#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
BANK1	55024	broad.mit.edu	37	4	102981427	102981427	+	Missense_Mutation	SNP	C	C	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr4:102981427C>A	ENST00000322953.4	+	12	2303	c.2029C>A	c.(2029-2031)Cag>Aag	p.Q677K	BANK1_ENST00000428908.1_Missense_Mutation_p.Q544K|BANK1_ENST00000444316.2_Missense_Mutation_p.Q647K|BANK1_ENST00000504592.1_Missense_Mutation_p.Q662K|BANK1_ENST00000508653.1_Missense_Mutation_p.Q544K	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	677					B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		AACTGATGGTCAGGAAGAACT	0.453																																						ENST00000504592.1																			0				NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44						c.(1984-1986)Cag>Aag		B-cell scaffold protein with ankyrin repeats 1							92.0	97.0	95.0					4																	102981427		2203	4300	6503	SO:0001583	missense	55024				B cell activation			g.chr4:102981427C>A	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"""Ankyrin repeat domain containing"""	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.2029C>A	4.37:g.102981427C>A	ENSP00000320509:p.Gln677Lys					BANK1_ENST00000322953.4_Missense_Mutation_p.Q677K|BANK1_ENST00000428908.1_Missense_Mutation_p.Q544K|BANK1_ENST00000508653.1_Missense_Mutation_p.Q544K|BANK1_ENST00000444316.2_Missense_Mutation_p.Q647K	p.Q662K			Q8NDB2	BANK1_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)	16	2402	+		Hepatocellular(203;0.217)	677					A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	37	c.1984C>A	CCDS34038.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.699691	0.68501	.	.	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	T;T;T;T;T	0.29917	2.23;2.19;1.55;1.55;2.23	5.59	5.59	0.84812	.	0.069929	0.56097	D	0.000028	T	0.52693	0.1750	L	0.61218	1.895	0.32109	N	0.589582	D;D;D	0.61697	0.99;0.986;0.986	D;P;P	0.73380	0.98;0.836;0.836	T	0.61603	-0.7029	10	0.66056	D	0.02	.	15.0983	0.72253	0.0:1.0:0.0:0.0	.	544;677;662	Q8NDB2-4;Q8NDB2;Q8NDB2-2	.;BANK1_HUMAN;.	K	662;677;544;544;647	ENSP00000421443:Q662K;ENSP00000320509:Q677K;ENSP00000412748:Q544K;ENSP00000422314:Q544K;ENSP00000388817:Q647K	ENSP00000320509:Q677K	Q	+	1	0	BANK1	103200450	0.992000	0.36948	0.944000	0.38274	0.666000	0.39218	3.857000	0.55972	2.644000	0.89710	0.561000	0.74099	CAG		0.453	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935		40	61	1	0	5.71845e-15	1	6.74265e-15	40	61				
CAMK2A	815	broad.mit.edu	37	5	149629830	149629830	+	Missense_Mutation	SNP	C	C	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr5:149629830C>T	ENST00000348628.6	-	11	1524	c.859G>A	c.(859-861)Gtg>Atg	p.V287M	CAMK2A_ENST00000398376.3_Missense_Mutation_p.V287M	NM_015981.3|NM_171825.2	NP_057065.2|NP_741960.1	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II alpha	287					calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|kinase activity (GO:0016301)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)	15		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGGCAGTCCACGGTCTCCTGT	0.602																																						ENST00000348628.6																			0				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)	15						c.(859-861)Gtg>Atg		calcium/calmodulin-dependent protein kinase II alpha							101.0	99.0	100.0					5																	149629830		2128	4259	6387	SO:0001583	missense	815				interferon-gamma-mediated signaling pathway|positive regulation of NF-kappaB transcription factor activity|synaptic transmission	cell junction|cytosol|endocytic vesicle membrane|nucleoplasm|presynaptic membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity	g.chr5:149629830C>T	AB023185	CCDS43386.1, CCDS43387.1	5q32	2013-09-20	2008-10-30		ENSG00000070808	ENSG00000070808	2.7.11.17		1460	protein-coding gene	gene with protein product	"""CaM-kinase II alpha chain"", ""calcium/calmodulin-dependent protein kinase II alpha-B subunit"", ""CaM kinase II alpha subunit"", ""CaMK-II alpha subunit"", ""calcium/calmodulin-dependent protein kinase type II alpha chain"""	114078	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha"""	CAMKA		10231032, 3475713	Standard	NM_015981		Approved	KIAA0968, CaMKIINalpha	uc003lrt.2	Q9UQM7	OTTHUMG00000134281	ENST00000348628.6:c.859G>A	5.37:g.149629830C>T	ENSP00000261793:p.Val287Met					CAMK2A_ENST00000398376.3_Missense_Mutation_p.V287M	p.V287M	NM_015981.3|NM_171825.2	NP_057065.2|NP_741960.1	Q9UQM7	KCC2A_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		11	1524	-		all_hematologic(541;0.224)	287					Q9UL21|Q9Y2H4|Q9Y352	Missense_Mutation	SNP	ENST00000348628.6	37	c.859G>A	CCDS43386.1	.	.	.	.	.	.	.	.	.	.	C	33	5.256226	0.95336	.	.	ENSG00000070808	ENST00000348628;ENST00000398376	T;T	0.69685	-0.42;-0.41	5.58	5.58	0.84498	Protein kinase-like domain (1);	0.086607	0.47093	D	0.000250	D	0.84674	0.5524	M	0.90425	3.115	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.997	P;D;P	0.63703	0.898;0.917;0.793	D	0.86960	0.2091	10	0.59425	D	0.04	.	19.1713	0.93578	0.0:1.0:0.0:0.0	.	287;287;287	Q9UQM7-2;Q9UQM7;A8K161	.;KCC2A_HUMAN;.	M	287	ENSP00000261793:V287M;ENSP00000381412:V287M	ENSP00000261793:V287M	V	-	1	0	CAMK2A	149610023	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.736000	0.84948	2.645000	0.89757	0.655000	0.94253	GTG		0.602	CAMK2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258869.2	NM_015981		23	41	0	0	0	1	0	23	41				
DEF8	54849	broad.mit.edu	37	16	90028152	90028152	+	Silent	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr16:90028152G>A	ENST00000268676.7	+	8	959	c.870G>A	c.(868-870)gtG>gtA	p.V290V	DEF8_ENST00000569453.1_Silent_p.V229V|DEF8_ENST00000563594.1_Silent_p.V229V|DEF8_ENST00000563795.1_Silent_p.V229V|DEF8_ENST00000563848.1_3'UTR|DEF8_ENST00000570182.1_Silent_p.V219V|DEF8_ENST00000567874.1_Silent_p.V169V	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	290					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		CAGGGGGTGTGCCCAGTGAGG	0.617																																						ENST00000563594.1																			0				central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						c.(685-687)gtG>gtA		differentially expressed in FDCP 8 homolog (mouse)							46.0	44.0	45.0					16																	90028152		2198	4300	6498	SO:0001819	synonymous_variant	54849				intracellular signal transduction		zinc ion binding	g.chr16:90028152G>A	AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.870G>A	16.37:g.90028152G>A						DEF8_ENST00000563848.1_3'UTR|DEF8_ENST00000570182.1_Silent_p.V219V|DEF8_ENST00000569453.1_Silent_p.V229V|DEF8_ENST00000563795.1_Silent_p.V229V|DEF8_ENST00000567874.1_Silent_p.V169V|DEF8_ENST00000268676.7_Silent_p.V290V	p.V229V	NM_001242818.1|NM_001242819.1	NP_001229747.1|NP_001229748.1	Q6ZN54	DEFI8_HUMAN		BRCA - Breast invasive adenocarcinoma(80;0.0274)	8	1684	+		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)	290					B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Silent	SNP	ENST00000268676.7	37	c.687G>A	CCDS10989.1																																																																																				0.617	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514		26	32	0	0	0	1	0	26	32				
FOXJ3	22887	broad.mit.edu	37	1	42660617	42660617	+	Missense_Mutation	SNP	C	C	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr1:42660617C>A	ENST00000372572.1	-	10	1189	c.878G>T	c.(877-879)aGt>aTt	p.S293I	FOXJ3_ENST00000372573.1_Missense_Mutation_p.S293I|FOXJ3_ENST00000361346.1_Missense_Mutation_p.S293I|FOXJ3_ENST00000361776.1_Missense_Mutation_p.S259I|FOXJ3_ENST00000545068.1_Missense_Mutation_p.S293I	NM_001198851.1	NP_001185780.1	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	293					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AAATGAGGCACTAAGATCTTC	0.348																																						ENST00000372572.1																			0				NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18						c.(877-879)aGt>aTt		forkhead box J3							181.0	191.0	188.0					1																	42660617		2203	4300	6503	SO:0001583	missense	22887				embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding	g.chr1:42660617C>A	AB028964	CCDS30689.1, CCDS55594.1	1p34.2	2008-04-10			ENSG00000198815	ENSG00000198815		"""Forkhead boxes"""	29178	protein-coding gene	gene with protein product							Standard	NM_014947		Approved	KIAA1041	uc001chf.3	Q9UPW0	OTTHUMG00000007026	ENST00000372572.1:c.878G>T	1.37:g.42660617C>A	ENSP00000361653:p.Ser293Ile					FOXJ3_ENST00000545068.1_Missense_Mutation_p.S293I|FOXJ3_ENST00000372573.1_Missense_Mutation_p.S293I|FOXJ3_ENST00000361776.1_Missense_Mutation_p.S259I|FOXJ3_ENST00000361346.1_Missense_Mutation_p.S293I	p.S293I	NM_001198851.1	NP_001185780.1	Q9UPW0	FOXJ3_HUMAN			10	1189	-	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)	293					A7MBL7|A7MD18|D3DPW2|Q9NSS7	Missense_Mutation	SNP	ENST00000372572.1	37	c.878G>T	CCDS30689.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.980494	0.92982	.	.	ENSG00000198815	ENST00000372573;ENST00000372572;ENST00000361346;ENST00000361776;ENST00000545068;ENST00000445886	T;T;T;T;T;T	0.00873	5.59;5.59;5.59;5.59;5.59;5.59	5.75	5.75	0.90469	.	1.163790	0.06228	N	0.688096	T	0.05318	0.0141	L	0.47190	1.495	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.78314	0.984;0.991	T	0.41431	-0.9509	10	0.87932	D	0	.	17.4293	0.87535	0.0:1.0:0.0:0.0	.	259;293	Q9UPW0-2;Q9UPW0	.;FOXJ3_HUMAN	I	293;293;293;259;293;259	ENSP00000361654:S293I;ENSP00000361653:S293I;ENSP00000354620:S293I;ENSP00000354449:S259I;ENSP00000439044:S293I;ENSP00000393408:S259I	ENSP00000354620:S293I	S	-	2	0	FOXJ3	42433204	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.297000	0.72757	2.711000	0.92665	0.655000	0.94253	AGT		0.348	FOXJ3-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018310.1	NM_014947		70	116	1	0	1.64915e-30	1	2.03567e-30	70	116				
ANKS1A	23294	broad.mit.edu	37	6	34957002	34957002	+	Splice_Site	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr6:34957002G>A	ENST00000360359.3	+	9	1349	c.1211G>A	c.(1210-1212)aGg>aAg	p.R404K	ANKS1A_ENST00000535627.1_Intron	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	404					ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						CTTCTGCAGAGGGAACGTCCA	0.393																																						ENST00000360359.3																			0				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						c.e9-1		ankyrin repeat and sterile alpha motif domain containing 1A							122.0	121.0	121.0					6																	34957002		2203	4300	6503	SO:0001630	splice_region_variant	23294					cytoplasm	protein binding	g.chr6:34957002G>A	D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	20961	protein-coding gene	gene with protein product		608994	"""ankyrin repeat and SAM domain containing 1"", ""ankyrin repeat and sterile alpha motif domain containing 1"""	ANKS1		9039502	Standard	NM_015245		Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	ENST00000360359.3:c.1210-1G>A	6.37:g.34957002G>A						ANKS1A_ENST00000535627.1_Intron	p.R404_splice	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN			9	1349	+			404					A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Splice_Site	SNP	ENST00000360359.3	37	c.1209_splice	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	G	16.80	3.222594	0.58668	.	.	ENSG00000064999	ENST00000544150;ENST00000360359	T	0.35789	1.29	5.73	4.87	0.63330	.	0.000000	0.49916	D	0.000139	T	0.24198	0.0586	N	0.11201	0.11	0.80722	D	1	D	0.58268	0.982	D	0.67548	0.952	T	0.15694	-1.0428	10	0.27785	T	0.31	-23.662	12.5438	0.56186	0.0767:0.0:0.9233:0.0	.	404	Q92625	ANS1A_HUMAN	K	404	ENSP00000353518:R404K	ENSP00000353518:R404K	R	+	2	0	ANKS1A	35064980	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.840000	0.55843	1.573000	0.49748	0.557000	0.71058	AGG		0.393	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478	Missense_Mutation	52	85	0	0	0	1	0	52	85				
MROH6	642475	broad.mit.edu	37	8	144650814	144650814	+	Silent	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr8:144650814G>A	ENST00000398882.3	-	10	1808	c.1552C>T	c.(1552-1554)Ctg>Ttg	p.L518L	MROH6_ENST00000533679.1_5'UTR|MROH6_ENST00000524906.1_5'UTR|MROH6_ENST00000532704.1_5'Flank|MROH6_ENST00000534459.1_5'UTR	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6	518	Leu-rich.																cggagccccagccggagcccg	0.741																																						ENST00000398882.3																			0											c.(1552-1554)Ctg>Ttg		maestro heat-like repeat family member 6							2.0	3.0	3.0					8																	144650814		1470	3355	4825	SO:0001819	synonymous_variant	642475							g.chr8:144650814G>A	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"""maestro heat-like repeat containing"""	27814	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 73"""	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164	ENST00000398882.3:c.1552C>T	8.37:g.144650814G>A						MROH6_ENST00000533679.1_5'UTR|MROH6_ENST00000524906.1_5'UTR|MROH6_ENST00000534459.1_5'UTR	p.L518L	NM_001100878.1	NP_001094348.1					10	1808	-								A8MWB1	Silent	SNP	ENST00000398882.3	37	c.1552C>T	CCDS47928.1	.	.	.	.	.	.	.	.	.	.	g	10.49	1.365960	0.24684	.	.	ENSG00000204839	ENST00000529971	T	0.30182	1.54	4.89	-9.77	0.00500	.	.	.	.	.	T	0.18964	0.0455	.	.	.	0.44261	D	0.997115	B	0.16396	0.017	B	0.15052	0.012	T	0.15607	-1.0431	8	0.87932	D	0	-8.4262	8.6604	0.34088	0.144:0.1985:0.5885:0.069	.	530	E9PPP7	.	V	530	ENSP00000436959:A530V	ENSP00000436959:A530V	A	-	2	0	C8orf73	144721957	0.000000	0.05858	0.504000	0.27639	0.164000	0.22412	-2.472000	0.00989	-1.596000	0.01611	0.543000	0.68304	GCT		0.741	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878		4	1	0	0	0	1	0	4	1				
