binding (GO:0035497)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|DNA-dependent protein kinase activity (GO:0004677)|MH1 domain binding (GO:0035501)|MH2 domain binding (GO:0035500)|nucleosomal DNA binding (GO:0031492)|regulatory region DNA binding (GO:0000975)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		HMGA2/RAD51B(11)|HMGA2/CCNB1IP1(2)|HMGA2/WIF1_ENST00000286574(14)|HMGA2/ALDH2_ENST00000261733(2)|HMGA2/EBF1(2)|HMGA2/LHFP(2)|HMGA2/NFIB_ENST00000397581(8)|HMGA2/LPP(161)|HMGA2/FHIT_ENST00000476844(4)|HMGA2/COX6C(2)	lung(2)	2	all_cancers(1;5.78e-46)		GBM - Glioblastoma multiforme(1;0.00179)|LUSC - Lung squamous cell carcinoma(43;0.156)	GBM - Glioblastoma multiforme(28;0.0386)		AGGAACCAACCGGTGAGCCCT	0.448			T	""" LHFP, RAD51L1, LPP, COX6C, CMKOR1, NFIB, ALDH2, CCNB1IP1, EBF1, WIF1, FHIT"""	"""lipoma, leiomyoma, pleiomorphic salivary gland adenoma"""																																	ENST00000541363.1				Dom	yes		12	12q15	8091	T	high mobility group AT-hook 2 (HMGIC)			M	""" LHFP, RAD51L1, LPP, COX6C, CMKOR1, NFIB, ALDH2, CCNB1IP1, EBF1, WIF1, FHIT"""		"""lipoma, leiomyoma, pleiomorphic salivary gland adenoma"""	HMGA2/RAD51B(11)|HMGA2/CCNB1IP1(2)|HMGA2/WIF1_ENST00000286574(14)|HMGA2/ALDH2_ENST00000261733(2)|HMGA2/EBF1(2)|HMGA2/LHFP(2)|HMGA2/NFIB_ENST00000397581(8)|HMGA2/LPP(161)|HMGA2/FHIT_ENST00000476844(4)|HMGA2/COX6C(2)	0				lung(2)	2						c.(118-120)acC>acT		high mobility group AT-hook 2							79.0	86.0	83.0					12																	66221789		2203	4300	6503	SO:0001819	synonymous_variant	8091				cell division|chromatin organization|mitosis|multicellular organismal development|regulation of growth|transcription, DNA-dependent	chromatin	AT DNA binding	g.chr12:66221789C>T	U28754	CCDS31854.1, CCDS44936.1, CCDS73491.1, CCDS73492.1	12q15	2011-07-01	2002-07-25	2002-07-26	ENSG00000149948	ENSG00000149948		"""High-mobility group / Canonical"""	5009	protein-coding gene	gene with protein product		600698	"""high-mobility group (nonhistone chromosomal) protein isoform I-C"""	HMGIC		8824803, 9003504	Standard	XM_006719620		Approved	BABL, LIPO	uc001ssx.3	P52926	OTTHUMG00000168936	ENST00000403681.2:c.120C>T	12.37:g.66221789C>T						HMGA2_ENST00000536545.1_Silent_p.T40T|HMGA2_ENST00000393578.3_Silent_p.T40T|HMGA2_ENST00000403681.2_Silent_p.T40T|HMGA2_ENST00000425208.2_Silent_p.T40T|HMGA2_ENST00000393577.3_Silent_p.T40T|HMGA2_ENST00000354636.3_Silent_p.T40T	p.T40T			P52926	HMGA2_HUMAN	GBM - Glioblastoma multiforme(1;0.00179)|LUSC - Lung squamous cell carcinoma(43;0.156)	GBM - Glioblastoma multiforme(28;0.0386)	2	493	+	all_cancers(1;5.78e-46)		40					E7EP85|E7EWA2|Q1M182|Q1M185|Q1M186|Q1M187|Q1M188	Silent	SNP	ENST00000403681.2	37	c.120C>T	CCDS44936.1																																																																																				0.448	HMGA2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401654.1	NM_003483		18	24	0	0	0	1	0	18	24				
OR6K3	391114	broad.mit.edu	37	1	158687537	158687537	+	Silent	SNP	G	G	A	rs376702655		TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr1:158687537G>A	ENST00000368146.1	-	1	416	c.417C>T	c.(415-417)taC>taT	p.Y139Y	OR6K3_ENST00000368145.1_Silent_p.Y123Y			Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K, member 3	139						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41	all_hematologic(112;0.0378)					AGATGGCAACGTATCTGTCAA	0.507																																						ENST00000368146.1																			0				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41						c.(415-417)taC>taT		olfactory receptor, family 6, subfamily K, member 3		G		0,4406		0,0,2203	113.0	119.0	117.0		369	-2.9	0.0	1		117	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	OR6K3	NM_001005327.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		123/316	158687537	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	391114				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:158687537G>A	AB065633	CCDS30903.1, CCDS30903.2	1q23.1	2012-08-09			ENSG00000203757	ENSG00000203757		"""GPCR / Class A : Olfactory receptors"""	15030	protein-coding gene	gene with protein product							Standard	NM_001005327		Approved		uc021pbn.1	Q8NGY3	OTTHUMG00000022770	ENST00000368146.1:c.417C>T	1.37:g.158687537G>A						OR6K3_ENST00000368145.1_Silent_p.Y123Y	p.Y139Y			Q8NGY3	OR6K3_HUMAN			1	416	-	all_hematologic(112;0.0378)		139					Q5VUV0|Q6IFR5	Silent	SNP	ENST00000368146.1	37	c.417C>T																																																																																					0.507	OR6K3-201	KNOWN	basic	protein_coding	protein_coding				4	81	0	0	0	1	0	4	81				
