#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
SYNE1	23345	broad.mit.edu	37	6	152539540	152539540	+	Splice_Site	SNP	T	T	C	rs35128811		TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr6:152539540T>C	ENST00000367255.5	-	121	22646		c.e121-2		SYNE1_ENST00000423061.1_Splice_Site|SYNE1_ENST00000356820.4_Splice_Site|SYNE1_ENST00000341594.5_Splice_Site|SYNE1_ENST00000448038.1_Splice_Site|SYNE1_ENST00000265368.4_Splice_Site	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1						cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AACTCCAGCCTTTTTTTCCAC	0.343										HNSCC(10;0.0054)																												ENST00000367255.5																			0				NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524						c.e121-2		spectrin repeat containing, nuclear envelope 1							125.0	136.0	132.0					6																	152539540		2203	4300	6503	SO:0001630	splice_region_variant	23345				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding	g.chr6:152539540T>C	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.22045-2A>G	6.37:g.152539540T>C		HNSCC(10;0.0054)				SYNE1_ENST00000265368.4_Splice_Site|SYNE1_ENST00000423061.1_Splice_Site|SYNE1_ENST00000356820.4_Splice_Site|SYNE1_ENST00000448038.1_Splice_Site|SYNE1_ENST00000341594.5_Splice_Site		NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)	121	22646	-		Ovarian(120;0.0955)						E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Splice_Site	SNP	ENST00000367255.5	37		CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	13.29	2.192011	0.38707	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000367251	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9247	0.79606	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SYNE1	152581233	1.000000	0.71417	0.823000	0.32752	0.548000	0.35241	6.065000	0.71176	2.160000	0.67779	0.528000	0.53228	.		0.343	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	Intron	4	131	0	0	0	1	0	4	131				
MED12L	116931	broad.mit.edu	37	3	151067935	151067935	+	Missense_Mutation	SNP	A	A	C			TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr3:151067935A>C	ENST00000474524.1	+	15	2272	c.2234A>C	c.(2233-2235)aAg>aCg	p.K745T	P2RY12_ENST00000302632.3_Intron|MED12L_ENST00000273432.4_Missense_Mutation_p.K605T|MED12L_ENST00000491549.1_3'UTR	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	745						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CATCAGCTGAAGAAGATTACC	0.418																																						ENST00000474524.1																			0				NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128						c.(2233-2235)aAg>aCg		mediator complex subunit 12-like							154.0	159.0	157.0					3																	151067935		2203	4300	6503	SO:0001583	missense	116931				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex		g.chr3:151067935A>C	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.2234A>C	3.37:g.151067935A>C	ENSP00000417235:p.Lys745Thr					P2RY12_ENST00000302632.3_Intron|MED12L_ENST00000273432.4_Missense_Mutation_p.K605T|MED12L_ENST00000491549.1_3'UTR	p.K745T	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		15	2272	+			745					Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	c.2234A>C	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	A	17.41	3.383166	0.61845	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.69561	-0.23;-0.41	5.81	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.75910	0.3914	L	0.52126	1.63	0.80722	D	1	D;B	0.69078	0.997;0.384	D;B	0.71184	0.972;0.159	T	0.77305	-0.2637	10	0.87932	D	0	-29.2242	12.5486	0.56214	0.8606:0.1394:0.0:0.0	.	605;745	F8WAE6;Q86YW9	.;MD12L_HUMAN	T	745;605	ENSP00000417235:K745T;ENSP00000273432:K605T	ENSP00000273432:K605T	K	+	2	0	MED12L	152550625	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.693000	0.74582	0.979000	0.38497	0.455000	0.32223	AAG		0.418	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		4	88	0	0	0	1	0	4	88				
MAML3	55534	broad.mit.edu	37	4	140811108	140811108	+	Silent	SNP	C	C	T			TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr4:140811108C>T	ENST00000509479.2	-	2	2338	c.1482G>A	c.(1480-1482)caG>caA	p.Q494Q	MAML3_ENST00000327122.5_Silent_p.Q338Q|MAML3_ENST00000398940.1_Silent_p.Q33Q	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgct	0.537																																						ENST00000509479.2																			0				breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25						c.(1480-1482)caG>caA		mastermind-like 3 (Drosophila)							14.0	19.0	17.0					4																	140811108		2165	4272	6437	SO:0001819	synonymous_variant	55534				Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity	g.chr4:140811108C>T	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1482G>A	4.37:g.140811108C>T						MAML3_ENST00000327122.5_Silent_p.Q338Q|MAML3_ENST00000398940.1_Silent_p.Q33Q	p.Q494Q	NM_018717.4	NP_061187.2	Q96JK9	MAML3_HUMAN			2	2338	-	all_hematologic(180;0.162)		494			Gln-rich.			Silent	SNP	ENST00000509479.2	37	c.1482G>A	CCDS54805.1																																																																																				0.537	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			4	22	0	0	0	1	0	4	22				
