#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	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_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	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_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
AARS2	57505	genome.wustl.edu	37	6	44278884	44278884	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr6:44278884C>T	ENST00000244571.4	-	4	598	c.596G>A	c.(595-597)cGt>cAt	p.R199H	RP11-444E17.6_ENST00000505802.1_Intron	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial									p.R199H(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GGAAAGCACACGGCTAGCAGG	0.587																																						dbGAP											1	Substitution - Missense(1)	breast(1)											63.0	64.0	63.0					6																	44278884		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	21022	protein-coding gene	gene with protein product	"""alanine tRNA ligase 2, mitochondrial"""	612035	"""alanyl-tRNA synthetase like"", ""alanyl-tRNA synthetase 2, mitochondrial (putative)"""	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.596G>A	6.37:g.44278884C>T	ENSP00000244571:p.Arg199His			Missense_Mutation	SNP	pfam_Ala-tRNA-synth_IIc_N,pfam_tRNA_SAD,superfamily_Ala-tRNA-synth_IIc_anticod-bd,superfamily_Thr/Ala-tRNA-synth_IIc_edit,smart_tRNA_SAD,prints_Ala-tRNA-synth_IIc,pfscan_Ala-tRNA-synth_IIc_core,tigrfam_Ala-tRNA-synth_IIc	p.R199H	ENST00000244571.4	37	c.596	CCDS34464.1	6	.	.	.	.	.	.	.	.	.	.	C	1.472	-0.559478	0.03967	.	.	ENSG00000124608	ENST00000244571	T	0.75154	-0.91	4.95	1.15	0.20763	Alanyl-tRNA synthetase, class IIc, core domain (1);Alanyl-tRNA synthetase, class IIc, N-terminal (1);	0.179581	0.50627	N	0.000107	T	0.34948	0.0915	L	0.28192	0.835	0.39622	D	0.970042	B	0.23937	0.094	B	0.26094	0.066	T	0.20505	-1.0273	10	0.07482	T	0.82	-3.7141	9.1822	0.37149	0.0:0.5654:0.0:0.4346	.	199	Q5JTZ9	SYAM_HUMAN	H	199	ENSP00000244571:R199H	ENSP00000244571:R199H	R	-	2	0	AARS2	44386862	0.008000	0.16893	0.991000	0.47740	0.547000	0.35210	0.167000	0.16602	0.295000	0.22570	-0.244000	0.11960	CGT	AARS2	-	pfam_Ala-tRNA-synth_IIc_N,pfscan_Ala-tRNA-synth_IIc_core,tigrfam_Ala-tRNA-synth_IIc	ENSG00000124608		0.587	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AARS2	HGNC	protein_coding	OTTHUMT00000040741.2	24	0.00	0	C	NM_020745		44278884	44278884	-1	no_errors	ENST00000244571	ensembl	human	known	69_37n	missense	21	57.14	28	SNP	0.908	T
ABCA4	24	genome.wustl.edu	37	1	94466444	94466444	+	Missense_Mutation	SNP	T	T	A			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr1:94466444T>A	ENST00000370225.3	-	47	6513	c.6427A>T	c.(6427-6429)Atg>Ttg	p.M2143L	ABCA4_ENST00000465352.1_5'Flank|ABCA4_ENST00000536513.1_Missense_Mutation_p.M413L|ABCA4_ENST00000535881.1_Missense_Mutation_p.M262L	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	2143	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)	p.M2143L(1)		NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		CCCTTTACCATGATGGCCAGC	0.582																																						dbGAP											1	Substitution - Missense(1)	breast(1)											155.0	120.0	132.0					1																	94466444		2203	4300	6503	-	-	-	SO:0001583	missense	0			U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.6427A>T	1.37:g.94466444T>A	ENSP00000359245:p.Met2143Leu		O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	pfam_ABC_transporter-like,smart_AAA+_ATPase,pfscan_ABC_transporter-like,tigrfam_Rim_ABC_transpt	p.M2143L	ENST00000370225.3	37	c.6427	CCDS747.1	1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.816404	0.90790	.	.	ENSG00000198691	ENST00000546054;ENST00000370225;ENST00000536513;ENST00000535881	D;D;D	0.99214	-5.57;-5.57;-5.57	5.84	5.84	0.93424	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.98560	0.9519	L	0.28556	0.865	0.80722	D	1	D	0.61080	0.989	P	0.62813	0.907	D	0.99934	1.1348	10	0.72032	D	0.01	.	16.2159	0.82217	0.0:0.0:0.0:1.0	.	2143	P78363	ABCA4_HUMAN	L	935;2143;413;262	ENSP00000359245:M2143L;ENSP00000439707:M413L;ENSP00000443203:M262L	ENSP00000359245:M2143L	M	-	1	0	ABCA4	94239032	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.982000	0.88131	2.243000	0.73865	0.533000	0.62120	ATG	ABCA4	-	smart_AAA+_ATPase,pfscan_ABC_transporter-like,tigrfam_Rim_ABC_transpt	ENSG00000198691		0.582	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ABCA4	HGNC	protein_coding	OTTHUMT00000029320.1	85	0.00	0	T	NM_000350		94466444	94466444	-1	no_errors	ENST00000370225	ensembl	human	known	69_37n	missense	65	50.76	67	SNP	1.000	A
ABCB4	5244	genome.wustl.edu	37	7	87074281	87074282	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr7:87074281_87074282insA	ENST00000265723.4	-	10	1126_1127	c.1015_1016insT	c.(1015-1017)tcafs	p.S339fs	ABCB4_ENST00000453593.1_Frame_Shift_Ins_p.S339fs|ABCB4_ENST00000545634.1_Frame_Shift_Ins_p.S339fs|ABCB4_ENST00000358400.3_Frame_Shift_Ins_p.S339fs|ABCB4_ENST00000359206.3_Frame_Shift_Ins_p.S339fs	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	339	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)	p.S339fs*3(1)		breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	AATTAGGATTGAAAAAAAAACC	0.347																																						dbGAP											1	Deletion - Frameshift(1)	lung(1)	GRCh37	CD034702|CI034710	ABCB4	D|I																																				-	-	-	SO:0001589	frameshift_variant	0			M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"""ATP binding cassette transporters / subfamily B"""	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.1016dupT	7.37:g.87074290_87074290dupA	ENSP00000265723:p.Ser339fs		A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Frame_Shift_Ins	INS	pfam_ABC_transptr_TM_dom,pfam_ABC_transporter-like,pfam_ABC_ATPase_put,pfam_Zeta_toxin_domain,superfamily_ABC_transptrTM_dom_typ1,smart_AAA+_ATPase,pfscan_ABC_transporter-like,pfscan_ABC_transporter_type1	p.S339fs	ENST00000265723.4	37	c.1016_1015	CCDS5606.1	7																																																																																			ABCB4	-	pfam_ABC_transptr_TM_dom,superfamily_ABC_transptrTM_dom_typ1,pfscan_ABC_transporter_type1	ENSG00000005471		0.347	ABCB4-002	KNOWN	basic|CCDS	protein_coding	ABCB4	HGNC	protein_coding	OTTHUMT00000336083.1	47	0.00	0	-	NM_000443		87074281	87074282	-1	no_errors	ENST00000265723	ensembl	human	known	69_37n	frame_shift_ins	40	27.27	15	INS	1.000:1.000	A
ACVR1B	91	genome.wustl.edu	37	12	52379131	52379131	+	Splice_Site	SNP	C	C	T			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr12:52379131C>T	ENST00000257963.4	+	6	1212	c.1135C>T	c.(1135-1137)Cga>Tga	p.R379*	ACVR1B_ENST00000563121.1_3'UTR|ACVR1B_ENST00000426655.2_Splice_Site_p.R379*|ACVR1B_ENST00000415850.2_Splice_Site_p.R379*|ACVR1B_ENST00000542485.1_Splice_Site_p.R327*|RNU6-574P_ENST00000384265.1_RNA|ACVR1B_ENST00000541224.1_Splice_Site_p.R420*	NM_004302.4|NM_020328.3	NP_004293.1|NP_064733.3	P36896	ACV1B_HUMAN	activin A receptor, type IB	379	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|central nervous system development (GO:0007417)|development of primary female sexual characteristics (GO:0046545)|extrinsic apoptotic signaling pathway (GO:0097191)|G1/S transition of mitotic cell cycle (GO:0000082)|hair follicle development (GO:0001942)|in utero embryonic development (GO:0001701)|negative regulation of cell growth (GO:0030308)|nodal signaling pathway (GO:0038092)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of trophoblast cell migration (GO:1901165)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|inhibin binding (GO:0034711)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|ubiquitin protein ligase binding (GO:0031625)	p.R420*(1)|p.R379*(1)		breast(5)|endometrium(4)|kidney(5)|large_intestine(12)|lung(10)|ovary(1)|pancreas(6)|prostate(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	GGGGACCAAACGGTAGGAGGG	0.547																																						dbGAP											2	Substitution - Nonsense(2)	breast(2)											127.0	116.0	120.0					12																	52379131		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0				CCDS8816.1, CCDS44893.1, CCDS44894.1, CCDS44893.2, CCDS44894.2	12q13	2006-11-09			ENSG00000135503	ENSG00000135503			172	protein-coding gene	gene with protein product		601300		ACVRLK4		8397373	Standard	NM_020327		Approved	ALK4, SKR2, ActRIB	uc010snn.2	P36896	OTTHUMG00000167920	ENST00000257963.4:c.1136+1C>T	12.37:g.52379131C>T			B7Z5L8|B7Z5W5|Q15479|Q15480|Q15481|Q15482	Nonsense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_TGF_beta_rcpt_GS,pfam_Activin_rcpt,superfamily_Kinase-like_dom,smart_TGF_beta_rcpt_GS,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.R379*	ENST00000257963.4	37	c.1135	CCDS8816.1	12	.	.	.	.	.	.	.	.	.	.	C	36	5.818764	0.96982	.	.	ENSG00000135503	ENST00000257963;ENST00000541224;ENST00000426655;ENST00000415850;ENST00000542485	.	.	.	4.76	2.77	0.32553	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.1374	0.59417	0.3895:0.6105:0.0:0.0	.	.	.	.	X	379;420;379;379;327	.	ENSP00000257963:R379X	R	+	1	2	ACVR1B	50665398	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	2.095000	0.41729	1.349000	0.45751	0.563000	0.77884	CGA	ACVR1B	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000135503		0.547	ACVR1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	ACVR1B	HGNC	protein_coding	OTTHUMT00000397000.1	63	0.00	0	C	NM_020328	Nonsense_Mutation	52379131	52379131	+1	no_errors	ENST00000257963	ensembl	human	known	69_37n	nonsense	51	42.70	38	SNP	1.000	T
AFF2	2334	genome.wustl.edu	37	X	148037946	148037946	+	Missense_Mutation	SNP	C	C	G			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chrX:148037946C>G	ENST00000370460.2	+	11	2850	c.2371C>G	c.(2371-2373)Cct>Gct	p.P791A	AFF2_ENST00000342251.3_Missense_Mutation_p.P758A|AFF2_ENST00000370457.5_Missense_Mutation_p.P758A|AFF2_ENST00000286437.5_Missense_Mutation_p.P432A	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	791					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)	p.P791A(2)|p.P432A(1)		breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					AATCCTGTCCCCTCTGCGAGA	0.468																																						dbGAP											3	Substitution - Missense(3)	breast(3)											125.0	112.0	116.0					X																	148037946		2203	4300	6503	-	-	-	SO:0001583	missense	0			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.2371C>G	X.37:g.148037946C>G	ENSP00000359489:p.Pro791Ala		A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	pfam_TF_AF4/FMR2	p.P791A	ENST00000370460.2	37	c.2371	CCDS14684.1	X	.	.	.	.	.	.	.	.	.	.	C	13.20	2.165699	0.38217	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6	5.87	4.99	0.66335	.	0.055211	0.64402	D	0.000001	D	0.91078	0.7192	M	0.86651	2.83	0.58432	D	0.999999	D;P;P;P;P;P	0.63046	0.992;0.944;0.944;0.944;0.944;0.955	P;P;P;P;P;P	0.61201	0.885;0.719;0.719;0.719;0.719;0.815	D	0.92170	0.5743	10	0.66056	D	0.02	.	15.2366	0.73436	0.1414:0.8586:0.0:0.0	.	432;756;758;752;781;791	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	A	791;758;758;432	ENSP00000359489:P791A;ENSP00000359486:P758A;ENSP00000345459:P758A;ENSP00000286437:P432A	ENSP00000286437:P432A	P	+	1	0	AFF2	147845646	1.000000	0.71417	0.554000	0.28268	0.075000	0.17131	5.008000	0.63991	1.172000	0.42781	0.600000	0.82982	CCT	AFF2	-	pfam_TF_AF4/FMR2	ENSG00000155966		0.468	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	AFF2	HGNC	protein_coding	OTTHUMT00000058673.2	183	0.00	0	C	NM_002025		148037946	148037946	+1	no_errors	ENST00000370460	ensembl	human	known	69_37n	missense	73	39.67	48	SNP	1.000	G