ELANE	1991	broad.mit.edu	37	19	853364	853364	+	Silent	SNP	C	C	T			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr19:853364C>T	ENST00000590230.1	+	4	468	c.327C>T	c.(325-327)taC>taT	p.Y109Y	ELANE_ENST00000263621.1_Silent_p.Y109Y			P08246	ELNE_HUMAN	elastase, neutrophil expressed	109	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acute inflammatory response to antigenic stimulus (GO:0002438)|cellular calcium ion homeostasis (GO:0006874)|collagen catabolic process (GO:0030574)|defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of chemotaxis (GO:0050922)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil mediated killing of fungus (GO:0070947)|phagocytosis (GO:0006909)|positive regulation of immune response (GO:0050778)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein catabolic process (GO:0030163)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)|response to UV (GO:0009411)|response to yeast (GO:0001878)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|transcriptional repressor complex (GO:0017053)	cytokine binding (GO:0019955)|endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|RNA polymerase II transcription corepressor activity (GO:0001106)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(1)|lung(4)|pancreas(1)	13					Alpha-1-proteinase inhibitor(DB00058)|Filgrastim(DB00099)|Pegfilgrastim(DB00019)	AAAACGGCTACGACCCCGTAA	0.706																																						ENST00000590230.1																			0				breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(1)|lung(4)|pancreas(1)	13						c.(325-327)taC>taT		elastase, neutrophil expressed	Alpha-1-proteinase inhibitor(DB00058)|Filgrastim(DB00099)|Pegfilgrastim(DB00019)						24.0	23.0	23.0					19																	853364		2184	4277	6461	SO:0001819	synonymous_variant	1991				cellular calcium ion homeostasis|negative regulation of chemokine biosynthetic process|negative regulation of chemotaxis|negative regulation of inflammatory response|negative regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 biosynthetic process|positive regulation of MAP kinase activity|positive regulation of smooth muscle cell proliferation|protein catabolic process|proteolysis|response to UV	cell surface|extracellular region|stored secretory granule	bacterial cell surface binding|cytokine binding|heparin binding	g.chr19:853364C>T		CCDS12045.1	19p13.3	2014-09-17	2009-05-05	2009-05-05	ENSG00000197561	ENSG00000197561	3.4.21.37		3309	protein-coding gene	gene with protein product	"""neutrophil elastase"", ""leukocyte elastase"", ""medullasin"""	130130	"""elastase 2, neutrophil"""	ELA2		2902087	Standard	XM_005259517		Approved	NE, HNE, HLE	uc002lqb.3	P08246		ENST00000590230.1:c.327C>T	19.37:g.853364C>T						ELANE_ENST00000263621.1_Silent_p.Y109Y	p.Y109Y			P08246	ELNE_HUMAN			4	468	+			109			Peptidase S1.		P09649|Q6B0D9|Q6LDP5	Silent	SNP	ENST00000590230.1	37	c.327C>T	CCDS12045.1																																																																																				0.706	ELANE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457890.2	NM_001972		8	14	0	0	0	1	0	8	14				