SERPINC1	462	broad.mit.edu	37	1	173873136	173873136	+	Missense_Mutation	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr1:173873136G>A	ENST00000367698.3	-	7	1404	c.1286C>T	c.(1285-1287)cCc>cTc	p.P429L		NM_000488.3	NP_000479.1	P01008	ANT3_HUMAN	serpin peptidase inhibitor, clade C (antithrombin), member 1	429					blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of inflammatory response (GO:0050728)|regulation of blood coagulation, intrinsic pathway (GO:2000266)|regulation of proteolysis (GO:0030162)|response to nutrient (GO:0007584)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(15)|ovary(1)	25					Ardeparin(DB00407)|Dalteparin(DB06779)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Nadroparin(DB08813)|Sulodexide(DB06271)|Tinzaparin(DB06822)	CACCCTGTTGGGGTTTAGCGA	0.458																																						ENST00000367698.3																			0				NS(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(15)|ovary(1)	25						c.(1285-1287)cCc>cTc		serpin peptidase inhibitor, clade C (antithrombin), member 1	Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)						80.0	78.0	78.0					1																	173873136		2203	4300	6503	SO:0001583	missense	462				blood coagulation|regulation of proteolysis	extracellular space|plasma membrane	heparin binding|protease binding|serine-type endopeptidase inhibitor activity	g.chr1:173873136G>A	X68793	CCDS1313.1	1q25.1	2014-02-18	2005-08-18		ENSG00000117601	ENSG00000117601		"""Serine (or cysteine) peptidase inhibitors"""	775	protein-coding gene	gene with protein product	"""antithrombin III"", ""signal peptide antithrombin part 1"", ""coding sequence signal peptide antithrombin part 1"", ""antithrombin (aa 375-432)"""	107300	"""serine (or cysteine) proteinase inhibitor, clade C (antithrombin), member 1"""	AT3		3979120, 24172014	Standard	NM_000488		Approved	ATIII, MGC22579	uc001gjt.3	P01008	OTTHUMG00000037276	ENST00000367698.3:c.1286C>T	1.37:g.173873136G>A	ENSP00000356671:p.Pro429Leu						p.P429L	NM_000488.3	NP_000479.1	P01008	ANT3_HUMAN			7	1404	-			429					B2R6P0|P78439|P78447|Q13815|Q5TC78|Q7KZ43|Q7KZ97|Q9UC78	Missense_Mutation	SNP	ENST00000367698.3	37	c.1286C>T	CCDS1313.1	.	.	.	.	.	.	.	.	.	.	G	6.971	0.549216	0.13374	.	.	ENSG00000117601	ENST00000367698;ENST00000351522	D	0.84442	-1.85	5.74	2.26	0.28386	Serpin domain (3);	0.671919	0.15262	N	0.271707	T	0.54870	0.1885	L	0.31926	0.97	0.09310	N	0.999998	B	0.06786	0.001	B	0.04013	0.001	T	0.43782	-0.9370	10	0.39692	T	0.17	.	1.4162	0.02302	0.2825:0.1516:0.4117:0.1542	.	429	P01008	ANT3_HUMAN	L	429;224	ENSP00000356671:P429L	ENSP00000307953:P224L	P	-	2	0	SERPINC1	172139759	0.113000	0.22115	0.986000	0.45419	0.974000	0.67602	0.677000	0.25262	0.695000	0.31675	0.650000	0.86243	CCC		0.458	SERPINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090734.1	NM_000488		43	57	0	0	0	1	0	43	57				
TTTY11	83866	broad.mit.edu	37	Y	8657050	8657050	+	lincRNA	SNP	C	C	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chrY:8657050C>T	ENST00000253470.4	-	0	414					NR_001548.2				testis-specific transcript, Y-linked 11 (non-protein coding)																		CTTTAAAATCCGCTTTAGTCG	0.373																																						ENST00000253470.4																			0																																																			83866							g.chrY:8657050C>T	AF332240		Yp11.2	2012-10-12	2009-08-21		ENSG00000180910	ENSG00000180910		"""Long non-coding RNAs"""	18492	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 134"""		"""testis-specific transcript, Y-linked 11"""				Standard	NR_001548		Approved	TTY11, NCRNA00134	uc004frk.2		OTTHUMG00000041259		Y.37:g.8657050C>T								NR_001548.2						0	414	-									RNA	SNP	ENST00000253470.4	37																																																																																						0.373	TTTY11-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000098854.2	NR_001548		18	0	0	0	0	1	0	18	0				
ZNF598	90850	broad.mit.edu	37	16	2051046	2051046	+	Missense_Mutation	SNP	C	C	T	rs373524057	byFrequency	TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr16:2051046C>T	ENST00000563630.1	-	7	1237	c.995G>A	c.(994-996)cGt>cAt	p.R332H	ZNF598_ENST00000431526.1_Missense_Mutation_p.R387H|ZNF598_ENST00000562103.1_Missense_Mutation_p.R332H|AC005606.15_ENST00000567515.1_lincRNA			Q86UK7	ZN598_HUMAN	zinc finger protein 598	387							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						CCGGGGGCCACGGGGATCCTC	0.692													C|||	2	0.000399361	0.0015	0.0	5008	,	,		14451	0.0		0.0	False		,,,				2504	0.0					ENST00000563630.1																			0				NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						c.(994-996)cGt>cAt		zinc finger protein 598		C	HIS/ARG	1,3917		0,1,1958	5.0	7.0	6.0		1162	2.8	0.4	16		6	0,8210		0,0,4105	no	missense	ZNF598	NM_178167.2	29	0,1,6063	TT,TC,CC		0.0,0.0255,0.0082	benign	387/905	2051046	1,12127	1959	4105	6064	SO:0001583	missense	90850					intracellular	zinc ion binding	g.chr16:2051046C>T	BC029270		16p13.3	2008-05-02				ENSG00000167962		"""Zinc fingers, C2H2-type"""	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.995G>A	16.37:g.2051046C>T	ENSP00000455882:p.Arg332His					ZNF598_ENST00000431526.1_Missense_Mutation_p.R387H|ZNF598_ENST00000562103.1_Missense_Mutation_p.R332H	p.R332H			Q86UK7	ZN598_HUMAN			7	1237	-			387					Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	37	c.995G>A		.	.	.	.	.	.	.	.	.	.	.	9.300	1.052967	0.19907	2.55E-4	0.0	ENSG00000167962	ENST00000431526	T	0.18810	2.19	4.79	2.84	0.33178	.	0.335675	0.30492	N	0.009506	T	0.18002	0.0432	L	0.55103	1.725	0.20074	N	0.999939	B	0.14805	0.011	B	0.09377	0.004	T	0.16808	-1.0390	10	0.36615	T	0.2	-3.72	7.3047	0.26440	0.0:0.7997:0.0:0.2003	.	387	Q86UK7	ZN598_HUMAN	H	387	ENSP00000411409:R387H	ENSP00000411409:R387H	R	-	2	0	ZNF598	1991047	0.001000	0.12720	0.448000	0.26945	0.053000	0.15095	0.877000	0.28106	0.620000	0.30215	0.591000	0.81541	CGT		0.692	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167		4	5	0	0	0	1	0	4	5				
HIST3H2BB	128312	broad.mit.edu	37	1	228645862	228645862	+	Missense_Mutation	SNP	C	C	T	rs562887286		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr1:228645862C>T	ENST00000369160.2	+	1	55	c.32C>T	c.(31-33)cCc>cTc	p.P11L	HIST3H2A_ENST00000366695.2_5'Flank	NM_175055.2	NP_778225.1	Q8N257	H2B3B_HUMAN	histone cluster 3, H2bb	11					chromatin organization (GO:0006325)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			skin(1)	1		Prostate(94;0.183)				GCTCCTGCGCCCAAGAAGGGT	0.527													C|||	1	0.000199681	0.0	0.0	5008	,	,		18396	0.0		0.0	False		,,,				2504	0.001					ENST00000369160.2																			0				skin(1)	1						c.(31-33)cCc>cTc		histone cluster 3, H2bb							62.0	66.0	64.0					1																	228645862		2203	4300	6503	SO:0001583	missense	128312				nucleosome assembly	nucleosome|nucleus	DNA binding	g.chr1:228645862C>T	AY131981	CCDS1574.1	1q42.13	2011-01-27	2006-10-11		ENSG00000196890	ENSG00000196890		"""Histones / Replication-dependent"""	20514	protein-coding gene	gene with protein product		615046	"""histone 3, H2bb"""			12408966	Standard	NM_175055		Approved		uc001hsz.3	Q8N257	OTTHUMG00000040045	ENST00000369160.2:c.32C>T	1.37:g.228645862C>T	ENSP00000375736:p.Pro11Leu						p.P11L	NM_175055.2	NP_778225.1	Q8N257	H2B3B_HUMAN			1	55	+		Prostate(94;0.183)	11					A4FU05|Q3ZCP6|Q5TA30	Missense_Mutation	SNP	ENST00000369160.2	37	c.32C>T	CCDS1574.1	.	.	.	.	.	.	.	.	.	.	.	14.54	2.566949	0.45694	.	.	ENSG00000196890	ENST00000369160	T	0.22743	1.94	3.98	3.98	0.46160	Histone-fold (2);	0.142675	0.31897	N	0.006897	T	0.29556	0.0737	M	0.81802	2.56	0.58432	D	0.999993	B	0.31485	0.325	B	0.31869	0.137	T	0.32079	-0.9920	10	0.87932	D	0	.	14.3736	0.66857	0.0:1.0:0.0:0.0	.	11	Q8N257	H2B3B_HUMAN	L	11	ENSP00000375736:P11L	ENSP00000375736:P11L	P	+	2	0	HIST3H2BB	226712485	1.000000	0.71417	0.959000	0.39883	0.165000	0.22458	7.107000	0.77047	2.496000	0.84212	0.591000	0.81541	CCC		0.527	HIST3H2BB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096597.1	NM_175055		46	69	0	0	0	1	0	46	69				
PCDHGA11	56105	broad.mit.edu	37	5	140801542	140801542	+	Missense_Mutation	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr5:140801542G>A	ENST00000398587.2	+	1	781	c.748G>A	c.(748-750)Gtg>Atg	p.V250M	PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA11_ENST00000518882.1_Missense_Mutation_p.V250M|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	250	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGTATATCGCGTGAGTGTTCC	0.498																																						ENST00000398587.2																			0				breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49						c.(748-750)Gtg>Atg									111.0	114.0	113.0					5																	140801542		1976	4164	6140	SO:0001583	missense	56105							g.chr5:140801542G>A	AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"""Cadherins / Protocadherins : Clustered"""	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.748G>A	5.37:g.140801542G>A	ENSP00000381589:p.Val250Met					PCDHGB1_ENST00000523390.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000518882.1_Missense_Mutation_p.V250M|PCDHGB7_ENST00000398594.2_Intron|PCDHGA9_ENST00000573521.1_Intron	p.V250M	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	781	+								B7ZVY8|Q9Y5D8|Q9Y5D9	Missense_Mutation	SNP	ENST00000398587.2	37	c.748G>A	CCDS47294.1	.	.	.	.	.	.	.	.	.	.	g	15.74	2.924006	0.52653	.	.	ENSG00000253873	ENST00000398587;ENST00000518882	T;T	0.01804	4.63;4.63	5.96	5.96	0.96718	Cadherin (4);Cadherin-like (1);	0.968814	0.08289	U	0.968708	T	0.09468	0.0233	M	0.80508	2.5	0.25266	N	0.98956	P;D;D	0.61697	0.94;0.99;0.982	P;P;P	0.50270	0.529;0.636;0.597	T	0.38757	-0.9646	10	0.72032	D	0.01	.	20.0324	0.97544	0.0:0.0:1.0:0.0	.	250;250;250	Q9Y5H2;Q9Y5H2-3;Q9Y5H2-2	PCDGB_HUMAN;.;.	M	250	ENSP00000381589:V250M;ENSP00000428333:V250M	ENSP00000381589:V250M	V	+	1	0	PCDHGA11	140781726	0.711000	0.27906	0.950000	0.38849	0.803000	0.45373	3.996000	0.57009	2.832000	0.97577	0.655000	0.94253	GTG		0.498	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914		82	100	0	0	0	1	0	82	100				
MDC1	9656	broad.mit.edu	37	6	30673819	30673819	+	Silent	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr6:30673819G>A	ENST00000376406.3	-	10	3788	c.3141C>T	c.(3139-3141)gcC>gcT	p.A1047A	MDC1_ENST00000376405.2_Silent_p.A783A|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1047	Pro-rich.			Missing (in Ref. 2; CAH18685). {ECO:0000305}.	DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						TTTGGGGTGGGGCTGGGGCTT	0.532								Other conserved DNA damage response genes																														ENST00000376406.3																			0				breast(2)|kidney(1)|ovary(1)	4						c.(3139-3141)gcC>gcT	Other conserved DNA damage response genes	mediator of DNA-damage checkpoint 1							55.0	66.0	62.0					6																	30673819		2202	4300	6502	SO:0001819	synonymous_variant	9656				cell cycle|double-strand break repair via homologous recombination|intra-S DNA damage checkpoint	focal adhesion|nucleoplasm	FHA domain binding|protein C-terminus binding	g.chr6:30673819G>A	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.3141C>T	6.37:g.30673819G>A						MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000376405.2_Silent_p.A783A	p.A1047A	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN			10	3788	-			1047	Missing (in Ref. 2; CAH18685).		Pro-rich.		A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Silent	SNP	ENST00000376406.3	37	c.3141C>T	CCDS34384.1	.	.	.	.	.	.	.	.	.	.	g	4.430	0.079583	0.08533	.	.	ENSG00000137337	ENST00000417033	.	.	.	4.83	-0.221	0.13126	.	.	.	.	.	T	0.09468	0.0233	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.35151	-0.9800	4	.	.	.	3.0787	4.4486	0.11609	0.3853:0.1605:0.4543:0.0	.	.	.	.	S	108	.	.	P	-	1	0	MDC1	30781798	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.215000	0.09279	0.006000	0.14734	-0.413000	0.06143	CCC		0.532	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		63	79	0	0	0	1	0	63	79				