ALG10B	144245	genome.wustl.edu	37	12	38714401	38714401	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr12:38714401G>A	ENST00000308742.4	+	3	1124	c.808G>A	c.(808-810)Gtt>Att	p.V270I	AC117372.1_ENST00000401168.2_RNA|ALG10B_ENST00000551464.1_Intron	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	270					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)	p.V270I(1)		breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				TTTTGTAGTAGTTAATGGTGG	0.353																																						dbGAP											1	Substitution - Missense(1)	breast(1)											177.0	181.0	180.0					12																	38714401		2203	4296	6499	-	-	-	SO:0001583	missense	0			AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"""potassium channel regulator 1"", ""dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"""		"""asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"""				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.808G>A	12.37:g.38714401G>A	ENSP00000310120:p.Val270Ile		B2RPF4	Missense_Mutation	SNP	pfam_Glycosyltransferase_ALG10,pirsf_Alpha1_2_glucosyltferase_Alg10	p.V270I	ENST00000308742.4	37	c.808	CCDS31772.1	12	.	.	.	.	.	.	.	.	.	.	g	1.536	-0.543034	0.04053	.	.	ENSG00000175548	ENST00000308742	T	0.55760	0.5	3.23	0.354	0.16063	.	0.601756	0.17987	N	0.155326	T	0.22742	0.0549	N	0.05383	-0.06	0.19945	N	0.999941	B	0.14012	0.009	B	0.12156	0.007	T	0.07790	-1.0754	10	0.24483	T	0.36	.	0.7507	0.00990	0.227:0.188:0.3926:0.1924	.	270	Q5I7T1	AG10B_HUMAN	I	270	ENSP00000310120:V270I	ENSP00000310120:V270I	V	+	1	0	ALG10B	37000668	0.000000	0.05858	0.103000	0.21229	0.663000	0.39108	-0.436000	0.06922	0.062000	0.16340	-0.162000	0.13425	GTT	ALG10B	-	pfam_Glycosyltransferase_ALG10,pirsf_Alpha1_2_glucosyltferase_Alg10	ENSG00000175548		0.353	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALG10B	HGNC	protein_coding	OTTHUMT00000403349.1	139	0.00	0	G	NM_001013620		38714401	38714401	+1	no_errors	ENST00000308742	ensembl	human	known	69_37n	missense	180	24.90	60	SNP	0.010	A
ANKRD18B	441459	genome.wustl.edu	37	9	33541181	33541182	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr9:33541181_33541182insA	ENST00000290943.6	+	7	941_942	c.845_846insA	c.(844-849)agaaaafs	p.RK282fs		NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	282										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						TTgaaaaaaagaaaaaaaagaa	0.361																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0					9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.853dupA	9.37:g.33541189_33541189dupA	ENSP00000290943:p.Arg282fs			Frame_Shift_Ins	INS	pfam_DUF3496,pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	p.R285fs	ENST00000290943.6	37	c.845_846		9																																																																																			ANKRD18B	-	NULL	ENSG00000230453		0.361	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	ANKRD18B	HGNC	protein_coding	OTTHUMT00000313729.2	11	0.00	0	-	XM_001718334		33541181	33541182	+1	no_errors	ENST00000290943	ensembl	human	known	69_37n	frame_shift_ins	27	30.77	12	INS	0.070:0.073	A
AOAH	313	genome.wustl.edu	37	7	36698846	36698846	+	Silent	SNP	A	A	G			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr7:36698846A>G	ENST00000258749.5	-	4	714	c.315T>C	c.(313-315)gaT>gaC	p.D105D	AOAH_ENST00000431169.1_Silent_p.D105D|AOAH_ENST00000535891.1_Silent_p.D73D	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	105	Saposin B-type. {ECO:0000255|PROSITE- ProRule:PRU00415}.				inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|lipopolysaccharide metabolic process (GO:0008653)|negative regulation of inflammatory response (GO:0050728)	extracellular region (GO:0005576)	acyloxyacyl hydrolase activity (GO:0050528)|catalytic activity (GO:0003824)|lipoprotein lipase activity (GO:0004465)	p.D105D(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(21)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	41						GACATACCACATCAGCATTCA	0.443																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											195.0	157.0	170.0					7																	36698846		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			BC025698	CCDS5448.1, CCDS55102.1, CCDS75584.1	7p14-p12	2014-03-14			ENSG00000136250	ENSG00000136250	3.1.1.77		548	protein-coding gene	gene with protein product		102593				1883828	Standard	NM_001637		Approved		uc022abu.1	P28039	OTTHUMG00000023566	ENST00000258749.5:c.315T>C	7.37:g.36698846A>G			A4D1Y5|B7Z490|Q53F13	Silent	SNP	pfam_Lipase_GDSL,pfam_SapB_2,superfamily_Saposin-like,superfamily_Esterase_SGNH_hydro-type,smart_SaposinB,pfscan_SaposinB	p.D105	ENST00000258749.5	37	c.315	CCDS5448.1	7																																																																																			AOAH	-	pfam_SapB_2,superfamily_Saposin-like,smart_SaposinB,pfscan_SaposinB	ENSG00000136250		0.443	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	AOAH	HGNC	protein_coding	OTTHUMT00000219829.2	246	0.00	0	A	NM_001637		36698846	36698846	-1	no_errors	ENST00000258749	ensembl	human	known	69_37n	silent	278	34.74	148	SNP	1.000	G
BRWD1	54014	genome.wustl.edu	37	21	40559077	40559078	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr21:40559077_40559078insT	ENST00000333229.2	-	42	7164_7165	c.6837_6838insA	c.(6835-6840)aaattafs	p.L2280fs	AF129408.17_ENST00000608767.1_RNA	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	2280					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				ACATTCAGTAATTTTTTCTTAG	0.351																																					Melanoma(170;988 1986 4794 16843 39731)	dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.6838dupA	21.37:g.40559083_40559083dupT	ENSP00000330753:p.Leu2280fs		C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Frame_Shift_Ins	INS	pfam_WD40_repeat,pfam_Bromodomain,superfamily_WD40_repeat_dom,superfamily_Bromodomain,smart_WD40_repeat,smart_Bromodomain,prints_Bromodomain,pfscan_Bromodomain,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.L2279fs	ENST00000333229.2	37	c.6838_6837	CCDS13662.1	21																																																																																			BRWD1	-	NULL	ENSG00000185658		0.351	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BRWD1	HGNC	protein_coding	OTTHUMT00000141398.3	55	0.00	0	-	NM_033656		40559077	40559078	-1	no_errors	ENST00000333229	ensembl	human	known	69_37n	frame_shift_ins	25	32.43	12	INS	0.662:0.249	T
C14orf37	145407	genome.wustl.edu	37	14	58598350	58598350	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr14:58598350G>A	ENST00000267485.7	-	4	1905	c.1711C>T	c.(1711-1713)Ccc>Tcc	p.P571S	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	571						integral component of membrane (GO:0016021)		p.P571S(1)		breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						GAAATGCTGGGTTCCCCCACC	0.498																																						dbGAP											1	Substitution - Missense(1)	breast(1)											113.0	106.0	109.0					14																	58598350		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.1711C>T	14.37:g.58598350G>A	ENSP00000267485:p.Pro571Ser		A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	NULL	p.P571S	ENST00000267485.7	37	c.1711	CCDS32089.1	14	.	.	.	.	.	.	.	.	.	.	G	8.383	0.837984	0.16891	.	.	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.20332	2.08	5.78	2.91	0.33838	.	0.981878	0.08326	N	0.963059	T	0.16685	0.0401	L	0.50333	1.59	0.09310	N	1	B;P;B;B	0.34462	0.225;0.454;0.225;0.225	B;B;B;B	0.28465	0.053;0.09;0.053;0.053	T	0.32929	-0.9888	10	0.54805	T	0.06	-1.1653	2.3481	0.04277	0.0981:0.3109:0.3436:0.2474	.	609;571;571;571	B4DMS4;Q86TY3-2;A8K990;Q86TY3	.;.;.;CN037_HUMAN	S	571;609	ENSP00000267485:P571S	ENSP00000267485:P571S	P	-	1	0	C14orf37	57668103	0.002000	0.14202	0.020000	0.16555	0.022000	0.10575	0.094000	0.15107	0.762000	0.33152	0.650000	0.86243	CCC	C14orf37	-	NULL	ENSG00000139971		0.498	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C14orf37	HGNC	protein_coding	OTTHUMT00000412059.1	51	0.00	0	G	NM_001001872		58598350	58598350	-1	no_errors	ENST00000267485	ensembl	human	known	69_37n	missense	19	78.02	71	SNP	0.000	A
CAMK2D	817	genome.wustl.edu	37	4	114434519	114434519	+	Missense_Mutation	SNP	A	A	G			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr4:114434519A>G	ENST00000342666.5	-	12	910	c.911T>C	c.(910-912)aTc>aCc	p.I304T	CAMK2D_ENST00000514328.1_Missense_Mutation_p.I304T|CAMK2D_ENST00000394522.3_Missense_Mutation_p.I304T|CAMK2D_ENST00000394524.3_Missense_Mutation_p.I304T|CAMK2D_ENST00000454265.2_Missense_Mutation_p.I304T|CAMK2D_ENST00000296402.5_Missense_Mutation_p.I304T|CAMK2D_ENST00000394526.2_Missense_Mutation_p.I304T|CAMK2D_ENST00000418639.2_Missense_Mutation_p.I304T|CAMK2D_ENST00000379773.2_Missense_Mutation_p.I304T|CAMK2D_ENST00000508738.1_Missense_Mutation_p.I304T|CAMK2D_ENST00000515496.1_Missense_Mutation_p.I304T|CAMK2D_ENST00000429180.1_Missense_Mutation_p.I304T|CAMK2D_ENST00000511664.1_Missense_Mutation_p.I304T|CAMK2D_ENST00000505990.1_Missense_Mutation_p.I304T			Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II delta	304					calcium ion transport (GO:0006816)|cardiac muscle cell contraction (GO:0086003)|cellular response to calcium ion (GO:0071277)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle cell action potential (GO:0098901)|regulation of cardiac muscle cell action potential involved in regulation of contraction (GO:0098909)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cell growth (GO:0001558)|regulation of cellular localization (GO:0060341)|regulation of generation of L-type calcium current (GO:1902514)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of histone deacetylase activity (GO:1901725)|regulation of membrane depolarization (GO:0003254)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of the force of heart contraction (GO:0002026)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|relaxation of cardiac muscle (GO:0055119)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|calcium channel complex (GO:0034704)|calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intercalated disc (GO:0014704)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|ion channel binding (GO:0044325)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|sodium channel inhibitor activity (GO:0019871)|titin binding (GO:0031432)	p.I304T(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	13		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)		AGTTGTCAAGATGGCACCCTG	0.373																																						dbGAP											1	Substitution - Missense(1)	breast(1)											88.0	88.0	88.0					4																	114434519		2203	4300	6503	-	-	-	SO:0001583	missense	0			U50361	CCDS3703.1, CCDS3704.1, CCDS43263.1, CCDS47127.1, CCDS54797.1	4q26	2008-10-30	2008-10-30		ENSG00000145349	ENSG00000145349			1462	protein-coding gene	gene with protein product		607708	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II delta"""	CAMKD			Standard	NM_001221		Approved		uc003ibi.3	Q13557	OTTHUMG00000132910	ENST00000342666.5:c.911T>C	4.37:g.114434519A>G	ENSP00000339740:p.Ile304Thr		A8MVS8|Q52PK4|Q59G21|Q8N553|Q9UGH6|Q9UQE9	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ca/CaM-dep_prot_kinase-assoc,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.I304T	ENST00000342666.5	37	c.911	CCDS3703.1	4	.	