APOA1	335	broad.mit.edu	37	11	116706628	116706628	+	Missense_Mutation	SNP	C	C	T			TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr11:116706628C>T	ENST00000236850.4	-	4	1065	c.700G>A	c.(700-702)Gcg>Acg	p.A234T	APOA1_ENST00000359492.2_Missense_Mutation_p.A234T|APOA1_ENST00000375323.1_Missense_Mutation_p.A234T|APOA1_ENST00000375329.2_Missense_Mutation_p.A212T|APOA1_ENST00000375320.1_Missense_Mutation_p.A234T|AP006216.12_ENST00000444200.1_RNA	NM_000039.1	NP_000030.1	P02647	APOA1_HUMAN	apolipoprotein A-I	234	10 X approximate tandem repeats.				adrenal gland development (GO:0030325)|blood coagulation (GO:0007596)|blood vessel endothelial cell migration (GO:0043534)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endothelial cell proliferation (GO:0001935)|G-protein coupled receptor signaling pathway (GO:0007186)|glucocorticoid metabolic process (GO:0008211)|high-density lipoprotein particle assembly (GO:0034380)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|integrin-mediated signaling pathway (GO:0007229)|lipid storage (GO:0019915)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein metabolic process (GO:0042157)|negative chemotaxis (GO:0050919)|negative regulation of cell adhesion molecule production (GO:0060354)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of lipase activity (GO:0060192)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of very-low-density lipoprotein particle remodeling (GO:0010903)|organ regeneration (GO:0031100)|peptidyl-methionine modification (GO:0018206)|peripheral nervous system axon regeneration (GO:0014012)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of hydrolase activity (GO:0051345)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transferase activity (GO:0051347)|protein oxidation (GO:0018158)|protein stabilization (GO:0050821)|regulation of Cdc42 protein signal transduction (GO:0032489)|regulation of intestinal cholesterol absorption (GO:0030300)|regulation of protein phosphorylation (GO:0001932)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to nutrient (GO:0007584)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|triglyceride homeostasis (GO:0070328)	blood microparticle (GO:0072562)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule lumen (GO:0034774)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)|vesicle (GO:0031982)	apolipoprotein A-I receptor binding (GO:0034191)|apolipoprotein receptor binding (GO:0034190)|beta-amyloid binding (GO:0001540)|chemorepellent activity (GO:0045499)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|enzyme binding (GO:0019899)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor binding (GO:0070653)|identical protein binding (GO:0042802)|lipase inhibitor activity (GO:0055102)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)			cervix(1)|endometrium(1)|lung(4)|prostate(1)|skin(2)	9	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.59e-05)|all cancers(92;0.000162)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		TCCTCGAGCGCGGGCTTGGCC	0.642																																						ENST00000236850.4																			0				cervix(1)|endometrium(1)|lung(4)|prostate(1)|skin(2)	9						c.(700-702)Gcg>Acg		apolipoprotein A-I							38.0	42.0	41.0					11																	116706628		2200	4287	6487	SO:0001583	missense	335				Cdc42 protein signal transduction|cholesterol efflux|cholesterol homeostasis|cholesterol import|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|negative regulation of cytokine secretion involved in immune response|negative regulation of interleukin-1 beta secretion|negative regulation of very-low-density lipoprotein particle remodeling|phosphatidylcholine biosynthetic process|phospholipid efflux|platelet activation|platelet degranulation|positive regulation of cholesterol esterification|positive regulation of hydrolase activity|protein stabilization|reverse