WDR35	57539	broad.mit.edu	37	2	20137643	20137643	+	Missense_Mutation	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr2:20137643G>A	ENST00000345530.3	-	20	2276	c.2161C>T	c.(2161-2163)Cgc>Tgc	p.R721C	WDR35_ENST00000281405.4_Missense_Mutation_p.R710C|WDR35_ENST00000416055.2_Missense_Mutation_p.R286C	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	721					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTTTGCAGCGCACAAATGCT	0.428																																						ENST00000345530.3																			0				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						c.(2161-2163)Cgc>Tgc		WD repeat domain 35							131.0	130.0	130.0					2																	20137643		2203	4299	6502	SO:0001583	missense	57539							g.chr2:20137643G>A	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.2161C>T	2.37:g.20137643G>A	ENSP00000314444:p.Arg721Cys					WDR35_ENST00000416055.2_Missense_Mutation_p.R286C|WDR35_ENST00000281405.4_Missense_Mutation_p.R710C	p.R721C	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN			20	2276	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)		721					B3KVI5|Q4ZG01|Q8NE11	Missense_Mutation	SNP	ENST00000345530.3	37	c.2161C>T	CCDS33152.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.857604	0.91433	.	.	ENSG00000118965	ENST00000345530;ENST00000281405;ENST00000416055;ENST00000453014	T;T;T;D	0.88201	-0.33;-0.33;-0.93;-2.35	5.18	5.18	0.71444	.	0.287526	0.40144	N	0.001173	D	0.94601	0.8260	M	0.86178	2.8	0.80722	D	1	D;D;B;P	0.71674	0.998;0.994;0.228;0.543	D;P;B;B	0.63877	0.919;0.821;0.102;0.081	D	0.95261	0.8369	10	0.87932	D	0	-1.3777	18.0251	0.89266	0.0:0.0:1.0:0.0	.	721;710;721;286	F8WB94;Q9P2L0-2;Q9P2L0;B3KR94	.;.;WDR35_HUMAN;.	C	721;710;286;256	ENSP00000314444:R721C;ENSP00000281405:R710C;ENSP00000399159:R286C;ENSP00000404409:R256C	ENSP00000281405:R710C	R	-	1	0	WDR35	20001124	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	9.813000	0.99286	2.576000	0.86940	0.591000	0.81541	CGC		0.428	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779		4	147	0	0	0	1	0	4	147				
LRP5	4041	broad.mit.edu	37	11	68125186	68125186	+	Missense_Mutation	SNP	G	G	A	rs146895334		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr11:68125186G>A	ENST00000294304.7	+	3	663	c.557G>A	c.(556-558)cGg>cAg	p.R186Q		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	186	Beta-propeller 1.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GGCAGCACCCGGAAGATCATT	0.587																																						ENST00000294304.7																			0				autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						c.(556-558)cGg>cAg		low density lipoprotein receptor-related protein 5		G	GLN/ARG	1,4399	2.1+/-5.4	0,1,2199	94.0	79.0	84.0		557	3.6	1.0	11	dbSNP_134	84	0,8588		0,0,4294	no	missense	LRP5	NM_002335.2	43	0,1,6493	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	186/1616	68125186	1,12987	2200	4294	6494	SO:0001583	missense	4041				adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity	g.chr11:68125186G>A	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.557G>A	11.37:g.68125186G>A	ENSP00000294304:p.Arg186Gln						p.R186Q	NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN			3	663	+			186			Beta-propeller 1.		Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	37	c.557G>A	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.324274	0.81580	2.27E-4	0.0	ENSG00000162337	ENST00000294304	D	0.97404	-4.37	3.56	3.56	0.40772	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.45606	U	0.000360	D	0.98601	0.9532	M	0.89904	3.07	0.58432	D	0.999992	D	0.89917	1.0	D	0.97110	1.0	D	0.99364	1.0918	10	0.87932	D	0	.	16.4484	0.83959	0.0:0.0:1.0:0.0	.	186	O75197	LRP5_HUMAN	Q	186	ENSP00000294304:R186Q	ENSP00000294304:R186Q	R	+	2	0	LRP5	67881762	1.000000	0.71417	0.992000	0.48379	0.770000	0.43624	9.158000	0.94723	2.291000	0.77112	0.455000	0.32223	CGG		0.587	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		3	39	0	0	0	1	0	3	39				
TRGV2	6974	broad.mit.edu	37	7	38403051	38403051	+	RNA	SNP	G	G	C	rs4993385	byFrequency	TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr7:38403051G>C	ENST00000426402.2	-	0	68									T cell receptor gamma variable 2																		GTAGGAGGAGGTGGTCTTCCT	0.527													C|||	930	0.185703	0.2035	0.2118	5008	,	,		20608	0.1647		0.2147	False		,,,				2504	0.135					ENST00000426402.2																			0																																																			6974							g.chr7:38403051G>C	M13429		7p14	2012-02-07			ENSG00000233306	ENSG00000233306		"""T cell receptors / TRG locus"""	12287	other	T cell receptor gene	"""T-cell receptor, gamma, variable region V2"""			TCRGV2		2938743, 2969332	Standard	NG_001336		Approved	VIS2			OTTHUMG00000155105		7.37:g.38403051G>C														0	68	-									RNA	SNP	ENST00000426402.2	37																																																																																						0.527	TRGV2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000338419.4	NG_001336		3	10	0	0	0	1	0	3	10				
KIAA0430	9665	broad.mit.edu	37	16	15694386	15694386	+	Missense_Mutation	SNP	G	G	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr16:15694386G>T	ENST00000396368.3	-	25	4918	c.4712C>A	c.(4711-4713)tCc>tAc	p.S1571Y	KIAA0430_ENST00000548025.1_Missense_Mutation_p.S1568Y|KIAA0430_ENST00000602337.1_Missense_Mutation_p.S1568Y|KIAA0430_ENST00000344181.3_Missense_Mutation_p.S1259Y|KIAA0430_ENST00000551742.1_Missense_Mutation_p.S1571Y|KIAA0430_ENST00000547936.1_5'Flank|KIAA0430_ENST00000540441.2_Missense_Mutation_p.S1406Y	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430	1571					double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						ATTGGCAGGGGAGAGACTGAG	0.562																																						ENST00000396368.3																			0				breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						c.(4711-4713)tCc>tAc		KIAA0430							95.0	96.0	96.0					16																	15694386		1957	4132	6089	SO:0001583	missense	9665					peroxisome	nucleotide binding|RNA binding	g.chr16:15694386G>T	AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29562	protein-coding gene	gene with protein product	"""limkain b1"", ""protein phosphatase 1, regulatory subunit 34"", ""meiosis arrest female 1"""	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.4712C>A	16.37:g.15694386G>T	ENSP00000379654:p.Ser1571Tyr					KIAA0430_ENST00000551742.1_Missense_Mutation_p.S1571Y|KIAA0430_ENST00000548025.1_Missense_Mutation_p.S1568Y|KIAA0430_ENST00000602337.1_Missense_Mutation_p.S1568Y|KIAA0430_ENST00000540441.2_Missense_Mutation_p.S1406Y|KIAA0430_ENST00000344181.3_Missense_Mutation_p.S1259Y	p.S1571Y	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	LKAP_HUMAN			25	4918	-			1570					A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Missense_Mutation	SNP	ENST00000396368.3	37	c.4712C>A	CCDS10562.2	.	.	.	.	.	.	.	.	.	.	G	14.19	2.462589	0.43736	.	.	ENSG00000166783	ENST00000396368;ENST00000540441;ENST00000321370;ENST00000344181;ENST00000548025;ENST00000551742;ENST00000551298	.	.	.	5.76	4.8	0.61643	.	0.662674	0.16523	N	0.210707	T	0.34948	0.0915	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.31790	0.029;0.34;0.34;0.017	B;B;B;B	0.35470	0.062;0.203;0.203;0.028	T	0.22243	-1.0222	9	0.35671	T	0.21	.	13.5575	0.61768	0.0728:0.0:0.9272:0.0	.	1570;1568;1567;1570	Q9Y4F3-5;F8VV09;Q9Y4F3-4;Q9Y4F3	.;.;.;LKAP_HUMAN	Y	1571;1406;1511;1259;1568;1571;1437	.	ENSP00000315718:S1511Y	S	-	2	0	KIAA0430	15601887	0.998000	0.40836	0.027000	0.17364	0.049000	0.14656	2.890000	0.48609	1.395000	0.46643	0.655000	0.94253	TCC		0.562	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	NM_014647		20	95	1	0	4.35082e-09	1	4.77381e-09	20	95				
SEMA3C	10512	broad.mit.edu	37	7	80430072	80430072	+	Splice_Site	SNP	C	C	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr7:80430072C>A	ENST00000265361.3	-	10	1548		c.e10+1		SEMA3C_ENST00000419255.2_Splice_Site|SEMA3C_ENST00000536800.1_Splice_Site|SEMA3C_ENST00000544525.1_Splice_Site	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C						axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TGAATAATTACCTTGATGTTG	0.289																																						ENST00000265361.3																			0				NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						c.e10+1		sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C							74.0	77.0	76.0					7																	80430072		2203	4289	6492	SO:0001630	splice_region_variant	10512				immune response|response to drug	membrane	receptor activity	g.chr7:80430072C>A	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.986+1G>T	7.37:g.80430072C>A						SEMA3C_ENST00000544525.1_Splice_Site|SEMA3C_ENST00000419255.2_Splice_Site|SEMA3C_ENST00000536800.1_Splice_Site		NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN			10	1548	-								B4DRL8	Splice_Site	SNP	ENST00000265361.3	37		CCDS5596.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.699671	0.88830	.	.	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525;ENST00000536800	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8893	0.96923	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SEMA3C	80268008	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	7.549000	0.82163	2.704000	0.92352	0.585000	0.79938	.		0.289	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	Intron	23	36	1	0	7.92952e-12	1	9.21224e-12	23	36				
CNGB3	54714	broad.mit.edu	37	8	87641258	87641258	+	Missense_Mutation	SNP	C	C	T	rs192568942	byFrequency	TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr8:87641258C>T	ENST00000320005.5	-	12	1416	c.1369G>A	c.(1369-1371)Gcc>Acc	p.A457T		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	457					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						TCCATGCAGGCGCGGAAGTAG	0.443													C|||	2	0.000399361	0.0	0.0	5008	,	,		18682	0.002		0.0	False		,,,				2504	0.0					ENST00000320005.5																			0				NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						c.(1369-1371)Gcc>Acc		cyclic nucleotide gated channel beta 3							249.0	234.0	239.0					8																	87641258		2203	4300	6503	SO:0001583	missense	54714				signal transduction|visual perception	integral to membrane	cGMP binding	g.chr8:87641258C>T	AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2153	protein-coding gene	gene with protein product		605080	"""achromatopsia (rod monochromacy) 3"", ""achromatopsia (rod monochromacy) 1"""	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.1369G>A	8.37:g.87641258C>T	ENSP00000316605:p.Ala457Thr						p.A457T	NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN			12	1416	-			457					C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	37	c.1369G>A	CCDS6244.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	9.652	1.141838	0.21205	.	.	ENSG00000170289	ENST00000320005	D	0.96587	-4.06	5.92	0.51	0.16983	Cyclic nucleotide-binding-like (1);	1.447980	0.04227	N	0.334592	D	0.94262	0.8157	M	0.65498	2.005	0.09310	N	1	B;B	0.32160	0.358;0.244	B;B	0.29353	0.101;0.047	D	0.83835	0.0254	10	0.51188	T	0.08	.	4.7431	0.13024	0.2532:0.4517:0.0:0.2951	.	457;457	Q9NQW8-2;Q9NQW8	.;CNGB3_HUMAN	T	457	ENSP00000316605:A457T	ENSP00000316605:A457T	A	-	1	0	CNGB3	87710374	0.003000	0.15002	0.000000	0.03702	0.260000	0.26232	0.476000	0.22180	-0.199000	0.10317	-0.300000	0.09419	GCC		0.443	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098		65	202	0	0	0	1	0	65	202				
PCDHGA4	56111	broad.mit.edu	37	5	140736453	140736453	+	Silent	SNP	C	C	A	rs207466434		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr5:140736453C>A	ENST00000571252.1	+	1	1686	c.1686C>A	c.(1684-1686)atC>atA	p.I562I	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	562	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCCTGAGATCCTGTACCCCA	0.582																																						ENST00000571252.1																			0				endometrium(1)|kidney(1)|lung(3)	5						c.(1684-1686)atC>atA									197.0	208.0	204.0					5																	140736453		2202	4297	6499	SO:0001819	synonymous_variant	56111							g.chr5:140736453C>A	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.1686C>A	5.37:g.140736453C>A						PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron	p.I562I	NM_018917.2	NP_061740.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	1686	+								Q9Y5D3	Silent	SNP	ENST00000571252.1	37	c.1686C>A	CCDS58979.1																																																																																				0.582	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		122	240	1	0	4.94232e-47	1	6.29747e-47	122	240				