.	.	.	.	.	.	.	.	.	A	24.3	4.513115	0.85389	.	.	ENSG00000145349	ENST00000394524;ENST00000454265;ENST00000429180;ENST00000418639;ENST00000394526;ENST00000296402;ENST00000511664;ENST00000342666;ENST00000515496;ENST00000514328;ENST00000394522;ENST00000505990;ENST00000379773;ENST00000508738;ENST00000509594	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.69685	-0.39;-0.38;-0.39;-0.35;-0.33;-0.39;-0.4;-0.4;-0.33;-0.42;-0.42;-0.38;-0.39;-0.4;1.47	5.37	5.37	0.77165	Protein kinase-like domain (1);	0.051073	0.85682	D	0.000000	D	0.86008	0.5830	M	0.92923	3.36	0.80722	D	1	P;P;P;P;P	0.45768	0.789;0.866;0.866;0.717;0.789	D;D;D;D;D	0.71656	0.964;0.966;0.966;0.974;0.926	D	0.89129	0.3508	10	0.87932	D	0	.	15.3589	0.74453	1.0:0.0:0.0:0.0	.	304;304;304;304;304	E9PF82;Q13557-3;Q13557-6;Q13557-12;Q13557	.;.;.;.;KCC2D_HUMAN	T	304;304;304;304;304;304;304;304;304;304;304;304;304;304;99	ENSP00000378032:I304T;ENSP00000415248:I304T;ENSP00000415707:I304T;ENSP00000406131:I304T;ENSP00000378034:I304T;ENSP00000296402:I304T;ENSP00000425824:I304T;ENSP00000339740:I304T;ENSP00000423482:I304T;ENSP00000423677:I304T;ENSP00000378030:I304T;ENSP00000424245:I304T;ENSP00000369098:I304T;ENSP00000422566:I304T;ENSP00000423753:I99T	ENSP00000296402:I304T	I	-	2	0	CAMK2D	114653968	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.289000	0.96061	2.028000	0.59812	0.533000	0.62120	ATC	CAMK2D	-	superfamily_Kinase-like_dom	ENSG00000145349		0.373	CAMK2D-003	KNOWN	basic|CCDS	protein_coding	CAMK2D	HGNC	protein_coding	OTTHUMT00000256420.2	77	0.00	0	A			114434519	114434519	-1	no_errors	ENST00000454265	ensembl	human	known	69_37n	missense	86	25.22	29	SNP	1.000	G
CHEK2P2	646096	genome.wustl.edu	37	15	20496657	20496657	+	RNA	SNP	C	C	T	rs7180374	byFrequency	TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr15:20496657C>T	ENST00000555186.1	+	0	710					NR_038836.1				checkpoint kinase 2 pseudogene 2																		GACCACAAAGCGCCCGGCTGT	0.438																																						dbGAP											0																																										-	-	-			0					15q11.1	2011-11-11			ENSG00000259156	ENSG00000259156			43578	pseudogene	pseudogene							Standard	NR_038836		Approved		uc001ytf.1		OTTHUMG00000171660		15.37:g.20496657C>T				RNA	SNP	-	NULL	ENST00000555186.1	37	NULL		15																																																																																			CHEK2P2	-	-	ENSG00000259156		0.438	CHEK2P2-002	KNOWN	basic	processed_transcript	CHEK2P2	HGNC	pseudogene	OTTHUMT00000414654.1	15	0.00	0	C	NR_038836		20496657	20496657	+1	no_errors	ENST00000555186	ensembl	human	known	69_37n	rna	15	34.78	8	SNP	0.921	T
COL14A1	7373	genome.wustl.edu	37	8	121222032	121222032	+	Silent	SNP	C	C	T			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr8:121222032C>T	ENST00000297848.3	+	12	1629	c.1359C>T	c.(1357-1359)gaC>gaT	p.D453D	COL14A1_ENST00000309791.4_Silent_p.D453D|COL14A1_ENST00000537875.1_Silent_p.D453D|COL14A1_ENST00000247781.3_Silent_p.D358D|COL14A1_ENST00000432943.2_3'UTR	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.D453D(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			TACTGTACGACGTGACTGAGA	0.458																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											116.0	108.0	111.0					8																	121222032		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.1359C>T	8.37:g.121222032C>T				Missense_Mutation	SNP	pfam_Fibronectin_type3,pfam_VWF_A,superfamily_Fibronectin_type3,smart_VWF_A,smart_Fibronectin_type3,pfscan_Fibronectin_type3,pfscan_VWF_A	p.R210C	ENST00000297848.3	37	c.628	CCDS34938.1	8	.	.	.	.	.	.	.	.	.	.	C	0.369	-0.935085	0.02340	.	.	ENSG00000187955	ENST00000523142	.	.	.	5.31	-2.89	0.05665	.	.	.	.	.	T	0.63558	0.2521	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62900	-0.6756	4	.	.	.	.	13.8741	0.63643	0.0:0.4475:0.0:0.5525	.	.	.	.	C	210	.	.	R	+	1	0	COL14A1	121291213	0.907000	0.30839	0.615000	0.29064	0.103000	0.19146	-0.075000	0.11431	-0.379000	0.07906	-1.874000	0.00550	CGT	COL14A1	-	pfam_Fibronectin_type3,superfamily_Fibronectin_type3,smart_VWF_A,smart_Fibronectin_type3,pfscan_Fibronectin_type3	ENSG00000187955		0.458	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL14A1	HGNC	protein_coding	OTTHUMT00000313657.2	49	0.00	0	C	NM_021110		121222032	121222032	+1	no_start_codon:pseudogene:no_stop_codon	ENST00000523142	ensembl	human	putative	69_37n	missense	62	47.90	57	SNP	0.956	T
DNAAF3	352909	genome.wustl.edu	37	19	55672058	55672059	+	Frame_Shift_Ins	INS	-	-	C	rs571791610		TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr19:55672058_55672059insC	ENST00000524407.2	-	9	1030_1031	c.997_998insG	c.(997-999)gacfs	p.D333fs	DNAAF3_ENST00000391720.4_Frame_Shift_Ins_p.D380fs|TNNI3_ENST00000590463.1_5'Flank|DNAAF3_ENST00000587789.2_5'Flank|CTD-2587H24.4_ENST00000587871.1_5'Flank|DNAAF3_ENST00000455045.1_Frame_Shift_Ins_p.D279fs|TNNI3_ENST00000344887.5_5'Flank|DNAAF3_ENST00000527223.2_Frame_Shift_Ins_p.D401fs|CTD-2587H24.5_ENST00000591665.1_RNA			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	333					axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)											CTCCTCCAGGTCCCCCCCGGTG	0.673											OREG0025678	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0										3,3607		0,3,1802						0.6	0.0			71	4,7842		0,4,3919	no	frameshift	C19orf51	NM_178837.3		0,7,5721	A1A1,A1R,RR		0.051,0.0831,0.0611				7,11449				-	-	-	SO:0001589	frameshift_variant	0			AK097388	CCDS12918.2, CCDS58679.1, CCDS58680.1, CCDS59422.1	19q13.42	2012-10-05	2012-03-09	2012-03-09	ENSG00000167646	ENSG00000167646			30492	protein-coding gene	gene with protein product		614566	"""chromosome 19 open reading frame 51"", ""ciliary dyskinesia, primary 2"""	C19orf51, CILD2		22387996	Standard	NM_001256714		Approved	FLJ40069, FLJ36139, PF22, PCD	uc002qjl.2	Q8N9W5	OTTHUMG00000128547	ENST00000524407.2:c.998dupG	19.37:g.55672065_55672065dupC	ENSP00000432046:p.Asp333fs	1009	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Frame_Shift_Ins	INS	NULL	p.D401fs	ENST00000524407.2	37	c.1202_1201	CCDS59422.1	19																																																																																			DNAAF3	-	NULL	ENSG00000167646		0.673	DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	DNAAF3	HGNC	protein_coding	OTTHUMT00000250388.5	16	0.00	0	-	NM_178837		55672058	55672059	-1	no_errors	ENST00000527223	ensembl	human	known	69_37n	frame_shift_ins	14	17.65	3	INS	0.001:0.002	C
DNHD1	144132	genome.wustl.edu	37	11	6579764	6579764	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr11:6579764G>A	ENST00000527990.2	+	24	9052	c.9052G>A	c.(9052-9054)Gat>Aat	p.D3018N	DNHD1_ENST00000254579.6_Missense_Mutation_p.D3018N			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3018					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)	p.D3018N(1)		NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CCTGATTGGAGATAAACAGGC	0.572																																						dbGAP											1	Substitution - Missense(1)	breast(1)											57.0	56.0	56.0					11																	6579764		692	1591	2283	-	-	-	SO:0001583	missense	0			AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.9052G>A	11.37:g.6579764G>A	ENSP00000436180:p.Asp3018Asn		Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	pfam_Dynein_heavy_dom-2,pfam_Dynein_heavy,superfamily_t-SNARE	p.D3018N	ENST00000527990.2	37	c.9052	CCDS44532.1	11	.	.	.	.	.	.	.	.	.	.	G	12.61	1.990667	0.35131	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000524401	T;T	0.28666	1.6;1.6	5.31	5.31	0.75309	.	.	.	.	.	T	0.24586	0.0596	N	0.14661	0.345	0.26773	N	0.969768	P	0.48162	0.906	P	0.46585	0.521	T	0.08597	-1.0714	9	0.16420	T	0.52	.	15.8971	0.79344	0.0:0.0:1.0:0.0	.	3018	Q96M86	DNHD1_HUMAN	N	3018;3018;83	ENSP00000254579:D3018N;ENSP00000436180:D3018N	ENSP00000254579:D3018N	D	+	1	0	DNHD1	6536340	0.992000	0.36948	0.975000	0.42487	0.905000	0.53344	2.599000	0.46231	2.471000	0.83476	0.591000	0.81541	GAT	DNHD1	-	NULL	ENSG00000179532		0.572	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	DNHD1	HGNC	protein_coding	OTTHUMT00000384673.2	60	0.00	0	G	NM_144666		6579764	6579764	+1	no_errors	ENST00000254579	ensembl	human	known	69_37n	missense	56	28.21	22	SNP	0.697	A
GAREML	150946	genome.wustl.edu	37	2	26405961	26405961	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr2:26405961G>A	ENST00000401533.2	+	3	509	c.379G>A	c.(379-381)Gtc>Atc	p.V127I	GAREML_ENST00000407684.1_Missense_Mutation_p.V50I	NM_001168241.1	NP_001161713.1	Q75VX8	GAREL_HUMAN	GRB2 associated, regulator of MAPK1-like	127	CABIT.					extracellular vesicular exosome (GO:0070062)		p.V127I(1)									CACCTTCAGCGTCAAGGTCAG	0.597																																						dbGAP											1	Substitution - Missense(1)	breast(1)											93.0	100.0	98.0					2																	26405961		692	1591	2283	-	-	-	SO:0001583	missense	0			AK090454, AB015349, AB124552	CCDS54336.1, CCDS54337.1	2p23.3	2012-11-30	2012-11-30	2012-11-30	ENSG00000157833	ENSG00000157833			27172	protein-coding gene	gene with protein product			"""family with sequence similarity 59, member B"""	FAM59B			Standard	NM_001168241		Approved	KIAA2038, FLJ00375	uc002rgw.2	Q75VX8	OTTHUMG00000151935	ENST00000401533.2:c.379G>A	2.37:g.26405961G>A	ENSP00000384593:p.Val127Ile		B5MC97|B7WNK9|Q8NF27|Q9UIK8	Missense_Mutation	SNP	superfamily_SAM/pointed	p.V127I	ENST00000401533.2	37	c.379	CCDS54336.1	2	.	.	.	.	.	.	.	.	.	.	G	31	5.083366	0.94050	.	.	ENSG00000157833	ENST00000401533;ENST00000407684	T;T	0.14766	2.48;2.48	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000007	T	0.38957	0.1060	M	0.73598	2.24	0.49483	D	0.999793	D;D	0.89917	1.0;0.989	D;D	0.85130	0.997;0.934	T	0.06041	-1.0849	10	0.46703	T	0.11	-33.6478	16.8926	0.86091	0.0:0.0:1.0:0.0	.	50;127	B7WNK9;Q75VX8	.;FA59B_HUMAN	I	127;50	ENSP00000384593:V127I;ENSP00000384581:V50I	ENSP00000384593:V127I	V	+	1	0	FAM59B	26259465	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.533000	0.81994	2.588000	0.87417	0.462000	0.41574	GTC	FAM59B	-	NULL	ENSG00000157833		0.597	GAREML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM59B	HGNC	protein_coding	OTTHUMT00000324498.2	37	0.00	0	G	NM_001168241		26405961	26405961	+1	no_errors	ENST00000401533	ensembl	human	known	69_37n	missense	20	35.48	11	SNP	1.000	A