cholesterol transport	endocytic vesicle|endoplasmic reticulum lumen|plasma membrane|spherical high-density lipoprotein particle|stored secretory granule|very-low-density lipoprotein particle	apolipoprotein A-I receptor binding|beta-amyloid binding|cholesterol binding|cholesterol transporter activity|enzyme binding|high-density lipoprotein particle receptor binding|identical protein binding|phosphatidylcholine-sterol O-acyltransferase activator activity|phospholipid binding	g.chr11:116706628C>T	X02162	CCDS8378.1	11q23-q24	2014-09-17			ENSG00000118137	ENSG00000118137		"""Apolipoproteins"""	600	protein-coding gene	gene with protein product		107680					Standard	NM_000039		Approved		uc001ppv.1	P02647	OTTHUMG00000046112	ENST00000236850.4:c.700G>A	11.37:g.116706628C>T	ENSP00000236850:p.Ala234Thr					APOA1_ENST00000375320.1_Missense_Mutation_p.A234T|APOA1_ENST00000375323.1_Missense_Mutation_p.A234T|APOA1_ENST00000375329.2_Missense_Mutation_p.A212T|APOA1_ENST00000359492.2_Missense_Mutation_p.A234T	p.A234T	NM_000039.1	NP_000030.1	P02647	APOA1_HUMAN		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.59e-05)|all cancers(92;0.000162)|OV - Ovarian serous cystadenocarcinoma(223;0.148)	4	1065	-	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)	234			10 X approximate tandem repeats.		A8K866|Q6LDN9|Q6Q785|Q9UCS8|Q9UCT8	Missense_Mutation	SNP	ENST00000236850.4	37	c.700G>A	CCDS8378.1	.	.	.	.	.	.	.	.	.	.	C	8.948	0.967438	0.18659	.	.	ENSG00000118137	ENST00000375320;ENST00000359492;ENST00000375329;ENST00000375323;ENST00000236850	T;T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72;-0.72	4.78	-0.0197	0.13958	.	0.849622	0.09829	U	0.750468	T	0.59390	0.2190	L	0.52364	1.645	0.09310	N	1	B	0.23891	0.093	B	0.19148	0.024	T	0.43782	-0.9370	10	0.25751	T	0.34	-14.8559	7.1552	0.25632	0.0:0.229:0.5581:0.213	.	234	P02647	APOA1_HUMAN	T	234;234;212;234;234	ENSP00000364469:A234T;ENSP00000352471:A234T;ENSP00000364478:A212T;ENSP00000364472:A234T;ENSP00000236850:A234T	ENSP00000236850:A234T	A	-	1	0	APOA1	116211838	0.000000	0.05858	0.014000	0.15608	0.420000	0.31355	0.029000	0.13666	0.147000	0.19030	-0.264000	0.10439	GCG		0.642	APOA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106281.2	NM_000039		3	54	0	0	0	1	0	3	54				
TULP1	7287	broad.mit.edu	37	6	35473863	35473863	+	Missense_Mutation	SNP	G	G	A			TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr6:35473863G>A	ENST00000229771.6	-	10	995	c.916C>T	c.(916-918)Cgc>Tgc	p.R306C	TULP1_ENST00000322263.4_Missense_Mutation_p.R253C	NM_003322.3	NP_003313.3	O00294	TULP1_HUMAN	tubby like protein 1	306					dendrite development (GO:0016358)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|phagocytosis (GO:0006909)|photoreceptor cell maintenance (GO:0045494)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|retina development in camera-type eye (GO:0060041)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|synapse (GO:0045202)	actin filament binding (GO:0051015)|G-protein coupled photoreceptor activity (GO:0008020)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	19						AGCCGGCAGCGCACCGTGCGG	0.677																																					GBM(55;1027 1091 11115 23439)	ENST00000229771.6																			0				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	19						c.(916-918)Cgc>Tgc		tubby like protein 1							48.0	55.0	53.0					6																	35473863		2203	4299	6502	SO:0001583	missense	7287				dendrite development|eye photoreceptor cell development|phagocytosis|photoreceptor cell maintenance|positive regulation of phagocytosis	cell junction|cytoplasm|extracellular region|photoreceptor inner segment|photoreceptor outer segment|synapse	actin filament binding|phosphatidylinositol-4,5-bisphosphate binding	g.chr6:35473863G>A	U82468	CCDS4807.1, CCDS75436.1	6p21.3	2014-01-28			ENSG00000112041	ENSG00000112041			12423	protein-coding gene	gene with protein product		602280		RP14		9096357, 9521870	Standard	NM_003322		Approved	TUBL1, LCA15	uc003okv.4	O00294	OTTHUMG00000014575	ENST00000229771.6:c.916C>T	6.37:g.35473863G>A	ENSP00000229771:p.Arg306Cys					TULP1_ENST00000322263.4_Missense_Mutation_p.R253C	p.R306C	NM_003322.3	NP_003313.3	O00294	TULP1_HUMAN			10	995	-			306					O43536|Q5TGM5|Q8N571	Missense_Mutation	SNP	ENST00000229771.6	37	c.916C>T	CCDS4807.1	.	.	.	.	.	.	.	.	.	.	G	18.29	3.591678	0.66219	.	.	ENSG00000112041	ENST00000229771;ENST00000322263	D;D	0.96716	-4.1;-4.1	4.88	4.88	0.63580	Tubby, C-terminal (3);	0.394694	0.25639	N	0.029286	D	0.91185	0.7223	L	0.60845	1.875	0.54753	D	0.999985	P;B	0.42161	0.772;0.1	B;B	0.32864	0.154;0.063	D	0.92612	0.6100	10	0.87932	D	0	-3.0E-4	10.9973	0.47585	0.0:0.0:0.6892:0.3108	.	253;306	O00294-2;O00294	.;TULP1_HUMAN	C	306;253	ENSP00000229771:R306C;ENSP00000319414:R253C	ENSP00000229771:R306C	R	-	1	0	TULP1	35581841	1.000000	0.71417	0.964000	0.40570	0.975000	0.68041	5.589000	0.67523	2.543000	0.85770	0.484000	0.47621	CGC		0.677	TULP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040307.2			14	42	0	0	0	1	0	14	42				