CSRNP3	80034	broad.mit.edu	37	2	166533063	166533063	+	Missense_Mutation	SNP	G	G	T	rs369735548		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr2:166533063G>T	ENST00000342316.4	+	4	922	c.650G>T	c.(649-651)cGa>cTa	p.R217L	CSRNP3_ENST00000314499.7_Missense_Mutation_p.R217L|CSRNP3_ENST00000409420.1_Missense_Mutation_p.R249L	NM_024969.3	NP_079245.2	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	217	Cys-rich.				apoptotic process (GO:0006915)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(3)|skin(2)	33						TGTGACTGCCGAGTGTTCTGT	0.542																																						ENST00000314499.7																			0				breast(2)|cervix(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(3)|skin(2)	33						c.(649-651)cGa>cTa		cysteine-serine-rich nuclear protein 3							67.0	64.0	65.0					2																	166533063		2203	4300	6503	SO:0001583	missense	80034				apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr2:166533063G>T	AB063300	CCDS2225.1	2q24.3	2012-04-17	2009-01-07	2009-01-07	ENSG00000178662	ENSG00000178662		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	30729	protein-coding gene	gene with protein product	"""TGF beta induced apotosis protein 2"", ""protein phosphatase 1, regulatory subunit 73"""		"""family with sequence similarity 130, member A2"""	FAM130A2		17726538	Standard	NM_024969		Approved	FLJ32093, TAIP-2, PPP1R73	uc002udg.3	Q8WYN3	OTTHUMG00000132145	ENST00000342316.4:c.650G>T	2.37:g.166533063G>T	ENSP00000344042:p.Arg217Leu					CSRNP3_ENST00000409420.1_Missense_Mutation_p.R249L|CSRNP3_ENST00000342316.4_Missense_Mutation_p.R217L	p.R217L	NM_001172173.1	NP_001165644.1	Q8WYN3	CSRN3_HUMAN			6	1026	+			217			Cys-rich.		B3KPR4|Q53SG0|Q6ZTX3|Q9HAF9	Missense_Mutation	SNP	ENST00000342316.4	37	c.650G>T	CCDS2225.1	.	.	.	.	.	.	.	.	.	.	G	35	5.592056	0.96590	.	.	ENSG00000178662	ENST00000421875;ENST00000431452;ENST00000314499;ENST00000342316;ENST00000409420	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.61726	0.2370	L	0.50333	1.59	0.54753	D	0.999988	D	0.89917	1.0	D	0.85130	0.997	T	0.59484	-0.7446	10	0.59425	D	0.04	-12.2647	19.3504	0.94381	0.0:0.0:1.0:0.0	.	217	Q8WYN3	CSRN3_HUMAN	L	217;224;217;217;249	ENSP00000412081:R217L;ENSP00000318258:R217L;ENSP00000344042:R217L;ENSP00000387195:R249L	ENSP00000318258:R217L	R	+	2	0	CSRNP3	166241309	1.000000	0.71417	0.979000	0.43373	0.995000	0.86356	7.965000	0.87945	2.885000	0.99019	0.655000	0.94253	CGA		0.542	CSRNP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255191.2	NM_024969		35	16	1	0	5.8336e-16	1	7.09007e-16	35	16				
MFSD2A	84879	broad.mit.edu	37	1	40421045	40421045	+	Silent	SNP	G	G	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr1:40421045G>T	ENST00000372809.5	+	1	224	c.81G>T	c.(79-81)ccG>ccT	p.P27P	MFSD2A_ENST00000420632.2_5'UTR|MFSD2A_ENST00000372811.5_Silent_p.P27P	NM_001136493.1	NP_001129965.1	Q8NA29	NLS1_HUMAN	major facilitator superfamily domain containing 2A	27					establishment of blood-brain barrier (GO:0060856)|fatty acid transport (GO:0015908)|lipid transport across blood brain barrier (GO:1990379)|transcytosis (GO:0045056)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phospholipid transporter activity (GO:0005548)|symporter activity (GO:0015293)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						CTGAACGCCCGGCCCAGGTGA	0.731																																						ENST00000372809.5																			0				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						c.(79-81)ccG>ccT		major facilitator superfamily domain containing 2A							11.0	15.0	13.0					1																	40421045		2182	4285	6467	SO:0001819	synonymous_variant	84879				transmembrane transport	endoplasmic reticulum membrane|integral to membrane		g.chr1:40421045G>T	AK093223	CCDS446.1, CCDS44118.1, CCDS72762.1	1p34.2	2009-09-08	2009-09-08	2009-09-08	ENSG00000168389	ENSG00000168389			25897	protein-coding gene	gene with protein product		614397	"""major facilitator superfamily domain containing 2"""	MFSD2		18694395	Standard	XM_005271285		Approved	FLJ14490	uc001cev.3	Q8NA29	OTTHUMG00000009293	ENST00000372809.5:c.81G>T	1.37:g.40421045G>T						MFSD2A_ENST00000420632.2_5'UTR|MFSD2A_ENST00000372811.5_Silent_p.P27P	p.P27P	NM_001136493.1	NP_001129965.1	Q8NA29	MFS2A_HUMAN			1	224	+			27					A8K675|Q6UWU5|Q96F59|Q9BRC8	Silent	SNP	ENST00000372809.5	37	c.81G>T	CCDS44118.1																																																																																				0.731	MFSD2A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025756.1	NM_032793		8	16	1	0	2.17888e-05	1	2.35796e-05	8	16				
OR13G1	441933	broad.mit.edu	37	1	247835701	247835701	+	Missense_Mutation	SNP	A	A	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr1:247835701A>T	ENST00000359688.2	-	1	664	c.643T>A	c.(643-645)Tat>Aat	p.Y215N	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	215						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			ATAAAACCATAGGAGATGCAG	0.458																																						ENST00000359688.2																			0				endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35						c.(643-645)Tat>Aat		olfactory receptor, family 13, subfamily G, member 1							104.0	98.0	100.0					1																	247835701		2203	4300	6503	SO:0001583	missense	441933				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:247835701A>T	AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"""GPCR / Class A : Olfactory receptors"""	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.643T>A	1.37:g.247835701A>T	ENSP00000352717:p.Tyr215Asn					RP11-634B7.4_ENST00000449298.1_RNA	p.Y215N	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.017)		1	664	-	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		215					B2RN80|Q5T2T2|Q6IF86	Missense_Mutation	SNP	ENST00000359688.2	37	c.643T>A	CCDS31094.1	.	.	.	.	.	.	.	.	.	.	A	14.23	2.473970	0.43942	.	.	ENSG00000197437	ENST00000359688	T	0.00518	6.86	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	0.187347	0.26173	N	0.025909	T	0.03739	0.0106	H	0.98918	4.37	0.25452	N	0.987992	D	0.89917	1.0	D	0.80764	0.994	T	0.19516	-1.0303	10	0.87932	D	0	-18.9462	11.5555	0.50745	1.0:0.0:0.0:0.0	.	215	Q8NGZ3	O13G1_HUMAN	N	215	ENSP00000352717:Y215N	ENSP00000352717:Y215N	Y	-	1	0	OR13G1	245902324	1.000000	0.71417	0.337000	0.25536	0.525000	0.34531	7.588000	0.82629	1.888000	0.54679	0.460000	0.39030	TAT		0.458	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487		29	45	0	0	0	1	0	29	45				
TAF1L	138474	broad.mit.edu	37	9	32631299	32631299	+	Missense_Mutation	SNP	G	G	C			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr9:32631299G>C	ENST00000242310.4	-	1	4368	c.4279C>G	c.(4279-4281)Cca>Gca	p.P1427A	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1427	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.P1427T(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		GCATTGACTGGAGTGTGGAAA	0.478																																						ENST00000242310.4																			1	Substitution - Missense(1)	p.P1427T(1)	lung(1)	breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159						c.(4279-4281)Cca>Gca		TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like							318.0	271.0	287.0					9																	32631299		2203	4300	6503	SO:0001583	missense	138474				male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding	g.chr9:32631299G>C	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.4279C>G	9.37:g.32631299G>C	ENSP00000418379:p.Pro1427Ala						p.P1427A	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)	1	4368	-			1427			Bromo 1.		Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	c.4279C>G	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	G	19.07	3.756234	0.69648	.	.	ENSG00000122728	ENST00000242310	T	0.26810	1.71	0.658	0.658	0.17855	Bromodomain (5);Bromodomain, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.42988	0.1227	M	0.93507	3.425	0.53005	D	0.999967	P	0.42973	0.796	P	0.48227	0.571	T	0.47341	-0.9125	10	0.56958	D	0.05	.	7.0823	0.25237	1.0E-4:0.0:0.9999:0.0	.	1427	Q8IZX4	TAF1L_HUMAN	A	1427	ENSP00000418379:P1427A	ENSP00000418379:P1427A	P	-	1	0	TAF1L	32621299	1.000000	0.71417	0.995000	0.50966	0.674000	0.39518	6.138000	0.71717	0.626000	0.30322	0.195000	0.17529	CCA		0.478	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			14	290	0	0	0	1	0	14	290				
HDAC7	51564	broad.mit.edu	37	12	48189110	48189110	+	Missense_Mutation	SNP	C	C	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr12:48189110C>T	ENST00000427332.2	-	11	1180	c.1024G>A	c.(1024-1026)Gag>Aag	p.E342K	HDAC7_ENST00000380610.4_Missense_Mutation_p.E398K|HDAC7_ENST00000354334.3_Missense_Mutation_p.E344K|HDAC7_ENST00000552960.1_Missense_Mutation_p.E364K|HDAC7_ENST00000080059.7_Missense_Mutation_p.E381K			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	342	Transcription repression 2. {ECO:0000250}.				cell-cell junction assembly (GO:0007043)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25				GBM - Glioblastoma multiforme(48;0.137)		GAGAGCCGCTCGGTGGTCATT	0.667																																						ENST00000080059.7																			0				breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						c.(1141-1143)Gag>Aag		histone deacetylase 7							13.0	16.0	15.0					12																	48189110		2194	4279	6473	SO:0001583	missense	51564				negative regulation of interleukin-2 production|negative regulation of osteoblast differentiation|positive regulation of cell migration involved in sprouting angiogenesis|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding	g.chr12:48189110C>T	AF239243	CCDS8756.2, CCDS41776.1	12q13.1	2008-02-25	2008-02-25	2008-02-25	ENSG00000061273	ENSG00000061273			14067	protein-coding gene	gene with protein product		606542	"""histone deacetylase 7A"""	HDAC7A		10922406, 10640276	Standard	NM_015401		Approved	DKFZP586J0917	uc010slo.2	Q8WUI4	OTTHUMG00000152968	ENST00000427332.2:c.1024G>A	12.37:g.48189110C>T	ENSP00000404394:p.Glu342Lys					HDAC7_ENST00000552960.1_Missense_Mutation_p.E364K|HDAC7_ENST00000380610.4_Missense_Mutation_p.E398K|HDAC7_ENST00000354334.3_Missense_Mutation_p.E344K|HDAC7_ENST00000427332.2_Missense_Mutation_p.E342K	p.E381K	NM_015401.3	NP_056216.2	Q8WUI4	HDAC7_HUMAN		GBM - Glioblastoma multiforme(48;0.137)	11	1140	-			342			Transcription repression 2 (By similarity).		B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Missense_Mutation	SNP	ENST00000427332.2	37	c.1141G>A		.	.	.	.	.	.	.	.	.	.	C	13.93	2.384725	0.42308	.	.	ENSG00000061273	ENST00000080059;ENST00000354334;ENST00000552960;ENST00000380610;ENST00000427332	T;T;T;T;T	0.57436	0.42;0.51;0.43;0.4;0.43	4.51	2.68	0.31781	.	0.471205	0.23506	N	0.047458	T	0.43634	0.1256	L	0.61218	1.895	0.26634	N	0.972413	P;P;P	0.40931	0.733;0.733;0.733	B;B;B	0.35899	0.213;0.213;0.213	T	0.27839	-1.0062	10	0.23302	T	0.38	.	9.9124	0.41415	0.0:0.83:0.0:0.17	.	381;364;344	Q8WUI4-5;Q8WUI4-6;Q8WUI4-7	.;.;.	K	381;344;364;398;342	ENSP00000080059:E381K;ENSP00000351326:E344K;ENSP00000448532:E364K;ENSP00000369984:E398K;ENSP00000404394:E342K	ENSP00000080059:E381K	E	-	1	0	HDAC7	46475377	0.999000	0.42202	0.998000	0.56505	0.739000	0.42172	2.162000	0.42367	0.638000	0.30545	-0.258000	0.10820	GAG		0.667	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2			12	22	0	0	0	1	0	12	22				
CYP2D7	1564	broad.mit.edu	37	22	42538870	42538870	+	RNA	SNP	A	A	C	rs2982057	byFrequency	TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr22:42538870A>C	ENST00000428786.1	-	0	0				CYP2D7P1_ENST00000433992.1_RNA|CYP2D7P1_ENST00000358097.4_RNA|CYP2D7P1_ENST00000424775.1_RNA																							CCATAGCGCGACAGGAACACC	0.687													N|||	80	0.0159744	0.0023	0.0317	5008	,	,		11900	0.0109		0.0348	False		,,,				2504	0.0092					ENST00000424775.1																			0				endometrium(1)	1																																														1564							g.chr22:42538870A>C																													22.37:g.42538870A>C						CYP2D7P1_ENST00000433992.1_RNA|CYP2D7P1_ENST00000358097.4_RNA								0	440	-									RNA	SNP	ENST00000428786.1	37			30	0.013736263736263736	1	0.0020325203252032522	5	0.013812154696132596	5	0.008741258741258742	19	0.025065963060686015	C	8.846	0.943329	0.18281	.	.	ENSG00000205702	ENST00000428297;ENST00000381321;ENST00000436260	.	.	.	3.26	3.26	0.37387	.	.	.	.	.	T	0.04724	0.0128	.	.	.	0.28613	N	0.908552	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.23154	-1.0196	7	0.02654	T	1	.	8.0614	0.30635	0.2422:0.7578:0.0:0.0	rs2982057	122;32	Q6XP50;F5H167	.;.	A	121;71;32	.	ENSP00000446103:S71A	S	-	1	0	CYP2D7P1	40868814	0.299000	0.24426	0.017000	0.16124	0.002000	0.02628	0.565000	0.23578	0.961000	0.38030	-0.290000	0.09829	TCG		0.687	RP4-669P10.16-001	KNOWN	basic|exp_conf	sense_intronic	sense_intronic	OTTHUMT00000320534.1			5	45	0	0	0	1	0	5	45				