FGF23	8074	genome.wustl.edu	37	12	4479739	4479739	+	Silent	SNP	G	G	T			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr12:4479739G>T	ENST00000237837.1	-	3	671	c.526C>A	c.(526-528)Cgg>Agg	p.R176R		NM_020638.2	NP_065689.1	Q9GZV9	FGF23_HUMAN	fibroblast growth factor 23	176			R -> Q (in ADHR; partially resistant to cleavage by furin). {ECO:0000269|PubMed:11062477}.		cell differentiation (GO:0030154)|cellular phosphate ion homeostasis (GO:0030643)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of bone mineralization (GO:0030502)|negative regulation of hormone secretion (GO:0046888)|negative regulation of osteoblast differentiation (GO:0045668)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphate ion homeostasis (GO:0055062)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vitamin D 24-hydroxylase activity (GO:0010980)|regulation of phosphate transport (GO:0010966)|vitamin D catabolic process (GO:0042369)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.R176R(1)		NS(1)|breast(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	22			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)|STAD - Stomach adenocarcinoma(119;0.206)			CGGGTGTGCCGCCGTGGTATG	0.672																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											32.0	37.0	36.0					12																	4479739		2203	4299	6502	-	-	-	SO:0001819	synonymous_variant	0			AF263537	CCDS8526.1	12p13	2008-07-04			ENSG00000118972	ENSG00000118972			3680	protein-coding gene	gene with protein product		605380				11032749, 18310961	Standard	NM_020638		Approved		uc001qmq.1	Q9GZV9	OTTHUMG00000168241	ENST00000237837.1:c.526C>A	12.37:g.4479739G>T			Q4V758	Silent	SNP	pfam_IL1_HBGF,superfamily_Cytokine_IL1-like,smart_IL1_HBGF,prints_IL1_HBGF	p.R176	ENST00000237837.1	37	c.526	CCDS8526.1	12																																																																																			FGF23	-	NULL	ENSG00000118972		0.672	FGF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FGF23	HGNC	protein_coding	OTTHUMT00000398936.1	29	0.00	0	G			4479739	4479739	-1	no_errors	ENST00000237837	ensembl	human	known	69_37n	silent	13	58.06	18	SNP	0.901	T
GPR39	2863	genome.wustl.edu	37	2	133175158	133175158	+	Silent	SNP	G	G	T			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr2:133175158G>T	ENST00000329321.3	+	1	1012	c.543G>T	c.(541-543)gtG>gtT	p.V181V		NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	181					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)	p.V181V(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ACCCCCTGGTGAACGTGCCCA	0.617																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											72.0	65.0	67.0					2																	133175158		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"""GPCR / Class A : Orphans"""	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.543G>T	2.37:g.133175158G>T			B2RC12|B6V9G4|Q08AS2|Q53R01	Silent	SNP	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn	p.V181	ENST00000329321.3	37	c.543	CCDS2170.1	2																																																																																			GPR39	-	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	ENSG00000183840		0.617	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR39	HGNC	protein_coding	OTTHUMT00000254582.1	53	0.00	0	G			133175158	133175158	+1	no_errors	ENST00000329321	ensembl	human	known	69_37n	silent	26	48.00	24	SNP	0.184	T
GRM3	2913	genome.wustl.edu	37	7	86415634	86415634	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr7:86415634G>A	ENST00000361669.2	+	3	1625	c.526G>A	c.(526-528)Gcc>Acc	p.A176T	AC005009.2_ENST00000418031.1_RNA|GRM3_ENST00000546348.1_Intron|GRM3_ENST00000536043.1_Missense_Mutation_p.A48T|AC005009.2_ENST00000452471.1_RNA|GRM3_ENST00000394720.2_Missense_Mutation_p.A174T|GRM3_ENST00000439827.1_Missense_Mutation_p.A176T	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	176					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)	p.A176T(2)		NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					ATCCACCAGCGCCAAACTCAG	0.552																																					GBM(52;969 1098 3139 52280)	dbGAP											2	Substitution - Missense(2)	prostate(1)|breast(1)											140.0	140.0	140.0					7																	86415634		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.526G>A	7.37:g.86415634G>A	ENSP00000355316:p.Ala176Thr		Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	pfam_ANF_lig-bd_rcpt,pfam_GPCR_3_C,pfam_GPCR_3_9-Cys_dom,prints_GPCR_3,prints_GPCR_3_mtglu_rcpt_3,prints_GPCR_3_mtglu_rcpt,prints_GPCR_3_mtglu_rcpt_2,prints_GPCR_3_GABA_rcpt_B,pfscan_GPCR_3_C	p.A176T	ENST00000361669.2	37	c.526	CCDS5600.1	7	.	.	.	.	.	.	.	.	.	.	G	33	5.206226	0.95033	.	.	ENSG00000198822	ENST00000361669;ENST00000454217;ENST00000536043;ENST00000439827;ENST00000394720	D;D;D;D;D	0.86366	-2.11;-2.11;-2.11;-2.11;-2.11	5.83	5.83	0.93111	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.91690	0.7373	L	0.56280	1.765	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	P;D;D	0.65573	0.895;0.923;0.936	D	0.90679	0.4604	10	0.45353	T	0.12	.	19.122	0.93367	0.0:0.0:1.0:0.0	.	48;176;176	F5GYZ2;G5E9K2;Q14832	.;.;GRM3_HUMAN	T	176;48;48;176;174	ENSP00000355316:A176T;ENSP00000405427:A48T;ENSP00000441407:A48T;ENSP00000398767:A176T;ENSP00000378209:A174T	ENSP00000355316:A176T	A	+	1	0	GRM3	86253570	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.756000	0.98918	2.770000	0.95276	0.655000	0.94253	GCC	GRM3	-	pfam_ANF_lig-bd_rcpt,prints_GPCR_3_GABA_rcpt_B	ENSG00000198822		0.552	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GRM3	HGNC	protein_coding	OTTHUMT00000253362.2	82	0.00	0	G			86415634	86415634	+1	no_errors	ENST00000361669	ensembl	human	known	69_37n	missense	77	36.36	44	SNP	1.000	A
HLA-DRB1	3123	genome.wustl.edu	37	6	32549525	32549525	+	Missense_Mutation	SNP	C	C	G			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr6:32549525C>G	ENST00000360004.5	-	3	566	c.461G>C	c.(460-462)gGc>gCc	p.G154A		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	154	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						TTCAATGCTGCCTGGATAGAA	0.542										Multiple Myeloma(14;0.17)																												dbGAP											0													97.0	115.0	109.0					6																	32549525		1511	2709	4220	-	-	-	SO:0001583	missense	0			AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.461G>C	6.37:g.32549525C>G	ENSP00000353099:p.Gly154Ala		P01914|Q9MYF5	Missense_Mutation	SNP	pfam_MHC_II_b_N,pfam_Ig_C1-set,superfamily_MHC_I/II-like_Ag-recog,smart_MHC_II_b_N,smart_Ig_C1-set,pfscan_Ig-like	p.G154A	ENST00000360004.5	37	c.461	CCDS47409.1	6	.	.	.	.	.	.	.	.	.	.	.	13.63	2.293183	0.40594	.	.	ENSG00000196126	ENST00000360004	T	0.08370	3.1	3.87	3.87	0.44632	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.367213	0.29551	N	0.011839	T	0.03011	0.0089	L	0.33137	0.985	0.27655	N	0.947267	B	0.30605	0.287	B	0.33454	0.164	T	0.27806	-1.0063	10	0.87932	D	0	.	9.8873	0.41268	0.0:0.7906:0.2094:0.0	rs1059352;rs1059620;rs3200389	154	P01911	2B1F_HUMAN	A	154	ENSP00000353099:G154A	ENSP00000353099:G154A	G	-	2	0	HLA-DRB1	32657503	0.002000	0.14202	0.957000	0.39632	0.929000	0.56500	1.302000	0.33459	1.883000	0.54544	0.453000	0.30009	GGC	HLA-DRB1	-	pfam_Ig_C1-set,smart_Ig_C1-set,pfscan_Ig-like	ENSG00000196126		0.542	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HLA-DRB1	HGNC	protein_coding	OTTHUMT00000076393.3	21	0.00	0	C	NM_002124		32549525	32549525	-1	no_errors	ENST00000360004	ensembl	human	known	69_37n	missense	152	14.61	26	SNP	0.607	G
HLA-DRB1	3123	genome.wustl.edu	37	6	32549531	32549531	+	Missense_Mutation	SNP	T	T	C	rs112796209	byFrequency	TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr6:32549531T>C	ENST00000360004.5	-	3	560	c.455A>G	c.(454-456)tAt>tGt	p.Y152C		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	152	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GCTGCCTGGATAGAAACCACT	0.532										Multiple Myeloma(14;0.17)																												dbGAP											0													101.0	120.0	113.0					6																	32549531		1511	2709	4220	-	-	-	SO:0001583	missense	0			AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.455A>G	6.37:g.32549531T>C	ENSP00000353099:p.Tyr152Cys		P01914|Q9MYF5	Missense_Mutation	SNP	pfam_MHC_II_b_N,pfam_Ig_C1-set,superfamily_MHC_I/II-like_Ag-recog,smart_MHC_II_b_N,smart_Ig_C1-set,pfscan_Ig-like	p.Y152C	ENST00000360004.5	37	c.455	CCDS47409.1	6	.	.	.	.	.	.	.	.	.	.	.	15.26	2.782128	0.49891	.	.	ENSG00000196126	ENST00000360004	T	0.04317	3.65	3.87	3.87	0.44632	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.113906	0.64402	D	0.000009	T	0.18882	0.0453	H	0.96398	3.815	0.44275	D	0.997133	D	0.89917	1.0	D	0.97110	1.0	T	0.02813	-1.1107	10	0.87932	D	0	.	6.8165	0.23833	0.2079:0.0:0.0:0.7921	.	152	P01911	2B1F_HUMAN	C	152	ENSP00000353099:Y152C	ENSP00000353099:Y152C	Y	-	2	0	HLA-DRB1	32657509	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	2.404000	0.44539	1.535000	0.49220	0.372000	0.22366	TAT	HLA-DRB1	-	pfam_Ig_C1-set,smart_Ig_C1-set,pfscan_Ig-like	ENSG00000196126		0.532	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HLA-DRB1	HGNC	protein_coding	OTTHUMT00000076393.3	24	0.00	0	T	NM_002124		32549531	32549531	-1	no_errors	ENST00000360004	ensembl	human	known	69_37n	missense	162	14.29	27	SNP	1.000	C
LAMA2	3908	genome.wustl.edu	37	6	129785500	129785500	+	Missense_Mutation	SNP	G	G	A	rs548483084		TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr6:129785500G>A	ENST00000421865.2	+	50	7107	c.7058G>A	c.(7057-7059)cGt>cAt	p.R2353H		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2353	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.R2353H(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		TTGGTCAGCCGTCCCATTCGC	0.453													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18973	0.0		0.0	False		,,,				2504	0.0					dbGAP											1	Substitution - Missense(1)	breast(1)											301.0	237.0	259.0					6																	129785500		2203	4300	6503	-	-	-	SO:0001583	missense	0			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.7058G>A	6.37:g.129785500G>A	ENSP00000400365:p.Arg2353His		Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	pfam_Laminin_G,pfam_EGF_laminin,pfam_Laminin_N,pfam_Laminin_I,pfam_Laminin_B_type_IV,pfam_Laminin_II,superfamily_ConA-like_lec_gl,superfamily_Galactose-bd-like,superfamily_t-SNARE,smart_Laminin_N,smart_EGF_laminin,smart_EGF-like,smart_Laminin_B_subgr,smart_Laminin_G,pfscan_Laminin_B_type_IV,pfscan_EGF_laminin,pfscan_Laminin_G,pfscan_Laminin_N	p.R2353H	ENST00000421865.2	37	c.7058	CCDS5138.1	6	.	.	.	.	.	.	.	.	.	.	G	34	5.303928	0.95601	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865;ENST00000443169	T	0.79352	-1.26	5.87	5.87	0.94306	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.094456	0.85682	D	0.000000	T	0.80696	0.4672	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.989	T	0.77099	-0.2713	9	.	.	.	.	20.1922	0.98231	0.0:0.0:1.0:0.0	.	2354;2353	A6NF00;P24043	.;LAMA2_HUMAN	H	2353;2352;2353;371	ENSP00000400365:R2353H	.	R	+	2	0	LAMA2	129827193	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.352000	0.97076	2.767000	0.95098	0.655000	0.94253	CGT	LAMA2	-	superfamily_ConA-like_lec_gl,pfscan_Laminin_G	ENSG00000196569		0.453	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LAMA2	HGNC	protein_coding	OTTHUMT00000042180.1	98	0.00	0	G			129785500	129785500	+1	no_errors	ENST00000421865	ensembl	human	known	69_37n	missense	186	23.46	57	SNP	1.000	A