LCA5	167691	broad.mit.edu	37	6	80201370	80201370	+	Missense_Mutation	SNP	G	G	A			TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr6:80201370G>A	ENST00000392959.1	-	7	1644	c.1033C>T	c.(1033-1035)Cct>Tct	p.P345S	LCA5_ENST00000467898.3_Missense_Mutation_p.P345S|LCA5_ENST00000369846.4_Missense_Mutation_p.P345S	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	345					intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		GGAGTTAAAGGATATTCTTCT	0.373																																						ENST00000392959.1																			0				haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32						c.(1033-1035)Cct>Tct		Leber congenital amaurosis 5							219.0	206.0	211.0					6																	80201370		2203	4300	6503	SO:0001583	missense	167691				protein transport	cilium axoneme|microtubule basal body	protein binding	g.chr6:80201370G>A		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"""lebercilin"""	611408	"""chromosome 6 open reading frame 152"""	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.1033C>T	6.37:g.80201370G>A	ENSP00000376686:p.Pro345Ser					LCA5_ENST00000369846.4_Missense_Mutation_p.P345S|LCA5_ENST00000467898.2_Missense_Mutation_p.P345S	p.P345S	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN		BRCA - Breast invasive adenocarcinoma(397;0.0657)	7	1644	-		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)	345					E1P542|Q9BWX7	Missense_Mutation	SNP	ENST00000392959.1	37	c.1033C>T	CCDS4990.1	.	.	.	.	.	.	.	.	.	.	G	4.324	0.059431	0.08339	.	.	ENSG00000135338	ENST00000369846;ENST00000392959	T;T	0.42131	0.98;0.98	5.11	0.893	0.19236	.	0.411149	0.26227	N	0.025586	T	0.19725	0.0474	M	0.61703	1.905	0.09310	N	0.999997	P	0.34724	0.465	B	0.37198	0.243	T	0.12578	-1.0542	10	0.45353	T	0.12	-0.418	7.5233	0.27641	0.4027:0.0:0.5973:0.0	.	345	Q86VQ0	LCA5_HUMAN	S	345	ENSP00000358861:P345S;ENSP00000376686:P345S	ENSP00000358861:P345S	P	-	1	0	LCA5	80258089	0.613000	0.27009	0.011000	0.14972	0.002000	0.02628	1.281000	0.33214	0.032000	0.15435	-0.229000	0.12294	CCT		0.373	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		21	111	0	0	0	1	0	21	111				
ARMC3	219681	broad.mit.edu	37	10	23248052	23248052	+	Missense_Mutation	SNP	C	C	G			TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr10:23248052C>G	ENST00000298032.5	+	5	430	c.346C>G	c.(346-348)Cag>Gag	p.Q116E	ARMC3_ENST00000464017.1_3'UTR|ARMC3_ENST00000409049.3_Missense_Mutation_p.Q116E|ARMC3_ENST00000376528.4_5'UTR|ARMC3_ENST00000409983.3_Missense_Mutation_p.Q116E	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	116						extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TGTCATTGCCCAGCTCGCTCC	0.284																																						ENST00000298032.5																			0				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						c.(346-348)Cag>Gag		armadillo repeat containing 3							108.0	110.0	110.0					10																	23248052		2203	4300	6503	SO:0001583	missense	219681						binding	g.chr10:23248052C>G	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"""Armadillo repeat containing"""	30964	protein-coding gene	gene with protein product	"""cancer/testis antigen 81"""	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.346C>G	10.37:g.23248052C>G	ENSP00000298032:p.Gln116Glu					ARMC3_ENST00000464017.1_3'UTR|ARMC3_ENST00000376528.4_5'UTR|ARMC3_ENST00000409049.3_Missense_Mutation_p.Q116E|ARMC3_ENST00000409983.3_Missense_Mutation_p.Q116E	p.Q116E	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN			5	430	+			116					A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Missense_Mutation	SNP	ENST00000298032.5	37	c.346C>G	CCDS7142.1	.	.	.	.	.	.	.	.	.	.	C	4.372	0.068543	0.08436	.	.	ENSG00000165309	ENST00000298032;ENST00000409983;ENST00000376523;ENST00000409049;ENST00000447081	T;T;T;T	0.51574	0.79;0.79;1.45;0.7	5.15	4.22	0.49857	Armadillo-like helical (1);Armadillo-type fold (1);	0.782790	0.12558	N	0.458421	T	0.41604	0.1166	L	0.44542	1.39	0.80722	D	1	B;B;B	0.28971	0.218;0.005;0.229	B;B;B	0.27076	0.076;0.008;0.058	T	0.13202	-1.0518	10	0.22706	T	0.39	-20.9269	14.7577	0.69579	0.1567:0.8433:0.0:0.0	.	116;28;116	Q5W041-4;C9JC46;Q5W041	.;.;ARMC3_HUMAN	E	116;116;116;116;28	ENSP00000298032:Q116E;ENSP00000386943:Q116E;ENSP00000387288:Q116E;ENSP00000396629:Q28E	ENSP00000298032:Q116E	Q	+	1	0	ARMC3	23288058	1.000000	0.71417	0.862000	0.33874	0.196000	0.23810	2.962000	0.49176	1.224000	0.43551	0.650000	0.86243	CAG		0.284	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081		9	73	0	0	0	1	0	9	73				