CALCRL	10203	broad.mit.edu	37	2	188225462	188225462	+	Missense_Mutation	SNP	G	G	C			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr2:188225462G>C	ENST00000409998.1	-	11	1425	c.644C>G	c.(643-645)tCc>tGc	p.S215C	CALCRL_ENST00000410068.1_Missense_Mutation_p.S215C|CALCRL_ENST00000392370.3_Missense_Mutation_p.S215C|AC007319.1_ENST00000412276.1_RNA|AC007319.1_ENST00000453517.1_RNA			Q16602	CALRL_HUMAN	calcitonin receptor-like	215					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|cAMP biosynthetic process (GO:0006171)|cellular response to sucrose stimulus (GO:0071329)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|heart development (GO:0007507)|negative regulation of inflammatory response (GO:0050728)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of muscle contraction (GO:0006937)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	adrenomedullin receptor activity (GO:0001605)|calcitonin gene-related polypeptide receptor activity (GO:0001635)|calcitonin receptor activity (GO:0004948)|G-protein coupled receptor activity (GO:0004930)|protein transporter activity (GO:0008565)			endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)			AATGAACTGGGACACTTTGCA	0.393																																						ENST00000409998.1																			0				endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1)	32						c.(643-645)tCc>tGc		calcitonin receptor-like							71.0	62.0	65.0					2																	188225462		2203	4300	6503	SO:0001583	missense	10203					integral to plasma membrane		g.chr2:188225462G>C	U17473	CCDS2293.1	2q21.1-q21.3	2012-08-10			ENSG00000064989	ENSG00000064989		"""GPCR / Class B : Calcitonin receptors"""	16709	protein-coding gene	gene with protein product		114190				7818539, 8626685	Standard	NM_005795		Approved	CGRPR, CRLR	uc010frt.4	Q16602	OTTHUMG00000132636	ENST00000409998.1:c.644C>G	2.37:g.188225462G>C	ENSP00000386972:p.Ser215Cys					CALCRL_ENST00000392370.3_Missense_Mutation_p.S215C|AC007319.1_ENST00000412276.1_RNA|AC007319.1_ENST00000453517.1_RNA|CALCRL_ENST00000410068.1_Missense_Mutation_p.S215C	p.S215C			Q16602	CALRL_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)		11	1425	-			215					A8K6G5|A8KAD3|Q53S02|Q53TS5	Missense_Mutation	SNP	ENST00000409998.1	37	c.644C>G	CCDS2293.1	.	.	.	.	.	.	.	.	.	.	G	17.21	3.331716	0.60853	.	.	ENSG00000064989	ENST00000392370;ENST00000409998;ENST00000410068	T;T;T	0.37915	1.17;1.17;1.17	5.6	1.86	0.25419	GPCR, family 2-like (1);	0.298941	0.28748	N	0.014278	T	0.49592	0.1566	L	0.60455	1.87	0.40400	D	0.979633	B	0.33171	0.4	P	0.51657	0.676	T	0.51795	-0.8660	10	0.72032	D	0.01	.	10.8814	0.46939	0.2333:0.0:0.7667:0.0	.	215	Q16602	CALRL_HUMAN	C	215	ENSP00000376177:S215C;ENSP00000386972:S215C;ENSP00000387190:S215C	ENSP00000376177:S215C	S	-	2	0	CALCRL	187933707	0.677000	0.27577	0.962000	0.40283	0.973000	0.67179	0.976000	0.29462	0.072000	0.16694	0.650000	0.86243	TCC		0.393	CALCRL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334648.1	NM_005795		28	28	0	0	0	1	0	28	28				
KIAA0430	9665	broad.mit.edu	37	16	15694388	15694388	+	Silent	SNP	G	G	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr16:15694388G>T	ENST00000396368.3	-	25	4916	c.4710C>A	c.(4708-4710)ctC>ctA	p.L1570L	KIAA0430_ENST00000548025.1_Silent_p.L1567L|KIAA0430_ENST00000602337.1_Silent_p.L1567L|KIAA0430_ENST00000344181.3_Silent_p.L1258L|KIAA0430_ENST00000551742.1_Silent_p.L1570L|KIAA0430_ENST00000547936.1_5'Flank|KIAA0430_ENST00000540441.2_Silent_p.L1405L	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430	1570					double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						TGGCAGGGGAGAGACTGAGTG	0.562																																						ENST00000396368.3																			0				breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						c.(4708-4710)ctC>ctA		KIAA0430							95.0	96.0	96.0					16																	15694388		1955	4133	6088	SO:0001819	synonymous_variant	9665					peroxisome	nucleotide binding|RNA binding	g.chr16:15694388G>T	AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29562	protein-coding gene	gene with protein product	"""limkain b1"", ""protein phosphatase 1, regulatory subunit 34"", ""meiosis arrest female 1"""	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.4710C>A	16.37:g.15694388G>T						KIAA0430_ENST00000551742.1_Silent_p.L1570L|KIAA0430_ENST00000548025.1_Silent_p.L1567L|KIAA0430_ENST00000602337.1_Silent_p.L1567L|KIAA0430_ENST00000540441.2_Silent_p.L1405L|KIAA0430_ENST00000344181.3_Silent_p.L1258L	p.L1570L	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	LKAP_HUMAN			25	4916	-			1569					A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Silent	SNP	ENST00000396368.3	37	c.4710C>A	CCDS10562.2																																																																																				0.562	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	NM_014647		19	95	1	0	2.4624e-09	1	2.73985e-09	19	95				
KLHL34	257240	broad.mit.edu	37	X	21675273	21675273	+	Missense_Mutation	SNP	G	G	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chrX:21675273G>T	ENST00000379499.2	-	1	1175	c.634C>A	c.(634-636)Cgc>Agc	p.R212S		NM_153270.1	NP_695002.1	Q8N239	KLH34_HUMAN	kelch-like family member 34	212	BACK.					extracellular space (GO:0005615)				cervix(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	26						TGTGCCAGGCGCTCAGTTGTG	0.692																																						ENST00000379499.2																			0				cervix(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	26						c.(634-636)Cgc>Agc		kelch-like family member 34							12.0	11.0	11.0					X																	21675273		2141	4173	6314	SO:0001583	missense	257240							g.chrX:21675273G>T	AK092279	CCDS14199.1	Xp22.12	2013-02-22	2013-02-22		ENSG00000185915	ENSG00000185915		"""Kelch-like"", ""BTB/POZ domain containing"""	26634	protein-coding gene	gene with protein product			"""kelch-like 34 (Drosophila)"""				Standard	NM_153270		Approved	FLJ34960, RP11-450P7.3	uc004czz.1	Q8N239	OTTHUMG00000021234	ENST00000379499.2:c.634C>A	X.37:g.21675273G>T	ENSP00000368813:p.Arg212Ser						p.R212S	NM_153270.1	NP_695002.1	Q8N239	KLH34_HUMAN			1	1175	-			212			BACK.			Missense_Mutation	SNP	ENST00000379499.2	37	c.634C>A	CCDS14199.1	.	.	.	.	.	.	.	.	.	.	G	10.38	1.334696	0.24253	.	.	ENSG00000185915	ENST00000379499	T	0.73258	-0.73	4.76	3.89	0.44902	BTB/Kelch-associated (2);	0.137252	0.47455	D	0.000232	T	0.74191	0.3684	M	0.64170	1.965	0.09310	N	1	P	0.49090	0.919	P	0.52481	0.7	T	0.67007	-0.5779	10	0.87932	D	0	.	9.5736	0.39442	0.105:0.0:0.895:0.0	.	212	Q8N239	KLH34_HUMAN	S	212	ENSP00000368813:R212S	ENSP00000368813:R212S	R	-	1	0	KLHL34	21585194	0.919000	0.31177	0.459000	0.27081	0.053000	0.15095	1.884000	0.39668	0.998000	0.38996	0.422000	0.28245	CGC		0.692	KLHL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056022.1	NM_153270		18	7	1	0	1.02788e-11	1	1.17685e-11	18	7				
ALG1L2	644974	broad.mit.edu	37	3	129817144	129817144	+	RNA	SNP	G	G	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr3:129817144G>T	ENST00000507643.1	+	0	726				AC083906.2_ENST00000578837.1_RNA			C9J202	AG1L2_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like 2								transferase activity, transferring glycosyl groups (GO:0016757)										TGCGGGAGTCGCAGCAGCTCT	0.527																																						ENST00000507643.1																			0																																																			644974				biosynthetic process		transferase activity, transferring glycosyl groups	g.chr3:129817144G>T	BC127756		3q22.1	2013-02-22	2013-02-22		ENSG00000251287	ENSG00000251287		"""Glycosyltransferase group 1 domain containing"""	37258	other	unknown			"""asparagine-linked glycosylation 1-like 2"""				Standard	NM_001136152		Approved		uc011bld.2	C9J202	OTTHUMG00000159782		3.37:g.129817144G>T										C9J202	AG1L2_HUMAN			0	726	+									RNA	SNP	ENST00000507643.1	37																																																																																						0.527	ALG1L2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000357289.1	NM_001136152		4	67	1	0	0.150653	1	0.150653	4	67				
HEPACAM	220296	broad.mit.edu	37	11	124794758	124794758	+	Missense_Mutation	SNP	C	C	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr11:124794758C>T	ENST00000298251.4	-	2	698	c.293G>A	c.(292-294)cGt>cAt	p.R98H		NM_152722.4	NP_689935.2			hepatic and glial cell adhesion molecule									p.R98H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		GAGTCGGATACGGTCTCGATA	0.587																																						ENST00000298251.4																			1	Substitution - Missense(1)	p.R98H(1)	ovary(1)	breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22						c.(292-294)cGt>cAt		hepatic and glial cell adhesion molecule							145.0	128.0	134.0					11																	124794758		2201	4299	6500	SO:0001583	missense	220296				cell adhesion|cell cycle arrest|regulation of growth	cytoplasm|integral to membrane		g.chr11:124794758C>T	AK098396	CCDS8456.1	11q24.2	2013-01-29	2011-02-11		ENSG00000165478	ENSG00000165478		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26361	protein-coding gene	gene with protein product	"""glial cell adhesion molecule"""	611642	"""hepatocyte cell adhesion molecule"""			15885354, 15917256	Standard	NM_152722		Approved	FLJ25530, hepaCAM, GLIALCAM	uc001qbk.3	Q14CZ8	OTTHUMG00000165938	ENST00000298251.4:c.293G>A	11.37:g.124794758C>T	ENSP00000298251:p.Arg98His						p.R98H	NM_152722.4	NP_689935.2	Q14CZ8	HECAM_HUMAN		BRCA - Breast invasive adenocarcinoma(274;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)	2	698	-	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)	98			Ig-like V-type.			Missense_Mutation	SNP	ENST00000298251.4	37	c.293G>A	CCDS8456.1	.	.	.	.	.	.	.	.	.	.	C	36	5.689530	0.96784	.	.	ENSG00000165478	ENST00000298251;ENST00000374961	T	0.39406	1.08	5.84	5.84	0.93424	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.69405	0.3107	M	0.81341	2.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.992;1.0	T	0.71777	-0.4490	10	0.87932	D	0	-17.862	20.1434	0.98067	0.0:1.0:0.0:0.0	.	98;98	Q14CZ8-2;Q14CZ8	.;HECAM_HUMAN	H	98	ENSP00000298251:R98H	ENSP00000298251:R98H	R	-	2	0	HEPACAM	124299968	1.000000	0.71417	0.998000	0.56505	0.910000	0.53928	7.796000	0.85898	2.769000	0.95229	0.563000	0.77884	CGT		0.587	HEPACAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387125.1	NM_152722		56	82	0	0	0	1	0	56	82				
GTF2IRD2P1	401375	broad.mit.edu	37	7	72664015	72664015	+	RNA	SNP	C	C	G	rs202030378|rs372212945	byFrequency	TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr7:72664015C>G	ENST00000425256.1	-	0	885									GTF2I repeat domain containing 2 pseudogene 1																		ATACCACCCCCGGGGCATGCC	0.507																																						ENST00000425256.1																			0																																																			401375							g.chr7:72664015C>G	AY312852		7q11.23	2010-03-19	2010-02-09	2010-02-09	ENSG00000214544	ENSG00000214544			33127	pseudogene	pseudogene			"""GTF2I repeat domain containing 2 pseudogene"""	GTF2IRD2P		15100712	Standard	NG_033736		Approved		uc003txs.1		OTTHUMG00000156803		7.37:g.72664015C>G								NR_002164.1						0	885	-									RNA	SNP	ENST00000425256.1	37																																																																																						0.507	GTF2IRD2P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000345921.1	NR_002164		3	21	0	0	0	1	0	3	21				
FRG1B	284802	broad.mit.edu	37	20	29628282	29628282	+	Missense_Mutation	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr20:29628282G>A	ENST00000278882.3	+	6	664	c.284G>A	c.(283-285)gGg>gAg	p.G95E	FRG1B_ENST00000358464.4_Missense_Mutation_p.G95E|FRG1B_ENST00000439954.2_Missense_Mutation_p.G100E			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	95										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						AATGAAGCAGGGGACATAGAA	0.373																																						ENST00000278882.3																			0				endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(283-285)gGg>gAg																																						SO:0001583	missense	284802							g.chr20:29628282G>A			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.284G>A	20.37:g.29628282G>A	ENSP00000278882:p.Gly95Glu					FRG1B_ENST00000358464.4_Missense_Mutation_p.G95E|FRG1B_ENST00000439954.2_Missense_Mutation_p.G100E	p.G95E							6	664	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.284G>A		.	.	.	.	.	.	.	.	.	.	g	18.02	3.529440	0.64860	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.56103	0.48	2.08	2.08	0.27032	Actin cross-linking (1);	0.051750	0.85682	D	0.000000	T	0.52092	0.1713	.	.	.	0.58432	D	0.999996	B;P	0.39940	0.309;0.696	P;P	0.46543	0.492;0.52	T	0.54221	-0.8326	9	0.45353	T	0.12	.	10.2211	0.43198	0.0:0.0:1.0:0.0	.	100;95	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	E	95;100;95	ENSP00000408863:G100E	ENSP00000278882:G95E	G	+	2	0	FRG1B	28241943	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	8.494000	0.90477	1.475000	0.48197	0.423000	0.28283	GGG		0.373	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		4	171	0	0	0	1	0	4	171				