NID1	4811	genome.wustl.edu	37	1	236205579	236205579	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr1:236205579C>T	ENST00000264187.6	-	4	848	c.766G>A	c.(766-768)Ggg>Agg	p.G256R	NID1_ENST00000366595.3_Missense_Mutation_p.G256R	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	256	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)	p.G256R(1)		breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	CCCTGCTGCCCAGAGTTACTA	0.572																																						dbGAP											1	Substitution - Missense(1)	breast(1)											145.0	155.0	152.0					1																	236205579		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"""nidogen (enactin)"""	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.766G>A	1.37:g.236205579C>T	ENSP00000264187:p.Gly256Arg		Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	pfam_G2_nidogen/fibulin_G2F,pfam_LDLR_classB_rpt,pfam_Nidogen_extracell_dom,pfam_Thyroglobulin_1,pfam_EGF-like_Ca-bd,superfamily_Green_fluorescent_prot-like,superfamily_Thyroglobulin_1,smart_Nidogen_extracell_dom,smart_EGF-like_Ca-bd,smart_EGF-like,smart_G2_nidogen/fibulin_G2F,smart_Thyroglobulin_1,smart_LDLR_classB_rpt,pfscan_EG-like_dom,pfscan_LDLR_classB_rpt,pfscan_G2_nidogen/fibulin_G2F,pfscan_Thyroglobulin_1	p.G256R	ENST00000264187.6	37	c.766	CCDS1608.1	1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.230257	0.79688	.	.	ENSG00000116962	ENST00000264187;ENST00000366595	T;T	0.80033	-1.33;-1.33	5.29	4.35	0.52113	Nidogen, extracellular domain (3);	0.150670	0.64402	N	0.000008	D	0.90655	0.7069	M	0.88704	2.975	0.49798	D	0.999823	B;D	0.89917	0.36;1.0	B;D	0.83275	0.181;0.996	D	0.92309	0.5856	10	0.72032	D	0.01	.	14.1874	0.65614	0.0:0.8505:0.1495:0.0	.	256;256	P14543-2;P14543	.;NID1_HUMAN	R	256	ENSP00000264187:G256R;ENSP00000355554:G256R	ENSP00000264187:G256R	G	-	1	0	NID1	234272202	1.000000	0.71417	0.957000	0.39632	0.892000	0.51952	6.578000	0.74032	1.420000	0.47138	0.563000	0.77884	GGG	NID1	-	pfam_Nidogen_extracell_dom,smart_Nidogen_extracell_dom	ENSG00000116962		0.572	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NID1	HGNC	protein_coding	OTTHUMT00000096647.2	13	0.00	0	C	NM_002508		236205579	236205579	-1	no_errors	ENST00000264187	ensembl	human	known	69_37n	missense	75	22.68	22	SNP	0.989	T
NKX2-5	1482	genome.wustl.edu	37	5	172659707	172659708	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr5:172659707_172659708insG	ENST00000329198.4	-	2	1112_1113	c.839_840insC	c.(838-840)ccafs	p.P280fs		NM_001166175.1|NM_001166176.1|NM_004387.3	NP_001159647.1|NP_001159648.1|NP_004378.1	P52952	NKX25_HUMAN	NK2 homeobox 5	280	Ala/Pro-rich.				adult heart development (GO:0007512)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial cardiac muscle cell development (GO:0055014)|atrial septum morphogenesis (GO:0060413)|atrioventricular node cell development (GO:0060928)|atrioventricular node cell fate commitment (GO:0060929)|BMP signaling pathway (GO:0030509)|bundle of His development (GO:0003166)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac ventricle formation (GO:0003211)|cell differentiation (GO:0030154)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|hemopoiesis (GO:0030097)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|pharyngeal system development (GO:0060037)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart contraction (GO:0045823)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of voltage-gated calcium channel activity (GO:1901387)|proepicardium development (GO:0003342)|pulmonary myocardium development (GO:0003350)|Purkinje myocyte differentiation (GO:0003168)|regulation of cardiac muscle cell proliferation (GO:0060043)|regulation of cardiac muscle contraction (GO:0055117)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|sarcomere organization (GO:0045214)|septum secundum development (GO:0003285)|spleen development (GO:0048536)|thyroid gland development (GO:0030878)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|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 distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)	12	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CCGGCTGCGCTGGGGAAGGCCC	0.673																																					Esophageal Squamous(72;810 1219 2387 13420 44943)	dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB021133	CCDS4387.1, CCDS54949.1, CCDS54950.1	5q34	2014-09-17	2011-06-01	2002-10-04	ENSG00000183072	ENSG00000183072		"""Homeoboxes / ANTP class : NKL subclass"""	2488	protein-coding gene	gene with protein product	"""tinman paralog (Drosophila)"""	600584	"""cardiac-specific homeo box"", ""NK2 transcription factor related, locus 5 (Drosophila)"""	CSX, NKX2E		7665173, 8900537	Standard	NM_004387		Approved	CSX1, NKX2.5, NKX4-1	uc003mcm.2	P52952	OTTHUMG00000130522	ENST00000329198.4:c.840dupC	5.37:g.172659711_172659711dupG	ENSP00000327758:p.Pro280fs		A8K3K0|B4DNB6|E9PBU6	Frame_Shift_Ins	INS	pfam_Homeodomain,superfamily_Homeodomain-like,smart_Homeodomain,prints_Homeobox_metazoa,pfscan_Homeodomain	p.A281fs	ENST00000329198.4	37	c.840_839	CCDS4387.1	5																																																																																			NKX2-5	-	NULL	ENSG00000183072		0.673	NKX2-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NKX2-5	HGNC	protein_coding	OTTHUMT00000252942.2	9	0.00	0	-			172659707	172659708	-1	no_errors	ENST00000329198	ensembl	human	known	69_37n	frame_shift_ins	6	40.00	4	INS	0.138:0.398	G
NTSR2	23620	genome.wustl.edu	37	2	11802135	11802135	+	Missense_Mutation	SNP	C	C	T	rs574844067		TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr2:11802135C>T	ENST00000306928.5	-	2	890	c.856G>A	c.(856-858)Gtg>Atg	p.V286M		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	286					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)	p.V286M(1)		breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	ATCCGGCGCACGTCTTTATGT	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		20172	0.001		0.0	False		,,,				2504	0.0					dbGAP											1	Substitution - Missense(1)	breast(1)											73.0	78.0	77.0					2																	11802135		2203	4300	6503	-	-	-	SO:0001583	missense	0			Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"""GPCR / Class A : Neurotensin receptors"""	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.856G>A	2.37:g.11802135C>T	ENSP00000303686:p.Val286Met		Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,prints_NT2_rcpt,prints_NT_rcpt,prints_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	p.V286M	ENST00000306928.5	37	c.856	CCDS1681.1	2	.	.	.	.	.	.	.	.	.	.	C	8.784	0.928873	0.18131	.	.	ENSG00000169006	ENST00000306928	T	0.71579	-0.58	4.31	-1.62	0.08372	GPCR, rhodopsin-like superfamily (1);	1.536130	0.03893	N	0.278944	T	0.53400	0.1794	N	0.14661	0.345	0.09310	N	1	D	0.60575	0.988	P	0.46389	0.515	T	0.47394	-0.9121	10	0.33141	T	0.24	-9.0853	2.4985	0.04628	0.3795:0.3908:0.1137:0.1159	.	286	O95665	NTR2_HUMAN	M	286	ENSP00000303686:V286M	ENSP00000303686:V286M	V	-	1	0	NTSR2	11719586	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.214000	0.02988	-0.192000	0.10432	0.455000	0.32223	GTG	NTSR2	-	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	ENSG00000169006		0.582	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NTSR2	HGNC	protein_coding	OTTHUMT00000239297.1	15	0.00	0	C			11802135	11802135	-1	no_errors	ENST00000306928	ensembl	human	known	69_37n	missense	16	27.27	6	SNP	0.000	T
NUP153	9972	genome.wustl.edu	37	6	17629273	17629273	+	Missense_Mutation	SNP	T	T	A			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr6:17629273T>A	ENST00000262077.2	-	18	3156	c.3157A>T	c.(3157-3159)Ata>Tta	p.I1053L	NUP153_ENST00000537253.1_Missense_Mutation_p.I1084L	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	1053					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)	p.I1053L(1)		NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			TTGGTTTCTATGGTTCCAAGG	0.448																																						dbGAP											1	Substitution - Missense(1)	breast(1)											103.0	98.0	100.0					6																	17629273		2203	4300	6503	-	-	-	SO:0001583	missense	0			Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"""nucleoporin 153kD"""			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.3157A>T	6.37:g.17629273T>A	ENSP00000262077:p.Ile1053Leu		B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Missense_Mutation	SNP	pfam_Nucleoporin_Nup153,pfam_Znf_RanBP2,pfam_Retro-transposon_transp_CS,smart_Znf_RanBP2,pfscan_Znf_RanBP2	p.I1084L	ENST00000262077.2	37	c.3250	CCDS4541.1	6	.	.	.	.	.	.	.	.	.	.	T	8.032	0.762070	0.15914	.	.	ENSG00000124789	ENST00000262077;ENST00000430136;ENST00000537253	T;T	0.06294	3.33;3.32	5.57	-7.52	0.01341	.	1.503030	0.04353	N	0.356079	T	0.00875	0.0029	N	0.25647	0.755	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.45116	-0.9283	10	0.10902	T	0.67	6.509	4.1263	0.10129	0.1118:0.393:0.3352:0.16	.	1084;1033;1053	F6QR24;Q4LE47;P49790	.;.;NU153_HUMAN	L	1053;1033;1084	ENSP00000262077:I1053L;ENSP00000444029:I1084L	ENSP00000262077:I1053L	I	-	1	0	NUP153	17737252	0.000000	0.05858	0.006000	0.13384	0.640000	0.38277	-1.315000	0.02713	-1.429000	0.01987	-0.256000	0.11100	ATA	NUP153	-	NULL	ENSG00000124789		0.448	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NUP153	HGNC	protein_coding	OTTHUMT00000039953.1	107	0.00	0	T			17629273	17629273	-1	no_errors	ENST00000537253	ensembl	human	known	69_37n	missense	98	14.78	17	SNP	0.000	A