VASP	7408	broad.mit.edu	37	19	46032458	46032458	+	IGR	SNP	G	G	A			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr19:46032458G>A	ENST00000245932.6	+	0	2305				OPA3_ENST00000323060.3_Silent_p.L133L	NM_003370.3	NP_003361.1	P50552	VASP_HUMAN	vasodilator-stimulated phosphoprotein						actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|neural tube closure (GO:0001843)|positive regulation of actin filament polymerization (GO:0030838)|protein homotetramerization (GO:0051289)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	profilin binding (GO:0005522)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)	18		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0145)|GBM - Glioblastoma multiforme(486;0.154)		GCAACTCCTCGAGCGCCAGCC	0.697																																						ENST00000323060.3																			0				cervix(1)|large_intestine(1)|lung(2)	4						c.(397-399)ctC>ctT		optic atrophy 3 (autosomal recessive, with chorea and spastic paraplegia)							18.0	19.0	19.0					19																	46032458		2194	4285	6479	SO:0001628	intergenic_variant	80207				response to stimulus|visual perception	mitochondrion		g.chr19:46032458G>A		CCDS33051.1	19q13.32	2012-02-22			ENSG00000125753	ENSG00000125753			12652	protein-coding gene	gene with protein product		601703				8812448	Standard	XM_005259199		Approved		uc002pcg.3	P50552			19.37:g.46032458G>A							p.L133L	NM_001017989.2	NP_001017989.2	Q9H6K4	OPA3_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00778)|GBM - Glioblastoma multiforme(486;0.0976)|Epithelial(262;0.242)	2	476	-		Ovarian(192;0.051)|all_neural(266;0.112)	133					B2RBT9|Q6PIZ1|Q93035	Silent	SNP	ENST00000245932.6	37	c.399C>T	CCDS33051.1																																																																																				0.697	VASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459589.1			13	13	0	0	0	1	0	13	13				
CHEK2	11200	broad.mit.edu	37	22	29091841	29091841	+	Silent	SNP	G	G	A	rs146546850	byFrequency	TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr22:29091841G>A	ENST00000405598.1	-	12	1307	c.1116C>T	c.(1114-1116)tcC>tcT	p.S372S	CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000544772.1_Silent_p.S151S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000464581.1_5'Flank			O96017	CHK2_HUMAN	checkpoint kinase 2	372	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.S372S(8)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCAAAATCTTGGAGTGCCCAA	0.413			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			8	Substitution - coding silent(8)	p.S372S(8)	kidney(4)|prostate(2)|endometrium(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(451-453)tcC>tcT	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2							43.0	44.0	44.0					22																	29091841		2203	4300	6503	SO:0001819	synonymous_variant	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091841G>A	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1116C>T	22.37:g.29091841G>A						CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000405598.1_Silent_p.S372S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000403642.1_Silent_p.S281S	p.S151S	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1889	-			372			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000405598.1	37	c.453C>T	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	G	5.792	0.330417	0.10956	.	.	ENSG00000183765	ENST00000434810	.	.	.	5.89	-2.11	0.07187	.	.	.	.	.	T	0.42154	0.1190	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33854	-0.9852	4	.	.	.	-7.6356	3.2532	0.06822	0.327:0.1103:0.4613:0.1014	.	.	.	.	L	116	.	.	P	-	2	0	CHEK2	27421841	0.997000	0.39634	0.996000	0.52242	0.470000	0.32858	0.318000	0.19504	-0.075000	0.12798	-0.907000	0.02831	CCA		0.413	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		4	22	0	0	0	1	0	4	22				