CCDC106	29903	broad.mit.edu	37	19	56160925	56160925	+	Silent	SNP	C	C	T	rs545356408		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr19:56160925C>T	ENST00000586790.1	+	3	1192	c.288C>T	c.(286-288)ttC>ttT	p.F96F	CCDC106_ENST00000591241.1_Silent_p.F61F|CCDC106_ENST00000308964.3_Silent_p.F96F|CCDC106_ENST00000588740.1_Silent_p.F96F|CCDC106_ENST00000591578.1_Silent_p.F96F			Q9BWC9	CC106_HUMAN	coiled-coil domain containing 106	96						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(2)|large_intestine(3)|lung(5)|skin(1)	11		Colorectal(82;0.00403)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)		TGGACAAATTCATCTCTTCTG	0.607													C|||	1	0.000199681	0.0	0.0	5008	,	,		18507	0.001		0.0	False		,,,				2504	0.0					ENST00000586790.1																			0				endometrium(2)|large_intestine(3)|lung(5)|skin(1)	11						c.(286-288)ttC>ttT		coiled-coil domain containing 106							63.0	60.0	61.0					19																	56160925		2203	4300	6503	SO:0001819	synonymous_variant	29903					nucleus		g.chr19:56160925C>T	AF054984	CCDS33118.1	19q13.42	2013-09-20			ENSG00000173581	ENSG00000173581			30181	protein-coding gene	gene with protein product		613478				8619474, 9110174	Standard	XM_005258827		Approved	HSU79303	uc002qlr.3	Q9BWC9	OTTHUMG00000180907	ENST00000586790.1:c.288C>T	19.37:g.56160925C>T						CCDC106_ENST00000308964.3_Silent_p.F96F|CCDC106_ENST00000591241.1_Silent_p.F61F|CCDC106_ENST00000588740.1_Silent_p.F96F|CCDC106_ENST00000591578.1_Silent_p.F96F	p.F96F			Q9BWC9	CC106_HUMAN	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)	3	1192	+		Colorectal(82;0.00403)|Ovarian(87;0.133)	96					B3KUF9|D3K183|Q99786	Silent	SNP	ENST00000586790.1	37	c.288C>T	CCDS33118.1																																																																																				0.607	CCDC106-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453593.1	NM_013301		15	27	0	0	0	1	0	15	27				
ZFYVE26	23503	broad.mit.edu	37	14	68228053	68228053	+	Missense_Mutation	SNP	C	C	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr14:68228053C>A	ENST00000555452.1	-	35	6754	c.6618G>T	c.(6616-6618)caG>caT	p.Q2206H	ZFYVE26_ENST00000347230.4_Intron|ZFYVE26_ENST00000557306.1_Intron			Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	0					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		AAGGCAGGCACTGCCTTTTTG	0.552																																						ENST00000555452.1																			0				NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94						c.(6616-6618)caG>caT		zinc finger, FYVE domain containing 26							84.0	67.0	73.0					14																	68228053		2203	4300	6503	SO:0001583	missense	23503				cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding	g.chr14:68228053C>A	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"""Zinc fingers, FYVE domain containing"""	20761	protein-coding gene	gene with protein product	"""spastizin"", ""FYVE-CENT"""	612012	"""spastic paraplegia 15 (complicated, autosomal recessive)"""	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000555452.1:c.6618G>T	14.37:g.68228053C>A	ENSP00000450603:p.Gln2206His					ZFYVE26_ENST00000557306.1_Intron|ZFYVE26_ENST00000347230.4_Intron	p.Q2206H			Q68DK2	ZFY26_HUMAN		all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)	35	6754	-			0					B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000555452.1	37	c.6618G>T		.	.	.	.	.	.	.	.	.	.	C	7.154	0.584429	0.13749	.	.	ENSG00000072121	ENST00000555452	T	0.27557	1.66	4.78	2.93	0.34026	.	.	.	.	.	T	0.27454	0.0674	.	.	.	0.09310	N	1	P	0.43094	0.799	P	0.44946	0.465	T	0.08146	-1.0736	7	.	.	.	.	6.2783	0.20993	0.0:0.7123:0.1875:0.1002	.	2206	G3V2D8	.	H	2206	ENSP00000450603:Q2206H	.	Q	-	3	2	ZFYVE26	67297806	0.003000	0.15002	0.030000	0.17652	0.056000	0.15407	0.110000	0.15437	0.600000	0.29862	-0.494000	0.04653	CAG		0.552	ZFYVE26-002	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000412740.1	NM_015346		7	12	1	0	0.0293803	1	0.029757	7	12				
TMTC4	84899	broad.mit.edu	37	13	101320926	101320926	+	Silent	SNP	C	C	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr13:101320926C>T	ENST00000376234.3	-	2	258	c.69G>A	c.(67-69)aaG>aaA	p.K23K	TMTC4_ENST00000342624.5_Silent_p.K42K|TMTC4_ENST00000328767.5_Silent_p.K23K	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	23						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CCACTACTAACTTAGCCCAGA	0.453																																						ENST00000342624.5																			0				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						c.(124-126)aaG>aaA		transmembrane and tetratricopeptide repeat containing 4							119.0	109.0	112.0					13																	101320926		1978	4170	6148	SO:0001819	synonymous_variant	84899					integral to membrane	binding	g.chr13:101320926C>T		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.69G>A	13.37:g.101320926C>T						TMTC4_ENST00000376234.3_Silent_p.K23K|TMTC4_ENST00000328767.5_Silent_p.K23K	p.K42K	NM_032813.2	NP_116202.2	Q5T4D3	TMTC4_HUMAN			3	384	-	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)		23					A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	ENST00000376234.3	37	c.126G>A	CCDS41904.1																																																																																				0.453	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813		18	34	0	0	0	1	0	18	34				
ALG1L2	644974	broad.mit.edu	37	3	129817138	129817138	+	RNA	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr3:129817138G>A	ENST00000507643.1	+	0	720				AC083906.2_ENST00000578837.1_RNA			C9J202	AG1L2_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like 2								transferase activity, transferring glycosyl groups (GO:0016757)										AGAACCTGCGGGAGTCGCAGC	0.522																																						ENST00000507643.1																			0																																																			644974				biosynthetic process		transferase activity, transferring glycosyl groups	g.chr3:129817138G>A	BC127756		3q22.1	2013-02-22	2013-02-22		ENSG00000251287	ENSG00000251287		"""Glycosyltransferase group 1 domain containing"""	37258	other	unknown			"""asparagine-linked glycosylation 1-like 2"""				Standard	NM_001136152		Approved		uc011bld.2	C9J202	OTTHUMG00000159782		3.37:g.129817138G>A										C9J202	AG1L2_HUMAN			0	720	+									RNA	SNP	ENST00000507643.1	37																																																																																						0.522	ALG1L2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000357289.1	NM_001136152		4	68	0	0	0	1	0	4	68				
TMED6	146456	broad.mit.edu	37	16	69383522	69383522	+	Silent	SNP	C	C	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr16:69383522C>T	ENST00000288025.3	-	2	301	c.246G>A	c.(244-246)cgG>cgA	p.R82R	RP11-343C2.7_ENST00000564737.1_Missense_Mutation_p.A75T|RP11-343C2.9_ENST00000563634.1_Intron	NM_144676.3	NP_653277.2	Q8WW62	TMED6_HUMAN	transmembrane emp24 protein transport domain containing 6	82	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	9						CAGCAACATGCCGGTCATGTG	0.532																																						ENST00000564737.1																			0											c.(223-225)Gca>Aca									117.0	107.0	110.0					16																	69383522		2198	4300	6498	SO:0001819	synonymous_variant	146456							g.chr16:69383522C>T	BC020827	CCDS10878.1	16q22.1	2008-02-05			ENSG00000157315	ENSG00000157315			28331	protein-coding gene	gene with protein product						12477932	Standard	NM_144676		Approved	MGC23911	uc002exc.2	Q8WW62	OTTHUMG00000137571	ENST00000288025.3:c.246G>A	16.37:g.69383522C>T						TMED6_ENST00000288025.3_Silent_p.R82R|RP11-343C2.9_ENST00000563634.1_Intron	p.A75T							2	222	-								Q6UXN5	Missense_Mutation	SNP	ENST00000288025.3	37	c.223G>A	CCDS10878.1																																																																																				0.532	TMED6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268951.1	NM_144676		4	155	0	0	0	1	0	4	155				
TRPM2	7226	broad.mit.edu	37	21	45861590	45861590	+	Missense_Mutation	SNP	G	G	A	rs145895219		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr21:45861590G>A	ENST00000397928.1	+	32	4847	c.4402G>A	c.(4402-4404)Gac>Aac	p.D1468N	TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Missense_Mutation_p.D1518N|TRPM2_ENST00000300481.9_Missense_Mutation_p.D1414N|TRPM2_ENST00000300482.5_Missense_Mutation_p.D1468N|snoZ6_ENST00000583496.1_RNA	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	1468	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GCACGCCTGCGACTCGGGGGC	0.662																																						ENST00000397928.1																			0				breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						c.(4402-4404)Gac>Aac		transient receptor potential cation channel, subfamily M, member 2		G	ASN/ASP	0,4406		0,0,2203	59.0	47.0	52.0		4402	1.1	0.0	21	dbSNP_134	52	4,8596	3.7+/-12.6	0,4,4296	no	missense	TRPM2	NM_003307.3	23	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	probably-damaging	1468/1504	45861590	4,13002	2203	4300	6503	SO:0001583	missense	7226					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity	g.chr21:45861590G>A	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.4402G>A	21.37:g.45861590G>A	ENSP00000381023:p.Asp1468Asn					TRPM2_ENST00000397932.2_Missense_Mutation_p.D1518N|TRPM2_ENST00000300482.5_Missense_Mutation_p.D1468N|TRPM2_ENST00000300481.9_Missense_Mutation_p.D1414N|TRPM2_ENST00000498430.1_3'UTR	p.D1468N	NM_003307.3	NP_003298.1	O94759	TRPM2_HUMAN			32	4847	+			1468			Nudix hydrolase.		D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	c.4402G>A	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.595264	0.28445	0.0	4.65E-4	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932;ENST00000540347	T;T;T;T	0.15487	2.42;2.42;2.42;2.42	4.01	1.14	0.20703	NUDIX hydrolase domain (1);NUDIX hydrolase domain-like (1);	0.250639	0.32028	N	0.006683	T	0.18341	0.0440	M	0.81682	2.555	0.09310	N	1	B;B;B;B	0.24651	0.108;0.021;0.021;0.021	B;B;B;B	0.18871	0.023;0.007;0.004;0.004	T	0.22836	-1.0205	10	0.87932	D	0	-25.3998	4.6951	0.12800	0.1902:0.0:0.6385:0.1713	.	149;1518;1254;1468	B4DVI8;E9PGK7;Q5KTC1;O94759	.;.;.;TRPM2_HUMAN	N	1468;1468;1414;1518;212	ENSP00000300482:D1468N;ENSP00000381023:D1468N;ENSP00000300481:D1414N;ENSP00000381026:D1518N	ENSP00000300481:D1414N	D	+	1	0	TRPM2	44686018	0.023000	0.18921	0.000000	0.03702	0.000000	0.00434	1.276000	0.33156	0.127000	0.18452	-0.748000	0.03510	GAC		0.662	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		24	26	0	0	0	1	0	24	26				
FOXP1	27086	broad.mit.edu	37	3	71247374	71247374	+	Silent	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr3:71247374G>A	ENST00000318789.4	-	6	684	c.159C>T	c.(157-159)caC>caT	p.H53H	FOXP1_ENST00000475937.1_Silent_p.H53H|FOXP1_ENST00000498215.1_Silent_p.H53H|FOXP1_ENST00000468577.1_Silent_p.H53H|FOXP1_ENST00000318779.3_Silent_p.H53H|FOXP1_ENST00000493089.1_Silent_p.H53H|FOXP1_ENST00000484350.1_Silent_p.H53H	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN	forkhead box P1	53					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		GCTGCTGGGCGTGGGCGAGGT	0.612			T	PAX5	ALL																																	ENST00000318789.4				Dom	yes		3	3p14.1	27086	T	forkhead box P1			L	PAX5		ALL		0				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						c.(157-159)caC>caT		forkhead box P1							48.0	53.0	51.0					3																	71247374		2203	4300	6503	SO:0001819	synonymous_variant	27086				cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	g.chr3:71247374G>A	AF146696	CCDS2914.1, CCDS33785.1, CCDS58837.1, CCDS58838.1, CCDS58839.1, CCDS74963.1, CCDS74964.1	3p14.1	2008-07-18			ENSG00000114861	ENSG00000114861		"""Forkhead boxes"""	3823	protein-coding gene	gene with protein product	"""fork head-related protein like B"", ""glutamine-rich factor 1"", ""PAX5/FOXP1 fusion protein"""	605515				8265594, 11751404	Standard	NM_032682		Approved	QRF1, 12CC4, HSPC215, hFKH1B	uc003doj.3	Q9H334	OTTHUMG00000158803	ENST00000318789.4:c.159C>T	3.37:g.71247374G>A						FOXP1_ENST00000468577.1_Silent_p.H53H|FOXP1_ENST00000475937.1_Silent_p.H53H|FOXP1_ENST00000493089.1_Silent_p.H53H|FOXP1_ENST00000484350.1_Silent_p.H53H|FOXP1_ENST00000318779.3_Silent_p.H53H|FOXP1_ENST00000498215.1_Silent_p.H53H	p.H53H	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)	6	684	-		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)	53					A3QVP8|B3KV70|G5E9V8|Q8NAN6|Q9BSG9|Q9H332|Q9H333|Q9P0R1	Silent	SNP	ENST00000318789.4	37	c.159C>T	CCDS2914.1																																																																																				0.612	FOXP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352250.1	NM_032682		4	164	0	0	0	1	0	4	164				