PGD	5226	genome.wustl.edu	37	1	10477067	10477067	+	Missense_Mutation	SNP	T	T	G			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr1:10477067T>G	ENST00000270776.8	+	9	906	c.868T>G	c.(868-870)Tta>Gta	p.L290V	PGD_ENST00000541529.1_Missense_Mutation_p.L268V|PGD_ENST00000538557.1_Missense_Mutation_p.L277V|PGD_ENST00000498356.1_3'UTR	NM_002631.2	NP_002622.2	P52209	6PGD_HUMAN	phosphogluconate dehydrogenase	290					carbohydrate metabolic process (GO:0005975)|D-gluconate metabolic process (GO:0019521)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	NADP binding (GO:0050661)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)	p.L290V(1)		NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	14	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.00832)|READ - Rectum adenocarcinoma(331;0.0487)	Dacarbazine(DB00851)|Furosemide(DB00695)|Gadopentetate dimeglumine(DB00789)|Ketotifen(DB00920)|Meloxicam(DB00814)|Methotrexate(DB00563)|Ritodrine(DB00867)	TGCTCGGTGCTTATCATCTCT	0.463																																						dbGAP											1	Substitution - Missense(1)	breast(1)											83.0	77.0	79.0					1																	10477067		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC000368	CCDS113.1	1p36.22	2012-10-02			ENSG00000142657	ENSG00000142657	1.1.1.43		8891	protein-coding gene	gene with protein product		172200					Standard	NM_002631		Approved		uc001arc.3	P52209	OTTHUMG00000001905	ENST00000270776.8:c.868T>G	1.37:g.10477067T>G	ENSP00000270776:p.Leu290Val		A8K2Y9|B4DQJ8|Q9BWD8	Missense_Mutation	SNP	pfam_6PGDH_C,pfam_6PGDH_NADP-bd,superfamily_6-PGluconate_DH_C-like,tigrfam_6PGDH_decarbox	p.L290V	ENST00000270776.8	37	c.868	CCDS113.1	1	.	.	.	.	.	.	.	.	.	.	T	17.29	3.352768	0.61293	.	.	ENSG00000142657	ENST00000541529;ENST00000543846;ENST00000270776;ENST00000538557	T;T;T	0.55052	0.54;0.54;0.54	4.82	2.42	0.29668	6-phosphogluconate dehydrogenase, C-terminal (1);Dehydrogenase, multihelical (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.000000	0.64402	D	0.000001	T	0.64427	0.2597	M	0.78456	2.415	0.58432	D	0.999997	D;D;D	0.61697	0.977;0.99;0.99	P;D;D	0.66084	0.671;0.941;0.941	T	0.61178	-0.7115	10	0.31617	T	0.26	-14.0631	6.1334	0.20217	0.0:0.4476:0.0:0.5524	.	268;290;290	F5H7U0;A8K2Y9;P52209	.;.;6PGD_HUMAN	V	268;236;290;277	ENSP00000442285:L268V;ENSP00000270776:L290V;ENSP00000437822:L277V	ENSP00000270776:L290V	L	+	1	2	PGD	10399654	0.997000	0.39634	0.999000	0.59377	0.995000	0.86356	0.921000	0.28718	0.793000	0.33875	0.529000	0.55759	TTA	PGD	-	pfam_6PGDH_C,superfamily_6-PGluconate_DH_C-like,tigrfam_6PGDH_decarbox	ENSG00000142657		0.463	PGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PGD	HGNC	protein_coding	OTTHUMT00000005398.1	104	0.00	0	T	NM_002631		10477067	10477067	+1	no_errors	ENST00000270776	ensembl	human	known	69_37n	missense	102	25.00	34	SNP	1.000	G
PHACTR1	221692	genome.wustl.edu	37	6	13287303	13287303	+	Missense_Mutation	SNP	G	G	T			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr6:13287303G>T	ENST00000379335.3	+	5	533	c.428G>T	c.(427-429)cGa>cTa	p.R143L	PHACTR1_ENST00000332995.7_Intron|RP1-257A7.4_ENST00000606150.1_RNA|PHACTR1_ENST00000457702.2_Intron|RP1-257A7.5_ENST00000606393.1_lincRNA			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	579					actin cytoskeleton reorganization (GO:0031532)|actomyosin structure organization (GO:0031032)|cell motility (GO:0048870)|stress fiber assembly (GO:0043149)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)|synapse (GO:0045202)	actin binding (GO:0003779)|protein phosphatase inhibitor activity (GO:0004864)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			AGGTTTCACCGACCTTAACAG	0.418																																						dbGAP											0													235.0	214.0	221.0					6																	13287303		1910	4129	6039	-	-	-	SO:0001583	missense	0			AB051520	CCDS75401.1	6p23	2013-01-24	2004-05-20	2004-05-21	ENSG00000112137	ENSG00000112137		"""Phosphatase and actin regulators"""	20990	protein-coding gene	gene with protein product		608723	"""RPEL repeat containing 1"""	RPEL1		11214970, 15107502	Standard	NM_030948		Approved	KIAA1733, dJ257A7.2	uc010jpc.3	Q9C0D0	OTTHUMG00000014270	ENST00000379335.3:c.428G>T	6.37:g.13287303G>T	ENSP00000368639:p.Arg143Leu		A8K1V2|Q3MJ93|Q5JSJ2	Missense_Mutation	SNP	pfam_RPEL_repeat,smart_RPEL_repeat,pfscan_RPEL_repeat	p.R143L	ENST00000379335.3	37	c.428		6	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.0|28.0	4.884749|4.884749	0.91814|0.91814	.|.	.|.	ENSG00000112137|ENSG00000112137	ENST00000415087|ENST00000379335	.|.	.|.	.|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	.|.	.|.	.|.	.|.	T|T	0.63058|0.63058	0.2479|0.2479	M|M	0.82630|0.82630	2.6|2.6	0.80722|0.80722	D|D	1|1	.|P	.|0.38300	.|0.626	.|B	.|0.39531	.|0.302	T|T	0.70883|0.70883	-0.4751|-0.4751	5|8	.|0.87932	.|D	.|0	.|.	19.045|19.045	0.93016|0.93016	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|579	.|Q9C0D0	.|PHAR1_HUMAN	Y|L	414|143	.|.	.|ENSP00000368639:R143L	D|R	+|+	1|2	0|0	PHACTR1|PHACTR1	13395282|13395282	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	7.380000|7.380000	0.79704|0.79704	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	GAC|CGA	PHACTR1	-	NULL	ENSG00000112137		0.418	PHACTR1-003	KNOWN	basic|appris_candidate	protein_coding	PHACTR1	HGNC	protein_coding	OTTHUMT00000039878.1	187	0.00	0	G	XM_166420		13287303	13287303	+1	no_errors	ENST00000379335	ensembl	human	known	69_37n	missense	168	23.98	53	SNP	1.000	T
PHLDA1	22822	genome.wustl.edu	37	12	76424820	76424820	+	Missense_Mutation	SNP	G	G	T			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr12:76424820G>T	ENST00000266671.5	-	1	2892	c.702C>A	c.(700-702)ttC>ttA	p.F234L	PHLDA1_ENST00000602540.1_Missense_Mutation_p.F93L|RP11-290L1.2_ENST00000547721.1_RNA|RP11-290L1.3_ENST00000552367.1_RNA			Q8WV24	PHLA1_HUMAN	pleckstrin homology-like domain, family A, member 1	234	PH.				apoptotic process (GO:0006915)|FasL biosynthetic process (GO:0045210)|forebrain neuron differentiation (GO:0021879)|positive regulation of apoptotic process (GO:0043065)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)|nucleus (GO:0005634)		p.F234L(1)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	14		Colorectal(145;0.09)				TCATGTTGGAGAAGTGCAGTT	0.632																																						dbGAP											1	Substitution - Missense(1)	breast(1)											95.0	75.0	82.0					12																	76424820		2203	4300	6503	-	-	-	SO:0001583	missense	0			Z50194	CCDS31861.1	12q15	2008-08-05				ENSG00000139289			8933	protein-coding gene	gene with protein product	"""proline-histidine rich protein"""	605335				12384558, 15037619	Standard	NM_007350		Approved	TDAG51, DT1P1B11, PHRIP	uc001sxu.3	Q8WV24		ENST00000266671.5:c.702C>A	12.37:g.76424820G>T	ENSP00000266671:p.Phe234Leu		A1A4G9|Q15184|Q2TAN2|Q9NZ17	Missense_Mutation	SNP	smart_Pleckstrin_homology	p.F234L	ENST00000266671.5	37	c.702	CCDS31861.1	12	.	.	.	.	.	.	.	.	.	.	G	25.4	4.629581	0.87660	.	.	ENSG00000139289	ENST00000266671;ENST00000421361	T	0.59224	0.28	4.66	1.03	0.20045	Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.51415	0.1673	L	0.42245	1.32	0.47245	D	0.999364	P	0.40970	0.734	P	0.46510	0.519	T	0.49661	-0.8916	10	0.87932	D	0	-7.4518	6.7627	0.23550	0.4154:0.0:0.5846:0.0	.	234	Q8WV24	PHLA1_HUMAN	L	234;93	ENSP00000266671:F234L	ENSP00000266671:F234L	F	-	3	2	PHLDA1	74711087	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.599000	0.54045	0.317000	0.23160	-0.367000	0.07326	TTC	PHLDA1	-	smart_Pleckstrin_homology	ENSG00000139289		0.632	PHLDA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PHLDA1	HGNC	protein_coding	OTTHUMT00000405846.2	87	0.00	0	G	NM_007350		76424820	76424820	-1	no_errors	ENST00000266671	ensembl	human	known	69_37n	missense	23	62.30	38	SNP	1.000	T
PKD1L2	114780	genome.wustl.edu	37	16	81242149	81242150	+	RNA	DEL	TT	TT	-	rs55980345|rs75398810|rs532218091|rs548490632|rs386792900	byFrequency	TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	TT	TT					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr16:81242149_81242150delTT	ENST00000525539.1	-	0	705_706				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.N236fs*26(6)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CGGACACAGGTTTCCAAAGTAG	0.554																																						dbGAP											6	Deletion - Frameshift(6)	breast(4)|lung(2)																																								-	-	-			0			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242149_81242150delTT			Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Frame_Shift_Del	DEL	pfam_Lectin_gal-bd_dom,pfam_C-type_lectin,pfam_PKD/REJ-like,superfamily_C-type_lectin_fold,superfamily_Coatomer/clathrin_app_Ig-like,superfamily_PKD_dom,smart_C-type_lectin,pfscan_C-type_lectin,pfscan_Lectin_gal-bd_dom,pfscan_REJ-like	p.N236fs	ENST00000525539.1	37	c.707_706		16																																																																																			PKD1L2	-	pfam_Lectin_gal-bd_dom,pfscan_Lectin_gal-bd_dom	ENSG00000166473		0.554	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	PKD1L2	HGNC	polymorphic_pseudogene	OTTHUMT00000387972.2	15	0.00	0	TT			81242149	81242150	-1	no_errors	ENST00000337114	ensembl	human	known	69_37n	frame_shift_del	23	48.08	25	DEL	0.998:0.999	-
PNKP	11284	genome.wustl.edu	37	19	50370371	50370372	+	Frame_Shift_Del	DEL	GG	GG	-			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	GG	GG					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr19:50370371_50370372delGG	ENST00000322344.3	-	2	199_200	c.90_91delCC	c.(88-93)gccctgfs	p.L31fs	PNKP_ENST00000600573.1_Frame_Shift_Del_p.L31fs|PNKP_ENST00000595792.1_5'UTR|PNKP_ENST00000600910.1_Frame_Shift_Del_p.L31fs|PNKP_ENST00000596014.1_Frame_Shift_Del_p.L31fs	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	31	FHA.				dephosphorylation (GO:0016311)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide phosphorylation (GO:0046939)|nucleotide-excision repair, DNA damage removal (GO:0000718)|polynucleotide 3' dephosphorylation (GO:0098506)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|endonuclease activity (GO:0004519)|nucleotide kinase activity (GO:0019201)|polynucleotide 3'-phosphatase activity (GO:0046403)|purine nucleotide binding (GO:0017076)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|urinary_tract(1)	19		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)		CCCAGGACCAGGGCTTGCCCGT	0.718								Other BER factors																														dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF126486	CCDS12783.1	19q13.3-q13.4	2008-02-05				ENSG00000039650			9154	protein-coding gene	gene with protein product		605610				10446192, 10446193	Standard	NM_007254		Approved	PNK	uc002pqj.3	Q96T60		ENST00000322344.3:c.90_91delCC	19.37:g.50370371_50370372delGG	ENSP00000323511:p.Leu31fs		Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	Frame_Shift_Del	DEL	pfam_PNK3P,superfamily_HAD-like_dom,superfamily_SMAD_FHA_domain,tigrfam_PNK_3Pase_met,tigrfam_Polynucleotide_phosphatase,tigrfam_HAD-SF_hydro_IIIA	p.L31fs	ENST00000322344.3	37	c.91_90	CCDS12783.1	19																																																																																			PNKP	-	superfamily_SMAD_FHA_domain,tigrfam_PNK_3Pase_met	ENSG00000039650		0.718	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PNKP	HGNC	protein_coding	OTTHUMT00000465830.1	11	0.00	0	GG	NM_007254		50370371	50370372	-1	no_errors	ENST00000322344	ensembl	human	known	69_37n	frame_shift_del	8	70.97	22	DEL	0.141:0.055	-