FAM221B	392307	broad.mit.edu	37	9	35819971	35819971	+	Missense_Mutation	SNP	G	G	T			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr9:35819971G>T	ENST00000423537.2	-	4	1038	c.769C>A	c.(769-771)Cat>Aat	p.H257N	TMEM8B_ENST00000377996.1_Intron	NM_001012446.3	NP_001012448.2	A6H8Z2	F221B_HUMAN	family with sequence similarity 221, member B	257										endometrium(2)|kidney(1)|lung(4)	7						CATAGGTAATGGGGGCAGCGC	0.483																																						ENST00000423537.2																			0				endometrium(2)|kidney(1)|lung(4)	7						c.(769-771)Cat>Aat		family with sequence similarity 221, member B							59.0	60.0	60.0					9																	35819971		1895	4120	6015	SO:0001583	missense	392307							g.chr9:35819971G>T	BX648702	CCDS43799.1, CCDS43799.2	9p13.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000204930	ENSG00000204930			30762	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 128"""	C9orf128			Standard	NM_001012446		Approved		uc010mlc.2	A6H8Z2	OTTHUMG00000019880	ENST00000423537.2:c.769C>A	9.37:g.35819971G>T	ENSP00000415299:p.His257Asn					TMEM8B_ENST00000377996.1_Intron	p.H257N	NM_001012446.3	NP_001012448.2	A6H8Z2	CI128_HUMAN			4	1038	-			257					Q5TCW2	Missense_Mutation	SNP	ENST00000423537.2	37	c.769C>A	CCDS43799.2	.	.	.	.	.	.	.	.	.	.	G	17.97	3.517348	0.64634	.	.	ENSG00000204930	ENST00000423537;ENST00000377984	T;T	0.15952	2.38;2.38	5.46	5.46	0.80206	.	.	.	.	.	T	0.23410	0.0566	M	0.62723	1.935	0.27859	N	0.940476	P	0.48694	0.914	B	0.42692	0.395	T	0.11591	-1.0581	9	0.42905	T	0.14	-7.2817	14.8065	0.69959	0.0:0.0:1.0:0.0	.	257	A6H8Z2	CI128_HUMAN	N	257	ENSP00000415299:H257N;ENSP00000367222:H257N	ENSP00000367222:H257N	H	-	1	0	C9orf128	35809971	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	3.964000	0.56780	2.552000	0.86080	0.655000	0.94253	CAT		0.483	FAM221B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355861.1	NM_001012446		5	72	1	0	8.12818e-05	1	8.12818e-05	5	72				
RPL36	25873	broad.mit.edu	37	19	5692054	5692054	+	IGR	SNP	C	C	A			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr19:5692054C>A	ENST00000577222.1	+	0	874				LONP1_ENST00000540670.2_Missense_Mutation_p.V761L|LONP1_ENST00000590729.1_Missense_Mutation_p.V827L|LONP1_ENST00000360614.3_Missense_Mutation_p.V957L|LONP1_ENST00000585374.1_Missense_Mutation_p.V843L|LONP1_ENST00000593119.1_Missense_Mutation_p.V893L			Q9Y3U8	RL36_HUMAN	ribosomal protein L36						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|upper_aerodigestive_tract(1)	2						CACCGTTCCACGGCCAGCGCC	0.687																																						ENST00000360614.3																			0				breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						c.(2869-2871)Gtg>Ttg		lon peptidase 1, mitochondrial							74.0	65.0	68.0					19																	5692054		2203	4300	6503	SO:0001628	intergenic_variant	9361				cellular chaperone-mediated protein complex assembly|cellular response to oxidative stress|misfolded or incompletely synthesized protein catabolic process|mitochondrial DNA metabolic process|oxidation-dependent protein catabolic process|protein homooligomerization|response to hypoxia	mitochondrial nucleoid	ADP binding|ATP binding|ATP-dependent peptidase activity|DNA polymerase binding|G-quadruplex DNA binding|mitochondrial heavy strand promoter anti-sense binding|mitochondrial light strand promoter anti-sense binding|sequence-specific DNA binding|serine-type endopeptidase activity|single-stranded DNA binding|single-stranded RNA binding	g.chr19:5692054C>A		CCDS12147.1	19p13.2	2011-04-06				ENSG00000130255		"""L ribosomal proteins"""	13631	protein-coding gene	gene with protein product							Standard	NM_033643		Approved	DKFZp566B023, L36	uc002mcv.3	Q9Y3U8			19.37:g.5692054C>A						LONP1_ENST00000590729.1_Missense_Mutation_p.V827L|LONP1_ENST00000593119.1_Missense_Mutation_p.V893L|LONP1_ENST00000540670.2_Missense_Mutation_p.V761L|LONP1_ENST00000585374.1_Missense_Mutation_p.V843L	p.V957L	NM_004793.2	NP_004784.2	P36776	LONM_HUMAN			18	3026	-			957					B2R4Y1|D6W634|Q6FIG1|Q9UQF6	Missense_Mutation	SNP	ENST00000577222.1	37	c.2869G>T	CCDS12147.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.913110	0.33815	.	.	ENSG00000196365	ENST00000360614;ENST00000358403;ENST00000540670	T;T	0.21932	2.28;1.98	3.9	3.9	0.45041	.	0.471044	0.18565	N	0.137488	T	0.17066	0.0410	L	0.36672	1.1	0.29103	N	0.881388	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.002	T	0.05920	-1.0856	10	0.40728	T	0.16	-32.6668	11.322	0.49428	0.0:1.0:0.0:0.0	.	957;893;957	E5KMH8;Q8N8K8;P36776	.;.;LONM_HUMAN	L	957;921;761	ENSP00000353826:V957L;ENSP00000441523:V761L	ENSP00000351177:V921L	V	-	1	0	LONP1	5643054	0.015000	0.18098	0.867000	0.34043	0.286000	0.27126	0.089000	0.15002	1.999000	0.58509	0.456000	0.33151	GTG		0.687	RPL36-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442561.1	NM_015414		29	34	1	0	2.49675e-24	1	2.74642e-24	29	34				