VPS8	23355	broad.mit.edu	37	3	184588531	184588531	+	Missense_Mutation	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr3:184588531G>A	ENST00000437079.3	+	21	1843	c.1672G>A	c.(1672-1674)Gat>Aat	p.D558N	VPS8_ENST00000446204.2_Missense_Mutation_p.D556N|VPS8_ENST00000287546.4_Missense_Mutation_p.D558N|VPS8_ENST00000436792.2_Missense_Mutation_p.D556N	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	558							zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			CCATTATGCAGATCGAGCTCT	0.408																																						ENST00000437079.3																			0				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54						c.(1672-1674)Gat>Aat		vacuolar protein sorting 8 homolog (S. cerevisiae)							73.0	69.0	70.0					3																	184588531		1849	4102	5951	SO:0001583	missense	23355						zinc ion binding	g.chr3:184588531G>A	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"""KIAA0804"""	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.1672G>A	3.37:g.184588531G>A	ENSP00000397879:p.Asp558Asn					VPS8_ENST00000446204.2_Missense_Mutation_p.D556N|VPS8_ENST00000436792.2_Missense_Mutation_p.D556N|VPS8_ENST00000287546.4_Missense_Mutation_p.D558N	p.D558N	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)		21	1843	+	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		558					A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	37	c.1672G>A	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.007130	0.75046	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.20598	2.07;2.08;2.08;2.06	5.35	5.35	0.76521	.	0.157476	0.56097	D	0.000033	T	0.30008	0.0751	L	0.29908	0.895	0.50813	D	0.999891	P;D	0.56746	0.532;0.977	B;P	0.55923	0.19;0.787	T	0.01182	-1.1426	10	0.29301	T	0.29	-15.9721	19.1024	0.93279	0.0:0.0:1.0:0.0	.	556;556	Q8N3P4-2;Q8N3P4-3	.;.	N	558;558;556;556	ENSP00000287546:D558N;ENSP00000397879:D558N;ENSP00000404704:D556N;ENSP00000405483:D556N	ENSP00000287546:D558N	D	+	1	0	VPS8	186071225	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.369000	0.79578	2.503000	0.84419	0.563000	0.77884	GAT		0.408	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303		11	14	0	0	0	1	0	11	14				
TMEM132A	54972	broad.mit.edu	37	11	60698020	60698020	+	Missense_Mutation	SNP	G	G	T	rs538143219		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr11:60698020G>T	ENST00000453848.2	+	5	1063	c.905G>T	c.(904-906)cGc>cTc	p.R302L	TMEM132A_ENST00000005286.4_Missense_Mutation_p.R302L			Q24JP5	T132A_HUMAN	transmembrane protein 132A	302						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						ACAGCCGCCCGCCCAGCCCAG	0.607																																						ENST00000005286.4																			0				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						c.(904-906)cGc>cTc		transmembrane protein 132A							96.0	104.0	101.0					11																	60698020		2203	4299	6502	SO:0001583	missense	54972					endoplasmic reticulum membrane|Golgi membrane|integral to membrane		g.chr11:60698020G>T	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"""heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"""	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.905G>T	11.37:g.60698020G>T	ENSP00000405823:p.Arg302Leu					TMEM132A_ENST00000453848.2_Missense_Mutation_p.R302L	p.R302L	NM_017870.3|NM_178031.2	NP_060340.2|NP_821174.1	Q24JP5	T132A_HUMAN			5	1058	+			302					Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	c.905G>T	CCDS44618.1	.	.	.	.	.	.	.	.	.	.	G	17.38	3.376263	0.61735	.	.	ENSG00000006118	ENST00000544065;ENST00000444690;ENST00000453848;ENST00000005286	T;T;T	0.15487	2.7;2.42;2.42	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000005	T	0.36771	0.0979	M	0.69358	2.11	0.41063	D	0.985395	P;D;B;B	0.71674	0.751;0.998;0.299;0.299	B;D;B;B	0.64595	0.327;0.927;0.078;0.078	T	0.08126	-1.0737	10	0.87932	D	0	.	12.1049	0.53807	0.0817:0.0:0.9183:0.0	.	291;52;302;302	Q24JP5-3;Q24JP5-4;Q24JP5;Q24JP5-2	.;.;T132A_HUMAN;.	L	40;52;302;302	ENSP00000442754:R40L;ENSP00000405823:R302L;ENSP00000005286:R302L	ENSP00000005286:R302L	R	+	2	0	TMEM132A	60454596	0.997000	0.39634	1.000000	0.80357	0.960000	0.62799	2.593000	0.46180	2.704000	0.92352	0.655000	0.94253	CGC		0.607	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870		110	152	1	0	5.10254e-61	1	6.6082e-61	110	152				
FRG1	2483	broad.mit.edu	37	4	190864424	190864424	+	Missense_Mutation	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr4:190864424G>A	ENST00000226798.4	+	2	352	c.130G>A	c.(130-132)Gtt>Att	p.V44I	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	44					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		GCTTGATATTGTTGGTGAGTC	0.313																																						ENST00000226798.4																			0				NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32						c.(130-132)Gtt>Att		FSHD region gene 1							52.0	64.0	60.0					4																	190864424		2200	4232	6432	SO:0001583	missense	2483				rRNA processing	Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus		g.chr4:190864424G>A	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.130G>A	4.37:g.190864424G>A	ENSP00000226798:p.Val44Ile					FRG1_ENST00000514482.1_3'UTR	p.V44I	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)	2	352	+		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)	44					A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	c.130G>A	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	7.527	0.657809	0.14645	.	.	ENSG00000109536	ENST00000226798	T	0.29917	1.55	3.1	2.26	0.28386	.	0.137370	0.48767	N	0.000173	T	0.22044	0.0531	L	0.42581	1.335	0.45806	D	0.998683	B	0.13594	0.008	B	0.12156	0.007	T	0.05954	-1.0854	10	0.38643	T	0.18	-5.4601	6.0443	0.19752	0.1424:0.0:0.8576:0.0	.	44	Q14331	FRG1_HUMAN	I	44	ENSP00000226798:V44I	ENSP00000226798:V44I	V	+	1	0	FRG1	191101418	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	2.809000	0.47971	0.880000	0.35969	0.549000	0.68633	GTT		0.313	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477		37	47	0	0	0	1	0	37	47				
UBE2Q1	55585	broad.mit.edu	37	1	154527222	154527222	+	Nonsense_Mutation	SNP	C	C	A	rs11542155		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr1:154527222C>A	ENST00000292211.4	-	4	656	c.577G>T	c.(577-579)Gag>Tag	p.E193*	UBE2Q1-AS1_ENST00000441613.1_RNA|UBE2Q1_ENST00000497453.1_5'UTR	NM_017582.6	NP_060052.3	Q7Z7E8	UB2Q1_HUMAN	ubiquitin-conjugating enzyme E2Q family member 1	193					embryo implantation (GO:0007566)|fertilization (GO:0009566)|mating behavior (GO:0007617)|prolactin secretion (GO:0070459)|protein ubiquitination (GO:0016567)|reproductive system development (GO:0061458)|suckling behavior (GO:0001967)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	16	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			TCAGGCATCTCCTCATCTTCA	0.527																																						ENST00000292211.4																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	16						c.(577-579)Gag>Tag		ubiquitin-conjugating enzyme E2Q family member 1							69.0	62.0	64.0					1																	154527222		2203	4300	6503	SO:0001587	stop_gained	55585						ATP binding|protein binding|ubiquitin-protein ligase activity	g.chr1:154527222C>A	AJ243666	CCDS1069.1	1q22	2008-05-02	2008-05-02	2005-08-05	ENSG00000160714	ENSG00000160714		"""Ubiquitin-conjugating enzymes E2"""	15698	protein-coding gene	gene with protein product			"""ubiquitin-conjugating enzyme E2Q (putative)"""	UBE2Q			Standard	NM_017582		Approved	PRO3094, NICE-5	uc001fff.1	Q7Z7E8	OTTHUMG00000037265	ENST00000292211.4:c.577G>T	1.37:g.154527222C>A	ENSP00000292211:p.Glu193*					UBE2Q1_ENST00000497453.1_5'UTR|UBE2Q1-AS1_ENST00000441613.1_RNA	p.E193*	NM_017582.6	NP_060052.3	Q7Z7E8	UB2Q1_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.185)		4	656	-	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		193					B4DF92|Q3B841|Q5I0X2|Q6IS04|Q6P7P2|Q96MV4|Q9BVX5|Q9UGL6	Nonsense_Mutation	SNP	ENST00000292211.4	37	c.577G>T	CCDS1069.1	.	.	.	.	.	.	.	.	.	.	C	36	5.802140	0.96960	.	.	ENSG00000160714	ENST00000292211	.	.	.	5.14	5.14	0.70334	.	0.120680	0.53938	D	0.000044	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-22.947	13.9879	0.64348	0.0:1.0:0.0:0.0	rs11542155	.	.	.	X	193	.	ENSP00000292211:E193X	E	-	1	0	UBE2Q1	152793846	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.199000	0.65152	2.663000	0.90544	0.557000	0.71058	GAG		0.527	UBE2Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090704.1	NM_017582		13	12	1	0	0.000151284	1	0.000159353	13	12				
LRP1B	53353	broad.mit.edu	37	2	141093256	141093256	+	Missense_Mutation	SNP	C	C	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr2:141093256C>A	ENST00000389484.3	-	78	13015	c.12044G>T	c.(12043-12045)gGc>gTc	p.G4015V		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4015					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.G4015D(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GCAGTTGGGGCCATTCAGCTG	0.418										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)	ENST00000389484.3																			1	Substitution - Missense(1)	p.G4015D(1)	lung(1)	NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606						c.(12043-12045)gGc>gTc		low density lipoprotein receptor-related protein 1B							141.0	137.0	138.0					2																	141093256		2203	4300	6503	SO:0001583	missense	53353				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding	g.chr2:141093256C>A	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.12044G>T	2.37:g.141093256C>A	ENSP00000374135:p.Gly4015Val	TSP Lung(27;0.18)					p.G4015V	NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)	78	13015	-		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)	4015					Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	c.12044G>T	CCDS2182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.8|26.8	4.769325|4.769325	0.90020|0.90020	.|.	.|.	ENSG00000168702|ENSG00000168702	ENST00000437977|ENST00000389484;ENST00000544579	.|D	.|0.93488	.|-3.23	5.49|5.49	5.49|5.49	0.81192|0.81192	.|Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.97365|0.97365	0.9138|0.9138	M|M	0.89214|0.89214	3.015|3.015	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	D|D	0.97724|0.97724	1.0198|1.0198	5|10	.|0.87932	.|D	.|0	.|.	19.7341|19.7341	0.96195|0.96195	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|4015	.|Q9NZR2	.|LRP1B_HUMAN	S|V	247|4015;3953	.|ENSP00000374135:G4015V	.|ENSP00000374135:G4015V	A|G	-|-	1|2	0|0	LRP1B|LRP1B	140809726|140809726	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	7.356000|7.356000	0.79445|0.79445	2.732000|2.732000	0.93576|0.93576	0.585000|0.585000	0.79938|0.79938	GCC|GGC		0.418	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		45	55	1	0	1.00953e-15	1	1.20838e-15	45	55				
NCF1	653361	broad.mit.edu	37	7	74193734	74193734	+	Missense_Mutation	SNP	C	C	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr7:74193734C>T	ENST00000289473.4	+	4	431	c.361C>T	c.(361-363)Cgc>Tgc	p.R121C	NCF1_ENST00000443956.3_3'UTR	NM_000265.4	NP_000256.4	P14598	NCF1_HUMAN	neutrophil cytosolic factor 1	121	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular defense response (GO:0006968)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|leukotriene metabolic process (GO:0006691)|negative regulation of smooth muscle contraction (GO:0045986)|neutrophil mediated killing of fungus (GO:0070947)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|protein targeting to membrane (GO:0006612)|respiratory burst (GO:0045730)|respiratory burst involved in defense response (GO:0002679)|response to yeast (GO:0001878)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagolysosome (GO:0032010)|rough endoplasmic reticulum (GO:0005791)	electron carrier activity (GO:0009055)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activity (GO:0016175)	p.R121C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|skin(3)	10					Dextromethorphan(DB00514)	CTTCAAGGTGCGCCCTGATGA	0.597																																						ENST00000289473.4																			1	Substitution - Missense(1)	p.R121C(1)	large_intestine(1)	breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|skin(3)	10						c.(361-363)Cgc>Tgc		neutrophil cytosolic factor 1							46.0	36.0	40.0					7																	74193734		2196	4283	6479	SO:0001583	missense	653361				cell communication|cellular defense response|innate immune response|protein targeting to membrane|respiratory burst|superoxide anion generation	cytosol|NADPH oxidase complex|soluble fraction	electron carrier activity|GTP binding|GTPase activity|phosphatidylinositol binding|SH3 domain binding|superoxide-generating NADPH oxidase activity	g.chr7:74193734C>T	M25665	CCDS34657.1	7q11.23	2014-09-17	2008-07-31		ENSG00000158517	ENSG00000158517			7660	protein-coding gene	gene with protein product	"""NADPH oxidase organizer 2"", ""chronic granulomatous disease, autosomal 1"""	608512	"""neutrophil cytosolic factor 1 (47kD, chronic granulomatous disease, autosomal 1)"""				Standard	NM_000265		Approved	p47phox, NOXO2, NCF1A, SH3PXD1A	uc022aft.1	P14598	OTTHUMG00000149965	ENST00000289473.4:c.361C>T	7.37:g.74193734C>T	ENSP00000289473:p.Arg121Cys					NCF1_ENST00000443956.3_3'UTR	p.R121C	NM_000265.4	NP_000256.3	P14598	NCF1_HUMAN			4	431	+			121			PX.		A6NEH2|A8K7S9|O43842|Q2PP07|Q53FR5|Q9BU90|Q9BXI7|Q9BXI8|Q9UDV9|Q9UMU2	Missense_Mutation	SNP	ENST00000289473.4	37	c.361C>T	CCDS34657.1	.	.	.	.	.	.	.	.	.	.	c	16.42	3.118318	0.56505	.	.	ENSG00000158517	ENST00000289473;ENST00000433458;ENST00000471594;ENST00000442021	T;T;T	0.70282	-0.47;-0.47;-0.47	3.48	2.5	0.30297	Phox homologous domain (4);	0.114786	0.56097	D	0.000040	D	0.83778	0.5328	M	0.88704	2.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.993;0.994	D	0.85789	0.1366	10	0.87932	D	0	-24.0235	10.0367	0.42133	0.3357:0.6643:0.0:0.0	.	121;121	P14598-2;P14598	.;NCF1_HUMAN	C	121;121;95;128	ENSP00000289473:R121C;ENSP00000392870:R121C;ENSP00000401935:R128C	ENSP00000289473:R121C	R	+	1	0	NCF1	73831670	0.963000	0.33076	0.992000	0.48379	0.940000	0.58332	1.549000	0.36212	1.690000	0.51089	0.442000	0.29010	CGC		0.597	NCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314560.1	NM_000265		9	52	0	0	0	1	0	9	52				