RFPL1	5988	genome.wustl.edu	37	22	29835418	29835418	+	Intron	SNP	C	C	A			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr22:29835418C>A	ENST00000354373.2	+	1	582				RFPL1S_ENST00000461286.3_RNA|RFPL1S_ENST00000539579.1_RNA	NM_021026.2	NP_066306.2	O75677	RFPL1_HUMAN	ret finger protein-like 1								zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(1)|lung(6)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	16						gtcaggagatcgggaccatcc	0.532																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			AJ010228	CCDS13857.2	22q12	2006-04-25			ENSG00000128250	ENSG00000128250		"""RING-type (C3HC4) zinc fingers"""	9977	protein-coding gene	gene with protein product		605968				10508838	Standard	NM_021026		Approved	RNF78	uc003afn.3	O75677	OTTHUMG00000150516	ENST00000354373.2:c.373+265C>A	22.37:g.29835418C>A			Q6IC06|Q9UJ97	RNA	SNP	-	NULL	ENST00000354373.2	37	NULL	CCDS13857.2	22																																																																																			RFPL1-AS1	-	-	ENSG00000225465		0.532	RFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RFPL1-AS1	HGNC	protein_coding	OTTHUMT00000318719.1	9	0.00	0	C	NM_021026		29835418	29835418	-1	no_errors	ENST00000461286	ensembl	human	known	69_37n	rna	1	92.31	12	SNP	0.000	A
SNRPN	6638	genome.wustl.edu	37	15	25222051	25222051	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr15:25222051G>T	ENST00000400100.1	+	10	1185	c.295G>T	c.(295-297)Gga>Tga	p.G99*	SNRPN_ENST00000444203.2_Nonsense_Mutation_p.G103*|SNRPN_ENST00000400097.1_Nonsense_Mutation_p.G99*|SNRPN_ENST00000390687.4_Nonsense_Mutation_p.G99*|SNHG14_ENST00000551631.2_RNA|SNRPN_ENST00000577565.1_Nonsense_Mutation_p.G99*|SNRPN_ENST00000554227.2_Nonsense_Mutation_p.G103*|SNRPN_ENST00000400098.1_Nonsense_Mutation_p.G99*|SNRPN_ENST00000346403.6_Nonsense_Mutation_p.G99*|SNURF_ENST00000338094.6_3'UTR|SNURF_ENST00000551312.2_Intron	NM_022807.2	NP_073718.1	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N	99					response to hormone (GO:0009725)|RNA splicing (GO:0008380)	small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U2 snRNP (GO:0005686)	RNA binding (GO:0003723)	p.G99*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(14)|ovary(1)|skin(2)	24		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)		ACCACTTGCTGGAGCTGCTGG	0.512									Prader-Willi syndrome																													dbGAP											1	Substitution - Nonsense(1)	breast(1)											85.0	88.0	87.0					15																	25222051		1941	4152	6093	-	-	-	SO:0001587	stop_gained	0	Familial Cancer Database	Prader-Labhart-Willi syndrome	L80005	CCDS10017.1	15q11.2	2013-07-16			ENSG00000128739	ENSG00000128739			11164	protein-coding gene	gene with protein product	"""tissue-specific splicing protein"", ""SM protein N"", ""small nuclear ribonucleoprotein N"""	182279	"""Prader-Willi syndrome chromosome region"""	PWCR		1533223	Standard	NM_022805		Approved	SMN, SM-D, HCERN3, SNRNP-N, SNURF-SNRPN, RT-LI	uc001ywt.1	P63162	OTTHUMG00000129180	ENST00000400100.1:c.295G>T	15.37:g.25222051G>T	ENSP00000382972:p.Gly99*		B3KVR1|P14648|P17135|Q0D2Q5	Nonsense_Mutation	SNP	pfam_Ribonucl_LSM,superfamily_LSM_dom,smart_Ribonucl_LSM_euk/arc,pirsf_snRNP-assoc_SmB/SmN	p.G103*	ENST00000400100.1	37	c.307	CCDS10017.1	15	.	.	.	.	.	.	.	.	.	.	G	44	10.886358	0.99483	.	.	ENSG00000128739	ENST00000400100;ENST00000400098;ENST00000400097;ENST00000554227;ENST00000390687;ENST00000444203	.	.	.	3.79	2.88	0.33553	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-12.8713	9.6315	0.39782	0.1056:0.0:0.8944:0.0	.	.	.	.	X	99;99;99;103;99;103	.	ENSP00000375105:G99X	G	+	1	0	SNRPN	22773144	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.116000	0.89574	1.180000	0.42898	0.561000	0.74099	GGA	SNRPN	-	pirsf_snRNP-assoc_SmB/SmN	ENSG00000128739		0.512	SNRPN-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	SNRPN	HGNC	protein_coding	OTTHUMT00000413849.10	72	0.00	0	G	NM_003097		25222051	25222051	+1	no_errors	ENST00000444203	ensembl	human	known	69_37n	nonsense	66	31.25	30	SNP	1.000	T
SUPT5H	6829	genome.wustl.edu	37	19	39955678	39955678	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr19:39955678G>A	ENST00000599117.1	+	12	1232	c.865G>A	c.(865-867)Gac>Aac	p.D289N	SUPT5H_ENST00000402194.2_Missense_Mutation_p.D285N|SUPT5H_ENST00000432763.2_Missense_Mutation_p.D289N|SUPT5H_ENST00000598725.1_Missense_Mutation_p.D289N|SUPT5H_ENST00000359191.6_Missense_Mutation_p.D285N			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	289	KOW 1.				7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)	p.D289N(1)		breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CTACAAGGATGACATTGCTCA	0.582																																						dbGAP											1	Substitution - Missense(1)	breast(1)											67.0	67.0	67.0					19																	39955678		2203	4300	6503	-	-	-	SO:0001583	missense	0			U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"""suppressor of Ty (S.cerevisiae) 5 homolog"""			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.865G>A	19.37:g.39955678G>A	ENSP00000470252:p.Asp289Asn		O43279|Q59G52|Q99639	Missense_Mutation	SNP	pfam_TF_Spt5_NGN-domain,pfam_KOW,pfam_Spt5_N,superfamily_Translation_prot_SH3-like,smart_Transcrpt_antiterm_NusG_N,smart_KOW,pirsf_TF_Spt5	p.D289N	ENST00000599117.1	37	c.865	CCDS12536.1	19	.	.	.	.	.	.	.	.	.	.	G	35	5.503361	0.96371	.	.	ENSG00000196235	ENST00000432763;ENST00000402194;ENST00000378524;ENST00000359191	.	.	.	5.65	5.65	0.86999	KOW (1);	0.000000	0.85682	D	0.000000	D	0.85159	0.5633	M	0.89095	3.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86881	0.2042	8	.	.	.	-35.3683	18.4891	0.90841	0.0:0.0:1.0:0.0	.	285;289	O00267-2;O00267	.;SPT5H_HUMAN	N	289;285;267;289	.	.	D	+	1	0	SUPT5H	44647518	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.670000	0.98625	2.670000	0.90874	0.563000	0.77884	GAC	SUPT5H	-	smart_KOW,pirsf_TF_Spt5	ENSG00000196235		0.582	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SUPT5H	HGNC	protein_coding	OTTHUMT00000464918.1	27	0.00	0	G	NM_003169		39955678	39955678	+1	no_errors	ENST00000359191	ensembl	human	known	69_37n	missense	27	22.86	8	SNP	1.000	A
TGFBR2	7048	genome.wustl.edu	37	3	30732950	30732950	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr3:30732950G>A	ENST00000295754.5	+	7	1945	c.1563G>A	c.(1561-1563)tgG>tgA	p.W521*	TGFBR2_ENST00000359013.4_Nonsense_Mutation_p.W546*	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)	521	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		W -> R (in LDS2). {ECO:0000269|PubMed:20358619}.		activation of protein kinase activity (GO:0032147)|aging (GO:0007568)|apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|cartilage development (GO:0051216)|common-partner SMAD protein phosphorylation (GO:0007182)|digestive tract development (GO:0048565)|embryo implantation (GO:0007566)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic hemopoiesis (GO:0035162)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lens development in camera-type eye (GO:0002088)|lens fiber cell apoptotic process (GO:1990086)|lung lobe morphogenesis (GO:0060463)|mammary gland morphogenesis (GO:0060443)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell tolerance induction (GO:0002663)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of tolerance induction to self antigen (GO:0002651)|protein phosphorylation (GO:0006468)|receptor-mediated endocytosis (GO:0006898)|regulation of cell proliferation (GO:0042127)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|smoothened signaling pathway (GO:0007224)|trachea formation (GO:0060440)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|wound healing (GO:0042060)	caveola (GO:0005901)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|glycosaminoglycan binding (GO:0005539)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type II (GO:0005026)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|type I transforming growth factor beta receptor binding (GO:0034713)|type III transforming growth factor beta receptor binding (GO:0034714)	p.W521*(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(15)|lung(10)|ovary(3)|pancreas(12)|skin(1)|stomach(5)|upper_aerodigestive_tract(2)	53						CTGAGTGCTGGGACCACGACC	0.617																																						dbGAP											2	Substitution - Nonsense(2)	large_intestine(1)|breast(1)											72.0	63.0	66.0					3																	30732950		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0				CCDS2648.1, CCDS33727.1	3p22	2014-09-17	2002-08-29		ENSG00000163513	ENSG00000163513			11773	protein-coding gene	gene with protein product		190182	"""transforming growth factor, beta receptor II (70-80kD)"""	MFS2		1319842, 15235604	Standard	NM_001024847		Approved		uc003cen.3	P37173	OTTHUMG00000130569	ENST00000295754.5:c.1563G>A	3.37:g.30732950G>A	ENSP00000295754:p.Trp521*		B4DTV5|Q15580|Q6DKT6|Q99474	Nonsense_Mutation	SNP	pirsf_Transform_growth_fac-b_typ-2,pfam_Transforming_GF_b_rcpt_2_ecto,pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Activin_II/TGFBeta-II_recpt,pfscan_Prot_kinase_cat_dom	p.W546*	ENST00000295754.5	37	c.1638	CCDS2648.1	3	.	.	.	.	.	.	.	.	.	.	G	41	9.033661	0.99042	.	.	ENSG00000163513	ENST00000295754;ENST00000359013;ENST00000439925	.	.	.	5.91	5.03	0.67393	.	0.054129	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.3682	0.83343	0.0:0.0:0.8671:0.1329	.	.	.	.	X	521;546;351	.	ENSP00000295754:W521X	W	+	3	0	TGFBR2	30707954	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	1.469000	0.48083	0.655000	0.94253	TGG	TGFBR2	-	pirsf_Transform_growth_fac-b_typ-2,pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Activin_II/TGFBeta-II_recpt,pfscan_Prot_kinase_cat_dom	ENSG00000163513		0.617	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TGFBR2	HGNC	protein_coding	OTTHUMT00000252994.2	99	0.00	0	G			30732950	30732950	+1	no_errors	ENST00000359013	ensembl	human	known	69_37n	nonsense	55	61.54	88	SNP	1.000	A