ARHGAP22	58504	broad.mit.edu	37	10	49667823	49667823	+	Missense_Mutation	SNP	A	A	T			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr10:49667823A>T	ENST00000249601.4	-	5	859	c.563T>A	c.(562-564)cTc>cAc	p.L188H	ARHGAP22_ENST00000417912.2_Missense_Mutation_p.L204H|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.L194H|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.L98H|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.L98H|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.L79H	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	188	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CTCCTCAGTGAGCCCGCGCTC	0.642																																						ENST00000249601.4																			0				endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						c.(562-564)cTc>cAc		Rho GTPase activating protein 22							108.0	100.0	102.0					10																	49667823		2203	4300	6503	SO:0001583	missense	58504				angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol|nucleus	GTPase activator activity	g.chr10:49667823A>T	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.563T>A	10.37:g.49667823A>T	ENSP00000249601:p.Leu188His					ARHGAP22_ENST00000374170.1_Missense_Mutation_p.L98H|ARHGAP22_ENST00000417912.2_Missense_Mutation_p.L204H|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.L98H|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.L79H|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.L194H	p.L188H	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN			5	859	-			188			Rho-GAP.		A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	37	c.563T>A	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.322550	0.81580	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62	4.9	4.9	0.64082	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.074399	0.56097	D	0.000031	T	0.67534	0.2903	H	0.96365	3.81	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;1.0;0.999;1.0;0.995	T	0.78892	-0.2025	10	0.87932	D	0	.	13.8597	0.63552	1.0:0.0:0.0:0.0	.	194;188;204;188;98	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3	.;.;.;RHG22_HUMAN;.	H	188;79;98;98;194;204	ENSP00000249601:L188H;ENSP00000363287:L79H;ENSP00000363285:L98H;ENSP00000410054:L98H;ENSP00000416701:L194H;ENSP00000412461:L204H	ENSP00000249601:L188H	L	-	2	0	ARHGAP22	49337829	1.000000	0.71417	0.944000	0.38274	0.667000	0.39255	9.033000	0.93741	2.074000	0.62210	0.260000	0.18958	CTC		0.642	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		52	69	0	0	0	1	0	52	69				
SEMA4G	57715	broad.mit.edu	37	10	102743064	102743066	+	In_Frame_Del	DEL	CCA	CCA	-			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr10:102743064_102743066delCCA	ENST00000370250.4	+	14	2066_2068	c.1693_1695delCCA	c.(1693-1695)ccadel	p.P568del	MRPL43_ENST00000299179.5_Intron|MRPL43_ENST00000493646.1_5'Flank|MRPL43_ENST00000370241.3_Intron|MRPL43_ENST00000342071.1_Intron|RP11-108L7.4_ENST00000447344.1_RNA|SEMA4G_ENST00000517724.1_Intron|MRPL43_ENST00000318325.2_Intron|MRPL43_ENST00000370242.4_Intron|SEMA4G_ENST00000210633.3_In_Frame_Del_p.P573del	NM_017893.3	NP_060363.2	Q9NTN9	SEM4G_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	568	Ig-like C2-type.|Poly-Pro.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		CCCCACAGGGCCACCACCACCAC	0.616																																						ENST00000210633.3																			0				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						c.