TRIML1	339976	broad.mit.edu	37	4	189060901	189060901	+	Silent	SNP	G	G	A	rs147444946	byFrequency	TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr4:189060901G>A	ENST00000332517.3	+	1	329	c.189G>A	c.(187-189)ccG>ccA	p.P63P	RP11-366H4.3_ENST00000501322.2_RNA	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	63					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		TGGAGGGCCCGCATTTCCAGT	0.602													G|||	4	0.000798722	0.003	0.0	5008	,	,		18184	0.0		0.0	False		,,,				2504	0.0				Melanoma(31;213 1036 16579 23968 32372)	ENST00000332517.3																			0				NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60						c.(187-189)ccG>ccA		tripartite motif family-like 1		G		5,4401	9.9+/-24.2	0,5,2198	83.0	88.0	86.0		189	-11.2	0.0	4	dbSNP_134	86	0,8600		0,0,4300	no	coding-synonymous	TRIML1	NM_178556.3		0,5,6498	AA,AG,GG		0.0,0.1135,0.0384		63/469	189060901	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	339976				multicellular organismal development		ligase activity|zinc ion binding	g.chr4:189060901G>A	AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108		"""RING-type (C3HC4) zinc fingers"""	26698	protein-coding gene	gene with protein product						12477932	Standard	NM_178556		Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.189G>A	4.37:g.189060901G>A							p.P63P	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)	1	329	+		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)	63					Q96BE5	Silent	SNP	ENST00000332517.3	37	c.189G>A	CCDS3851.1																																																																																				0.602	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556		7	73	0	0	0	1	0	7	73				
TCHH	7062	broad.mit.edu	37	1	152082552	152082552	+	Silent	SNP	C	C	T	rs375526947		TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr1:152082552C>T	ENST00000368804.1	-	2	3140	c.3141G>A	c.(3139-3141)gaG>gaA	p.E1047E		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1047	10 X 30 AA tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GATATTGCCTCTCCCGCTCCT	0.582																																						ENST00000368804.1																			0				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105						c.(3139-3141)gaG>gaA		trichohyalin							122.0	125.0	124.0					1																	152082552		1959	4139	6098	SO:0001819	synonymous_variant	7062				keratinization	cytoskeleton	calcium ion binding	g.chr1:152082552C>T	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.3141G>A	1.37:g.152082552C>T							p.E1047E	NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		2	3140	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		1047			10 X 30 AA tandem repeats.		Q5VUI3	Silent	SNP	ENST00000368804.1	37	c.3141G>A	CCDS41396.1																																																																																				0.582	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		4	105	0	0	0	1	0	4	105				
NLGN1	22871	broad.mit.edu	37	3	173322724	173322724	+	Silent	SNP	A	A	G			TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr3:173322724A>G	ENST00000457714.1	+	3	765	c.336A>G	c.(334-336)caA>caG	p.Q112Q	NLGN1_ENST00000361589.4_Silent_p.Q112Q|NLGN1_ENST00000401917.3_Silent_p.Q112Q|NLGN1_ENST00000545397.1_Silent_p.Q112Q	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	112					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			ATGCCACTCAATTTGCTCCTG	0.463																																						ENST00000457714.1																			0				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83						c.(334-336)caA>caG		neuroligin 1							167.0	162.0	164.0					3																	173322724		2203	4300	6503	SO:0001819	synonymous_variant	22871				calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity	g.chr3:173322724A>G	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.336A>G	3.37:g.173322724A>G						NLGN1_ENST00000545397.1_Silent_p.Q112Q|NLGN1_ENST00000401917.3_Silent_p.Q112Q|NLGN1_ENST00000361589.4_Silent_p.Q112Q	p.Q112Q	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)		3	765	+	Ovarian(172;0.0025)		112					Q9UPT2	Silent	SNP	ENST00000457714.1	37	c.336A>G	CCDS3222.1																																																																																				0.463	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		18	69	0	0	0	1	0	18	69				