TOR1AIP1	26092	genome.wustl.edu	37	1	179870511	179870511	+	Missense_Mutation	SNP	G	G	T			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr1:179870511G>T	ENST00000606911.2	+	5	918	c.727G>T	c.(727-729)Gat>Tat	p.D243Y	TOR1AIP1_ENST00000271583.3_Missense_Mutation_p.D244Y|RN7SL230P_ENST00000580835.1_RNA|TOR1AIP1_ENST00000474875.1_3'UTR|TOR1AIP1_ENST00000435319.4_Missense_Mutation_p.D122Y|TOR1AIP1_ENST00000528443.2_Missense_Mutation_p.D244Y			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1	243					positive regulation of ATPase activity (GO:0032781)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)	p.D243Y(1)		breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	18						CAGGGATTCTGATGAATCTGG	0.333																																						dbGAP											1	Substitution - Missense(1)	breast(1)											65.0	60.0	62.0					1																	179870511		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS1335.1, CCDS65737.1	1q24.2	2008-02-05			ENSG00000143337	ENSG00000143337			29456	protein-coding gene	gene with protein product	"""lamina associated polypeptide 1B"""	614512				12061773, 15767459	Standard	NM_015602		Approved	LAP1B, FLJ13142	uc001gnp.2	Q5JTV8	OTTHUMG00000035257	ENST00000606911.2:c.727G>T	1.37:g.179870511G>T	ENSP00000476687:p.Asp243Tyr		A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Missense_Mutation	SNP	pfam_Lamina-ass_polypeptide_CLAP1C	p.D243Y	ENST00000606911.2	37	c.727	CCDS1335.1	1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.248|8.248	0.808356|0.808356	0.16467|0.16467	.|.	.|.	ENSG00000143337|ENSG00000143337	ENST00000528443;ENST00000325993;ENST00000271583;ENST00000435319|ENST00000527391	T;T;T|.	0.23950|.	1.88;1.88;1.88|.	4.05|4.05	-1.67|-1.67	0.08238|0.08238	.|.	1.542140|.	0.04306|.	N|.	0.348149|.	T|.	0.18257|.	0.0438|.	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	0.999997|0.999997	P;P|.	0.49696|.	0.534;0.927|.	B;P|.	0.48952|.	0.212;0.596|.	T|.	0.29671|.	-1.0004|.	9|.	.|.	.|.	.|.	0.0143|0.0143	5.8007|5.8007	0.18412|0.18412	0.2052:0.4696:0.3252:0.0|0.2052:0.4696:0.3252:0.0	.|.	243;244|.	Q5JTV8;E9PKD1|.	TOIP1_HUMAN;.|.	Y|L	244;243;244;243|119	ENSP00000435365:D244Y;ENSP00000271583:D244Y;ENSP00000393292:D243Y|.	.|.	D|X	+|+	1|2	0|2	TOR1AIP1|TOR1AIP1	178137134|178137134	0.005000|0.005000	0.15991|0.15991	0.054000|0.054000	0.19295|0.19295	0.080000|0.080000	0.17528|0.17528	-0.398000|-0.398000	0.07259|0.07259	-0.287000|-0.287000	0.09064|0.09064	0.563000|0.563000	0.77884|0.77884	GAT|TGA	TOR1AIP1	-	pfam_Lamina-ass_polypeptide_CLAP1C	ENSG00000143337		0.333	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	TOR1AIP1	HGNC	protein_coding	OTTHUMT00000100313.4	49	0.00	0	G	NM_015602		179870511	179870511	+1	no_errors	ENST00000435319	ensembl	human	known	69_37n	missense	63	19.23	15	SNP	0.068	T
TP53	7157	genome.wustl.edu	37	17	7574003	7574003	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr17:7574003G>A	ENST00000269305.4	-	10	1213	c.1024C>T	c.(1024-1026)Cga>Tga	p.R342*	TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Intron|TP53_ENST00000455263.2_3'UTR|TP53_ENST00000445888.2_Nonsense_Mutation_p.R342*|TP53_ENST00000420246.2_3'UTR	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	342	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		R -> L (in a sporadic cancer; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R342*(70)|p.0?(8)|p.R342fs*3(8)|p.?(1)|p.R342_N345delRELN(1)|p.I332fs*5(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)	TTCAGCTCTCGGAACATCTCG	0.557		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	dbGAP	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	89	Substitution - Nonsense(70)|Whole gene deletion(8)|Deletion - Frameshift(7)|Insertion - Frameshift(2)|Deletion - In frame(1)|Unknown(1)	breast(16)|upper_aerodigestive_tract(11)|large_intestine(9)|central_nervous_system(9)|ovary(7)|lung(6)|skin(5)|liver(5)|haematopoietic_and_lymphoid_tissue(4)|pancreas(4)|bone(4)|stomach(2)|urinary_tract(2)|oesophagus(2)|kidney(1)|peritoneum(1)|endometrium(1)	GRCh37	CM004908	TP53	M							62.0	48.0	53.0					17																	7574003		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0	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.1024C>T	17.37:g.7574003G>A	ENSP00000269305:p.Arg342*		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	Nonsense_Mutation	SNP	pfam_p53_DNA-bd,pfam_p53_tetrameristn,pfam_p53_transactivation_domain,superfamily_p53-like_TF_DNA-bd,superfamily_p53_tetrameristn,prints_p53_tumour_suppressor	p.R342*	ENST00000269305.4	37	c.1024	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	G	37	6.061927	0.97246	.	.	ENSG00000141510	ENST00000269305;ENST00000445888;ENST00000396473	.	.	.	5.43	3.43	0.39272	.	0.217683	0.37906	N	0.001893	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-0.3792	6.4477	0.21885	0.0845:0.0:0.5925:0.323	.	.	.	.	X	342;342;331	.	ENSP00000269305:R342X	R	-	1	2	TP53	7514728	0.820000	0.29190	0.702000	0.30337	0.859000	0.49053	2.169000	0.42434	0.657000	0.30906	0.561000	0.74099	CGA	TP53	-	pfam_p53_tetrameristn,superfamily_p53_tetrameristn,prints_p53_tumour_suppressor	ENSG00000141510		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	HGNC	protein_coding	OTTHUMT00000367397.1	37	0.00	0	G	NM_000546		7574003	7574003	-1	no_errors	ENST00000269305	ensembl	human	known	69_37n	nonsense	19	68.33	41	SNP	0.307	A
USP5	8078	genome.wustl.edu	37	12	6964674	6964674	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr12:6964674G>A	ENST00000229268.8	+	2	273	c.221G>A	c.(220-222)cGg>cAg	p.R74Q	USP5_ENST00000389231.5_Missense_Mutation_p.R74Q	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	74					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)	p.R74Q(2)		breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						TTGCACCTCCGGCGGACCCGG	0.542																																						dbGAP											2	Substitution - Missense(2)	breast(2)											85.0	97.0	92.0					12																	6964674		2203	4300	6503	-	-	-	SO:0001583	missense	0			U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"""Ubiquitin-specific peptidases"""	12628	protein-coding gene	gene with protein product		601447	"""ubiquitin specific protease 5 (isopeptidase T)"""			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.221G>A	12.37:g.6964674G>A	ENSP00000229268:p.Arg74Gln		D3DUS7|D3DUS8|Q96J22	Missense_Mutation	SNP	pfam_Peptidase_C19,pfam_UBA/transl_elong_EF1B_N,pfam_Znf_UBP,superfamily_UBA-like,smart_Znf_UBP,smart_UBA/transl_elong_EF1B_N_euk,pirsf_Ubiquitinyl_hydrolase,pfscan_UBA/transl_elong_EF1B_N_euk,pfscan_Znf_UBP,pfscan_Peptidase_C19	p.R74Q	ENST00000229268.8	37	c.221	CCDS41743.1	12	.	.	.	.	.	.	.	.	.	.	G	17.52	3.410948	0.62399	.	.	ENSG00000111667	ENST00000229268;ENST00000389231;ENST00000542087	T;T	0.21734	1.99;1.99	5.85	4.86	0.63082	.	0.246954	0.38217	N	0.001766	T	0.09468	0.0233	N	0.11313	0.125	0.41589	D	0.988782	B;B	0.06786	0.0;0.001	B;B	0.08055	0.002;0.003	T	0.20773	-1.0265	10	0.37606	T	0.19	-5.8905	3.8595	0.08990	0.3234:0.0:0.6766:0.0	.	74;74	P45974;P45974-2	UBP5_HUMAN;.	Q	74	ENSP00000229268:R74Q;ENSP00000373883:R74Q	ENSP00000229268:R74Q	R	+	2	0	USP5	6834935	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.093000	0.57714	2.767000	0.95098	0.655000	0.94253	CGG	USP5	-	pirsf_Ubiquitinyl_hydrolase	ENSG00000111667		0.542	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	USP5	HGNC	protein_coding	OTTHUMT00000402982.1	19	0.00	0	G			6964674	6964674	+1	no_errors	ENST00000229268	ensembl	human	known	69_37n	missense	25	23.53	8	SNP	0.995	A
USP9X	8239	genome.wustl.edu	37	X	41076559	41076559	+	Missense_Mutation	SNP	C	C	G			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chrX:41076559C>G	ENST00000324545.8	+	36	6805	c.6172C>G	c.(6172-6174)Cac>Gac	p.H2058D	USP9X_ENST00000378308.2_Missense_Mutation_p.H2058D	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	2058					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)	p.H2051D(1)|p.H2058D(1)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						TACAGGATTTCACACAAAGAA	0.373																																					Ovarian(172;1807 2695 35459 49286)	dbGAP											2	Substitution - Missense(2)	breast(2)											130.0	123.0	125.0					X																	41076559		2045	4220	6265	-	-	-	SO:0001583	missense	0			X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.6172C>G	X.37:g.41076559C>G	ENSP00000316357:p.His2058Asp		O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	pfam_Peptidase_C19,superfamily_ARM-type_fold,pfscan_Peptidase_C19	p.H2058D	ENST00000324545.8	37	c.6172	CCDS43930.1	X	.	.	.	.	.	.	.	.	.	.	C	24.3	4.513550	0.85389	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.03441	3.93;3.93	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.11196	0.0273	M	0.72118	2.19	0.80722	D	1	P;P	0.47762	0.9;0.839	P;B	0.47786	0.557;0.347	T	0.00766	-1.1575	10	0.62326	D	0.03	.	18.2166	0.89887	0.0:1.0:0.0:0.0	.	2058;2058	Q93008-1;Q93008	.;USP9X_HUMAN	D	2058	ENSP00000367558:H2058D;ENSP00000316357:H2058D	ENSP00000316357:H2058D	H	+	1	0	USP9X	40961503	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.487000	0.81328	2.240000	0.73641	0.600000	0.82982	CAC	USP9X	-	NULL	ENSG00000124486		0.373	USP9X-003	KNOWN	basic|CCDS	protein_coding	USP9X	HGNC	protein_coding	OTTHUMT00000056250.4	117	0.00	0	C	NM_004652		41076559	41076559	+1	no_errors	ENST00000324545	ensembl	human	known	69_37n	missense	34	39.29	22	SNP	1.000	G
VWA5B2	90113	genome.wustl.edu	37	3	183952089	183952090	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr3:183952089_183952090insC	ENST00000426955.2	+	5	824_825	c.724_725insC	c.(724-726)gccfs	p.A242fs	EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_Frame_Shift_Ins_p.A23fs	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	253										breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						GCGGGCAGATGCCCCCCCTCAT	0.614																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0				CCDS54686.1	3q27.1	2008-07-25	2008-07-25		ENSG00000145198	ENSG00000145198			25144	protein-coding gene	gene with protein product						15231747	Standard	NM_138345		Approved	DKFZp761K032, LOC90113	uc011bra.2	Q8N398	OTTHUMG00000156820	ENST00000426955.2:c.731dupC	3.37:g.183952096_183952096dupC	ENSP00000398688:p.Ala242fs		B9EGN7	Frame_Shift_Ins	INS	NULL	p.H245fs	ENST00000426955.2	37	c.724_725	CCDS54686.1	3																																																																																			VWA5B2	-	NULL	ENSG00000145198		0.614	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VWA5B2	HGNC	protein_coding	OTTHUMT00000346004.2	25	0.00	0	-	XM_291077		183952089	183952090	+1	no_errors	ENST00000426955	ensembl	human	known	69_37n	frame_shift_ins	23	11.54	3	INS	1.000:1.000	C
ALG1L9P	285407	genome.wustl.edu	37	11	71527792	71527792	+	RNA	SNP	T	T	C	rs11235112	byFrequency	TCGA-AN-A0G0-01A-11W-A050-09	TCGA-AN-A0G0-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	9eb55dd2-a956-4dfe-8631-04722c49819f	eb7cc6da-9544-4308-8627-1b4015493c58	g.chr11:71527792T>C	ENST00000508969.2	-	0	0				ZNF705E_ENST00000525199.1_RNA	NR_073387.1																						GTCTCTCTCCTGTGTGAGTTT	0.418													.|||	2490	0.497204	0.3253	0.4366	5008	,	,		17827	0.4563		0.6531	False		,,,				2504	0.6544					dbGAP											0																																										-	-	-			0																															11.37:g.71527792T>C				RNA	SNP	-	NULL	ENST00000508969.2	37	NULL		11																																																																																			ZNF705E	-	-	ENSG00000214534		0.418	CTD-2313N18.5-002	KNOWN	basic	processed_transcript	ZNF705E	HGNC	processed_transcript	OTTHUMT00000394764.1	12	0.00	0	T			71527792	71527792	-1	no_errors	ENST00000525199	ensembl	human	known	69_37n	rna	25	59.68	37	SNP	0.761	C