(1708-1710)del		sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G			,,,,	20,0,4218		0,0,20,0,0,2099					,,,,	2.9	1.0		dbSNP_134	28	58,3,8161		1,0,56,0,3,4051	no	intron,intron,intron,codingComplex,intron	SEMA4G,MRPL43	NM_176794.1,NM_176793.1,NM_176792.2,NM_017893.3,NM_001203244.1	,,,,	1,0,76,0,3,6150	A1A1,A1A2,A1R,A2A2,A2R,RR		0.7419,0.4719,0.6501	,,,,	,,,,		78,3,12379				SO:0001651	inframe_deletion	57715				cell differentiation|nervous system development	integral to membrane	receptor activity	g.chr10:102743064_102743066delCCA	AB046839	CCDS7501.1, CCDS55724.1	10q24.31	2013-01-11			ENSG00000095539	ENSG00000095539		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10735	protein-coding gene	gene with protein product							Standard	NM_017893		Approved	FLJ20590, KIAA1619	uc001krw.2	Q9NTN9	OTTHUMG00000018922	ENST00000370250.4:c.1693_1695delCCA	10.37:g.102743073_102743075delCCA	ENSP00000359270:p.Pro568del					MRPL43_ENST00000318325.2_Intron|MRPL43_ENST00000299179.5_Intron|MRPL43_ENST00000342071.1_Intron|MRPL43_ENST00000370241.3_Intron|SEMA4G_ENST00000517724.1_Intron|RP11-108L7.4_ENST00000447344.1_RNA|MRPL43_ENST00000370242.4_Intron|SEMA4G_ENST00000370250.4_In_Frame_Del_p.P568del	p.P573del			Q9NTN9	SEM4G_HUMAN		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)	14	1786_1788	+		Colorectal(252;0.234)	568			Ig-like C2-type.		A1A5C6|A6NJY8|Q58EY1|Q9HCF3	In_Frame_Del	DEL	ENST00000370250.4	37	c.1708_1710delCCA																																																																																					0.616	SEMA4G-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049920.2			2	4						2	4	---	---	---	---
CTB-134H23.3	0	broad.mit.edu	37	16	29118702	29118704	+	RNA	DEL	AGC	AGC	-	rs374747642		TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr16:29118702_29118704delAGC	ENST00000562618.1	-	0	328_330				RRN3P2_ENST00000564580.1_RNA																							GCCAGGTCCAagcagcagcagca	0.66																																						ENST00000564580.1																			0																																																			653390							g.chr16:29118702_29118704delAGC																													16.37:g.29118711_29118713delAGC						CTB-134H23.3_ENST00000562618.1_RNA								0	1448	+									RNA	DEL	ENST00000562618.1	37																																																																																						0.660	CTB-134H23.3-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000433241.1			2	4						2	4	---	---	---	---
PLXNB3	5365	broad.mit.edu	37	X	153044463	153044463	+	Frame_Shift_Del	DEL	C	C	-			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chrX:153044463delC	ENST00000361971.5	+	36	5813	c.5699delC	c.(5698-5700)gccfs	p.A1900fs	PLXNB3_ENST00000538776.1_Frame_Shift_Del_p.A1553fs|SRPK3_ENST00000393786.3_5'Flank|SRPK3_ENST00000370100.1_5'Flank|SRPK3_ENST00000370108.3_5'Flank|SRPK3_ENST00000370101.3_5'Flank|SRPK3_ENST00000489426.1_5'UTR|PLXNB3_ENST00000538966.1_Frame_Shift_Del_p.A1923fs|SRPK3_ENST00000370104.1_5'Flank	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1900					axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGTCGCCGCCCTGGTGGAA	0.647																																						ENST00000538966.1																			0				central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32						c.(5767-5769)gcfs		plexin B3							19.0	18.0	18.0					X																	153044463		2197	4289	6486	SO:0001589	frameshift_variant	5365				axon guidance	integral to membrane|intracellular|plasma membrane	protein binding|receptor activity	g.chrX:153044463delC	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.5699delC	X.37:g.153044463delC	ENSP00000355378:p.Ala1900fs					PLXNB3_ENST00000361971.5_Frame_Shift_Del_p.A1900fs|PLXNB3_ENST00000538776.1_Frame_Shift_Del_p.A1553fs|SRPK3_ENST00000489426.1_5'UTR	p.A1923fs	NM_001163257.1	NP_001156729.1	Q9ULL4	PLXB3_HUMAN			37	6039	+	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)		1900					B7Z3E6|F5H773|Q9HDA4	Frame_Shift_Del	DEL	ENST00000361971.5	37	c.5768delC	CCDS14729.1																																																																																				0.647	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			2	4						2	4	---	---	---	---