CROCCP2	84809	broad.mit.edu	37	1	16952952	16952952	+	lincRNA	SNP	G	G	A	rs1762946	byFrequency	TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr1:16952952G>A	ENST00000412962.1	-	0	664							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											TCTGCCCTCAGCTTGGTCACG	0.622																																						ENST00000412962.1																			0																																																			84809							g.chr1:16952952G>A	AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16952952G>A														0	664	-								Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																						0.622	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1	NR_026752.1		4	21	0	0	0	1	0	4	21				
BMS1P20	96610	broad.mit.edu	37	22	22664606	22664606	+	RNA	SNP	A	A	G	rs187344612		TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr22:22664606A>G	ENST00000426066.1	+	0	787					NR_027293.1				BMS1 pseudogene 20																		GTCTTCATGCAAACTTGGTAT	0.398																																						ENST00000426066.1																			0																																																			96610							g.chr22:22664606A>G			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22664606A>G								NR_027293.1						0	787	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.398	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			3	18	0	0	0	1	0	3	18				
POM121L9P	29774	broad.mit.edu	37	22	24659536	24659536	+	RNA	SNP	C	C	T	rs564427351	byFrequency	TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr22:24659536C>T	ENST00000414583.2	+	0	3061					NR_003714.1				POM121 transmembrane nucleoporin-like 9, pseudogene																		GATCTCATCGCGGACACCACT	0.512													C|||	2	0.000399361	0.0008	0.0	5008	,	,		24328	0.0		0.001	False		,,,				2504	0.0					ENST00000414583.2																			0																																																			29774							g.chr22:24659536C>T	AL040062, AL117401		22q11.22	2012-03-13	2012-03-13		ENSG00000128262	ENSG00000128262			30080	pseudogene	pseudogene			"""POM121 membrane glycoprotein-like 9, pseudogene"""				Standard	NR_003714		Approved				OTTHUMG00000150763		22.37:g.24659536C>T								NR_003714.1						0	3061	+									RNA	SNP	ENST00000414583.2	37																																																																																						0.512	POM121L9P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000319991.1	NM_014549		3	8	0	0	0	1	0	3	8				
SLC25A44	9673	broad.mit.edu	37	1	156177746	156177746	+	Missense_Mutation	SNP	C	C	T			TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr1:156177746C>T	ENST00000359511.4	+	3	867	c.695C>T	c.(694-696)gCt>gTt	p.A232V	SLC25A44_ENST00000469537.1_3'UTR|SLC25A44_ENST00000423538.2_Missense_Mutation_p.A209V	NM_014655.2	NP_055470.1	Q96H78	S2544_HUMAN	solute carrier family 25, member 44	232					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Hepatocellular(266;0.158)					GGGCCCCTGGCTGCAGCCACT	0.557																																						ENST00000359511.4																			0				breast(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						c.(694-696)gCt>gTt		solute carrier family 25, member 44							98.0	82.0	87.0					1																	156177746		2203	4300	6503	SO:0001583	missense	9673				transmembrane transport	integral to membrane|mitochondrial inner membrane	binding	g.chr1:156177746C>T	AB007915	CCDS1133.1, CCDS72943.1	1q22	2013-05-22			ENSG00000160785	ENSG00000160785		"""Solute carriers"""	29036	protein-coding gene	gene with protein product		610824				16949250	Standard	NM_001286184		Approved	FLJ90431, KIAA0446	uc001fnp.3	Q96H78	OTTHUMG00000014816	ENST00000359511.4:c.695C>T	1.37:g.156177746C>T	ENSP00000352497:p.Ala232Val					SLC25A44_ENST00000469537.1_3'UTR|SLC25A44_ENST00000423538.2_Missense_Mutation_p.A209V	p.A232V	NM_014655.2	NP_055470.1	Q96H78	S2544_HUMAN			3	867	+	Hepatocellular(266;0.158)		232					O75034	Missense_Mutation	SNP	ENST00000359511.4	37	c.695C>T	CCDS1133.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.955019	0.92726	.	.	ENSG00000160785	ENST00000359511;ENST00000423538	D;D	0.87256	-2.23;-2.23	5.17	5.17	0.71159	Mitochondrial carrier domain (2);	0.056219	0.64402	D	0.000001	D	0.94062	0.8097	M	0.91612	3.225	0.80722	D	1	D;D;D	0.67145	0.992;0.996;0.989	P;D;D	0.71656	0.894;0.962;0.974	D	0.94855	0.8017	10	0.87932	D	0	-7.6045	16.2196	0.82251	0.0:1.0:0.0:0.0	.	209;209;232	E9PGQ0;B4DGC4;Q96H78	.;.;S2544_HUMAN	V	232;209	ENSP00000352497:A232V;ENSP00000407560:A209V	ENSP00000352497:A232V	A	+	2	0	SLC25A44	154444370	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	7.435000	0.80391	2.677000	0.91161	0.637000	0.83480	GCT		0.557	SLC25A44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040856.1	NM_014655		9	41	0	0	0	1	0	9	41				
PTPN18	26469	broad.mit.edu	37	2	131129929	131129934	+	In_Frame_Del	DEL	GACGGG	GACGGG	-	rs112040677	byFrequency	TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr2:131129929_131129934delGACGGG	ENST00000175756.5	+	13	1214_1219	c.1113_1118delGACGGG	c.(1111-1119)cagacgggg>cag	p.TG378del	PTPN18_ENST00000347849.3_In_Frame_Del_p.TG271del	NM_014369.3	NP_055184.2	Q99952	PTN18_HUMAN	protein tyrosine phosphatase, non-receptor type 18 (brain-derived)	378				Missing (in Ref. 1; CAA56105). {ECO:0000305}.	peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)	p.T378_G379delTG(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)	15	Colorectal(110;0.1)					gtgggacgcagacggggacggggacg	0.777														1724	0.344249	0.6324	0.2349	5008	,	,		12983	0.3214		0.2008	False		,,,				2504	0.2035					ENST00000175756.5																			1	Deletion - In frame(1)	p.T378_G379delTG(1)	prostate(1)	endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)	15						c.(1111-1119)cag>ca		protein tyrosine phosphatase, non-receptor type 18 (brain-derived)			,	1068,966		446,176,395					,	-3.8	0.0		dbSNP_132	3	951,4205		280,391,1907	no	coding,coding	PTPN18	NM_014369.3,NM_001142370.1	,	726,567,2302	A1A1,A1R,RR		18.4445,47.4926,28.0807	,	,		2019,5171				SO:0001651	inframe_deletion	26469					cytoplasm|nucleus	non-membrane spanning protein tyrosine phosphatase activity	g.chr2:131129929_131129934delGACGGG	X79568	CCDS2161.1, CCDS46410.1	2q21	2011-06-09			ENSG00000072135	ENSG00000072135		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9649	protein-coding gene	gene with protein product		606587				8950995	Standard	NM_014369		Approved	BDP1	uc002trc.3	Q99952	OTTHUMG00000131630	ENST00000175756.5:c.1113_1118delGACGGG	2.37:g.131129935_131129940delGACGGG	ENSP00000175756:p.Thr378_Gly379del					PTPN18_ENST00000347849.3_In_Frame_Del_p.QTG264del	p.QTG371del	NM_014369.3	NP_055184.2	Q99952	PTN18_HUMAN			13	1214_1219	+	Colorectal(110;0.1)		371					B4E1E6|Q53P42	In_Frame_Del	DEL	ENST00000175756.5	37	c.1113_1118delGACGGG	CCDS2161.1																																																																																				0.777	PTPN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254523.2			3	3						3	3	---	---	---	---
PMS2P4	5382	broad.mit.edu	37	7	66762448	66762449	+	RNA	INS	-	-	T	rs371810458	byFrequency	TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr7:66762448_66762449insT	ENST00000414507.1	-	0	184				Y_RNA_ENST00000364695.1_RNA					postmeiotic segregation increased 2 pseudogene 4																		aaaaaaaaaaaaTGGACCCATG	0.401																																						ENST00000414507.1																			0																																																			5382							g.chr7:66762448_66762449insT	D38438		7q11.22	2010-10-26	2010-10-26	2010-10-26	ENSG00000067601	ENSG00000067601			9129	pseudogene	pseudogene	"""PMS2 pseudogene"""		"""postmeiotic segregation increased 2-like 4"", ""postmeiotic segregation increased 2-like 4 pseudogene"""	PMS2L4		8586419	Standard	NR_046297		Approved	PMS6	uc003tvo.3		OTTHUMG00000156923		7.37:g.66762448_66762449insT														0	184	-									RNA	INS	ENST00000414507.1	37																																																																																						0.401	PMS2P4-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000346632.1	NR_022007		2	4						2	4	---	---	---	---
TRUB1	142940	broad.mit.edu	37	10	116698250	116698250	+	Frame_Shift_Del	DEL	C	C	-			TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr10:116698250delC	ENST00000298746.3	+	1	299	c.238delC	c.(238-240)cccfs	p.P80fs	TRUB1_ENST00000485065.1_3'UTR	NM_139169.4	NP_631908.1	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase family member 1	80					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(2)|kidney(2)|large_intestine(1)|lung(5)|urinary_tract(2)	12		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)		Epithelial(162;0.00879)|all cancers(201;0.0243)		GCCCAAAGGGCCCACTTCAGC	0.657																																						ENST00000298746.3																			0				breast(2)|kidney(2)|large_intestine(1)|lung(5)|urinary_tract(2)	12						c.(238-240)ccfs		TruB pseudouridine (psi) synthase family member 1							12.0	13.0	13.0					10																	116698250		2202	4298	6500	SO:0001589	frameshift_variant	142940				pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding	g.chr10:116698250delC	AF448144	CCDS7591.1	10q25.3	2013-09-02	2013-09-02		ENSG00000165832	ENSG00000165832			16060	protein-coding gene	gene with protein product		610726	"""TruB pseudouridine (psi) synthase homolog 1 (E. coli)"""			12736709	Standard	NM_139169		Approved	PUS4	uc001lcd.3	Q8WWH5	OTTHUMG00000019094	ENST00000298746.3:c.238delC	10.37:g.116698250delC	ENSP00000298746:p.Pro80fs					TRUB1_ENST00000485065.1_3'UTR	p.P80fs	NM_139169.4	NP_631908.1	Q8WWH5	TRUB1_HUMAN		Epithelial(162;0.00879)|all cancers(201;0.0243)	1	299	+		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)	80					B2R716|Q53ES2	Frame_Shift_Del	DEL	ENST00000298746.3	37	c.238delC	CCDS7591.1																																																																																				0.657	TRUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050504.1	NM_139169		2	4						2	4	---	---	---	---
CCDC137	339230	broad.mit.edu	37	17	79639622	79639622	+	Frame_Shift_Del	DEL	A	A	-	rs35963091		TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chr17:79639622delA	ENST00000329214.8	+	6	1161	c.758delA	c.(757-759)gagfs	p.E254fs		NM_199287.2	NP_954981.1	Q6PK04	CC137_HUMAN	coiled-coil domain containing 137	254							poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(2)	12	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			ATTGTGGAGGAGGAGAGAGAG	0.672																																						ENST00000329214.8																			0				NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(2)	12						c.(757-759)ggfs		coiled-coil domain containing 137							13.0	17.0	16.0					17																	79639622		2001	4148	6149	SO:0001589	frameshift_variant	339230							g.chr17:79639622delA	BC009369	CCDS42400.1	17q25.3	2008-07-04				ENSG00000185298			33451	protein-coding gene	gene with protein product		614271					Standard	NM_199287		Approved	MGC16597	uc002kbc.4	Q6PK04		ENST00000329214.8:c.758delA	17.37:g.79639622delA	ENSP00000329360:p.Glu254fs						p.E254fs	NM_199287.2	NP_954981.1	Q6PK04	CC137_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)		6	1161	+	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		254						Frame_Shift_Del	DEL	ENST00000329214.8	37	c.758delA	CCDS42400.1																																																																																				0.672	CCDC137-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440387.1			2	4						2	4	---	---	---	---
EFNB1	1947	broad.mit.edu	37	X	68058545	68058545	+	Frame_Shift_Del	DEL	C	C	-			TCGA-QR-A6H0-01A-11D-A35D-08	TCGA-QR-A6H0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a7beead6-bfb3-41cd-8d66-b630a1d927ca	8c64013f-3fef-4ace-ae3d-75f927c4c567	g.chrX:68058545delC	ENST00000204961.4	+	2	994	c.214delC	c.(214-216)cccfs	p.P72fs		NM_004429.4	NP_004420.1	P98172	EFNB1_HUMAN	ephrin-B1	72	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|embryonic pattern specification (GO:0009880)|ephrin receptor signaling pathway (GO:0048013)|neural crest cell migration (GO:0001755)|positive regulation of T cell proliferation (GO:0042102)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ephrin receptor binding (GO:0046875)			breast(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	22						AGCAGGGCGGCCCTATGAGTA	0.572																																						ENST00000204961.4																			0				breast(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	22						c.(214-216)ccfs		ephrin-B1							61.0	47.0	52.0					X																	68058545		2203	4300	6503	SO:0001589	frameshift_variant	1947				cell adhesion|cell-cell signaling	integral to plasma membrane|soluble fraction|synapse	ephrin receptor binding	g.chrX:68058545delC	U09303	CCDS14391.1	Xq12	2011-03-09			ENSG00000090776	ENSG00000090776		"""Ephrins"""	3226	protein-coding gene	gene with protein product		300035	"""craniofrontonasal syndrome (craniofrontonasal dysplasia)"""	EPLG2, CFNS		7774950, 16526919	Standard	NM_004429		Approved	LERK2, Elk-L	uc004dxd.4	P98172	OTTHUMG00000021751	ENST00000204961.4:c.214delC	X.37:g.68058545delC	ENSP00000204961:p.Pro72fs						p.P72fs	NM_004429.4	NP_004420.1	P98172	EFNB1_HUMAN			2	994	+			72					D3DVU0	Frame_Shift_Del	DEL	ENST00000204961.4	37	c.214delC	CCDS14391.1																																																																																				0.572	EFNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057029.1	NM_004429		2	4						2	4	---	---	---	---