ALPK2	115701	broad.mit.edu	37	18	56204900	56204900	+	Missense_Mutation	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr18:56204900G>A	ENST00000361673.3	-	5	2732	c.2519C>T	c.(2518-2520)aCg>aTg	p.T840M	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	840						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TGCCAGTTCCGTATCTACAGA	0.398																																						ENST00000361673.3																			0				NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						c.(2518-2520)aCg>aTg		alpha-kinase 2							72.0	70.0	71.0					18																	56204900		2203	4300	6503	SO:0001583	missense	115701						ATP binding|protein serine/threonine kinase activity	g.chr18:56204900G>A	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.2519C>T	18.37:g.56204900G>A	ENSP00000354991:p.Thr840Met					RP11-1151B14.4_ENST00000591360.1_RNA	p.T840M	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN			5	2732	-			840					Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	c.2519C>T	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	G	3.965	-0.009562	0.07727	.	.	ENSG00000198796	ENST00000361673	T	0.42900	0.96	5.57	-6.55	0.01854	.	3.138150	0.00639	N	0.000517	T	0.24198	0.0586	N	0.08118	0	0.09310	N	1	B;B	0.12630	0.001;0.006	B;B	0.06405	0.0;0.002	T	0.31194	-0.9952	10	0.56958	D	0.05	10.7019	11.614	0.51078	0.1856:0.0:0.6834:0.131	.	840;840	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	M	840	ENSP00000354991:T840M	ENSP00000354991:T840M	T	-	2	0	ALPK2	54355880	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.214000	0.09292	-1.192000	0.02691	-1.279000	0.01387	ACG		0.398	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		22	48	0	0	0	1	0	22	48				
RBPJL	11317	broad.mit.edu	37	20	43936862	43936862	+	Silent	SNP	C	C	T	rs533358769		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr20:43936862C>T	ENST00000343694.3	+	2	174	c.102C>T	c.(100-102)gaC>gaT	p.D34D	MATN4_ENST00000372754.1_5'Flank|MATN4_ENST00000372756.1_5'Flank|MATN4_ENST00000372751.4_5'UTR|MATN4_ENST00000353917.5_5'UTR|RBPJL_ENST00000372741.3_Silent_p.D34D|RBPJL_ENST00000372743.1_Silent_p.D34D|MATN4_ENST00000360607.6_5'UTR|MATN4_ENST00000342716.4_5'UTR|MATN4_ENST00000537548.1_5'UTR	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	34					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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 (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				GCGAAGCCGACAGGCGGAGCC	0.647																																						ENST00000343694.3																			0				NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						c.(100-102)gaC>gaT		recombination signal binding protein for immunoglobulin kappa J region-like							51.0	55.0	53.0					20																	43936862		2203	4300	6503	SO:0001819	synonymous_variant	11317				signal transduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr20:43936862C>T	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.102C>T	20.37:g.43936862C>T						MATN4_ENST00000342716.4_5'UTR|RBPJL_ENST00000372743.1_Silent_p.D34D|MATN4_ENST00000353917.5_5'UTR|MATN4_ENST00000360607.5_5'UTR|RBPJL_ENST00000372741.3_Silent_p.D34D|MATN4_ENST00000372751.4_5'UTR|MATN4_ENST00000537548.1_5'UTR	p.D34D	NM_014276.2	NP_055091.2	Q9UBG7	RBPJL_HUMAN			2	174	+		Myeloproliferative disorder(115;0.0122)	34					O95723|Q5QPU9|Q5QPV0|Q9ULV9	Silent	SNP	ENST00000343694.3	37	c.102C>T	CCDS13349.1																																																																																				0.647	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276		39	108	0	0	0	1	0	39	108				
KNDC1	85442	broad.mit.edu	37	10	135015258	135015258	+	Silent	SNP	C	C	T	rs550328756	byFrequency	TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr10:135015258C>T	ENST00000304613.3	+	17	3264	c.3243C>T	c.(3241-3243)ccC>ccT	p.P1081P	KNDC1_ENST00000368571.2_Silent_p.P1016P|KNDC1_ENST00000368572.2_Silent_p.P1083P			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1081					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CCTTGTCCCCCGGCCCAGCCG	0.697													C|||	2	0.000399361	0.0008	0.0	5008	,	,		14217	0.0		0.0	False		,,,				2504	0.001					ENST00000304613.3																			0				NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60						c.(3241-3243)ccC>ccT		kinase non-catalytic C-lobe domain (KIND) containing 1							11.0	14.0	13.0					10																	135015258		2191	4283	6474	SO:0001819	synonymous_variant	85442				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction			g.chr10:135015258C>T	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.3243C>T	10.37:g.135015258C>T						KNDC1_ENST00000368571.2_Silent_p.P1016P|KNDC1_ENST00000368572.2_Silent_p.P1083P	p.P1081P			Q76NI1	VKIND_HUMAN		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)	17	3264	+		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)	1081					B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Silent	SNP	ENST00000304613.3	37	c.3243C>T	CCDS7674.1																																																																																				0.697	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		13	16	0	0	0	1	0	13	16				
SUSD4	55061	broad.mit.edu	37	1	223396790	223396790	+	Silent	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr1:223396790G>A	ENST00000343846.3	-	7	1878	c.1245C>T	c.(1243-1245)ccC>ccT	p.P415P	SUSD4_ENST00000366878.4_Silent_p.P415P|SUSD4_ENST00000484758.2_Silent_p.P346P|SUSD4_ENST00000454695.2_Silent_p.P255P|SUSD4_ENST00000494793.2_Silent_p.P415P|SUSD4_ENST00000478605.1_5'UTR			Q5VX71	SUSD4_HUMAN	sushi domain containing 4	415						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(131;0.0611)		CCCCTGAGCCGGGGTATGCTG	0.637																																						ENST00000343846.3																			0				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1)	17						c.(1243-1245)ccC>ccT		sushi domain containing 4							27.0	31.0	29.0					1																	223396790		1977	4141	6118	SO:0001819	synonymous_variant	55061					integral to membrane		g.chr1:223396790G>A	AK096265	CCDS31034.1, CCDS41471.1	1q41	2008-05-14			ENSG00000143502	ENSG00000143502			25470	protein-coding gene	gene with protein product		615827				12477932	Standard	NM_017982		Approved	FLJ10052	uc001hny.4	Q5VX71	OTTHUMG00000037936	ENST00000343846.3:c.1245C>T	1.37:g.223396790G>A						SUSD4_ENST00000454695.2_Silent_p.P255P|SUSD4_ENST00000478605.1_5'UTR|SUSD4_ENST00000366878.4_Silent_p.P415P	p.P415P			Q5VX71	SUSD4_HUMAN		GBM - Glioblastoma multiforme(131;0.0611)	7	1878	-			415					D3DTB9|Q6UX62|Q9BSR0|Q9NWG0	Silent	SNP	ENST00000343846.3	37	c.1245C>T	CCDS41471.1	.	.	.	.	.	.	.	.	.	.	G	8.911	0.958689	0.18507	.	.	ENSG00000143502	ENST00000271787	.	.	.	5.16	-8.41	0.00961	.	0.143817	0.32608	N	0.005873	T	0.29288	0.0729	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37753	-0.9692	6	0.09843	T	0.71	-18.1687	7.9376	0.29939	0.6492:0.0835:0.1834:0.084	.	.	.	.	L	190	.	ENSP00000271787:P190L	P	-	2	0	SUSD4	221463413	0.000000	0.05858	0.767000	0.31495	0.848000	0.48234	-2.623000	0.00876	-1.478000	0.01869	-0.812000	0.03155	CCG		0.637	SUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092592.2	NM_017982		11	29	0	0	0	1	0	11	29				
SSUH2	51066	broad.mit.edu	37	3	8671394	8671394	+	Missense_Mutation	SNP	C	C	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr3:8671394C>A	ENST00000317371.4	-	14	1703	c.478G>T	c.(478-480)Ggg>Tgg	p.G160W	SSUH2_ENST00000415132.1_Missense_Mutation_p.G160W|SSUH2_ENST00000341795.3_Missense_Mutation_p.G160W|SSUH2_ENST00000544814.1_Missense_Mutation_p.G182W			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	160	Cys-rich.					cytoplasm (GO:0005737)											CGCCCACGCCCATGGCATTTG	0.582																																						ENST00000317371.4																			0											c.(478-480)Ggg>Tgg		ssu-2 homolog (C. elegans)							95.0	98.0	97.0					3																	8671394		2203	4300	6503	SO:0001583	missense	51066							g.chr3:8671394C>A	AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 32"""	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.478G>T	3.37:g.8671394C>A	ENSP00000324551:p.Gly160Trp					SSUH2_ENST00000341795.3_Missense_Mutation_p.G160W|SSUH2_ENST00000415132.1_Missense_Mutation_p.G160W|SSUH2_ENST00000544814.1_Missense_Mutation_p.G182W	p.G160W							14	1703	-								A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Missense_Mutation	SNP	ENST00000317371.4	37	c.478G>T	CCDS2568.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.935115	0.73442	.	.	ENSG00000125046	ENST00000341795;ENST00000317371;ENST00000415132;ENST00000544814	T;T;T;T	0.62941	0.0;0.0;-0.01;0.04	4.75	4.75	0.60458	.	0.109887	0.64402	D	0.000008	T	0.80232	0.4585	M	0.86028	2.79	0.44282	D	0.997146	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.83673	0.0167	10	0.87932	D	0	-41.3205	13.2679	0.60144	0.0:1.0:0.0:0.0	.	182;160	F5H2S5;Q9Y2M2	.;CC032_HUMAN	W	160;160;160;182	ENSP00000339150:G160W;ENSP00000324551:G160W;ENSP00000410757:G160W;ENSP00000439378:G182W	ENSP00000324551:G160W	G	-	1	0	C3orf32	8646394	0.868000	0.29978	0.935000	0.37517	0.987000	0.75469	2.836000	0.48183	2.189000	0.69895	0.467000	0.42956	GGG		0.582	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931		63	52	1	0	5.80444e-35	1	7.27858e-35	63	52				
KIAA0195	9772	broad.mit.edu	37	17	73481511	73481511	+	Silent	SNP	C	C	T	rs376940052		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr17:73481511C>T	ENST00000314256.7	+	3	421	c.27C>T	c.(25-27)ggC>ggT	p.G9G	KIAA0195_ENST00000375248.5_Silent_p.G19G|KIAA0195_ENST00000579208.1_Intron	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	9						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCCTGCAGGGCGAGCCTCCCT	0.677																																						ENST00000314256.7																			0				breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42						c.(25-27)ggC>ggT		KIAA0195		C		0,4406		0,0,2203	49.0	48.0	48.0		27	2.8	1.0	17		48	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIAA0195	NM_014738.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		9/1357	73481511	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9772				ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism	g.chr17:73481511C>T		CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.27C>T	17.37:g.73481511C>T						KIAA0195_ENST00000375248.5_Silent_p.G19G|KIAA0195_ENST00000579208.1_Intron	p.G9G	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)		3	421	+	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		9					O75536|Q86XF1	Silent	SNP	ENST00000314256.7	37	c.27C>T	CCDS32732.1																																																																																				0.677	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738		4	109	0	0	0	1	0	4	109				
PROSC	11212	broad.mit.edu	37	8	37623065	37623065	+	Missense_Mutation	SNP	C	C	T	rs376835563		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr8:37623065C>T	ENST00000328195.3	+	2	188	c.121C>T	c.(121-123)Cgg>Tgg	p.R41W		NM_007198.3	NP_009129.1	O94903	PROSC_HUMAN	proline synthetase co-transcribed homolog (bacterial)	41					alpha-amino acid metabolic process (GO:1901605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrion (GO:0005739)	pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)	7		Lung NSC(58;0.174)	BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)		L-Proline(DB00172)	CATCCAGCCCCGGCTAGTGGC	0.532																																						ENST00000328195.3																			0				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)	7						c.(121-123)Cgg>Tgg		proline synthetase co-transcribed homolog (bacterial)	L-Proline(DB00172)|Pyridoxal Phosphate(DB00114)	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	180.0	187.0	185.0		121	5.6	1.0	8		185	0,8600		0,0,4300	no	missense	PROSC	NM_007198.3	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	41/276	37623065	1,13005	2203	4300	6503	SO:0001583	missense	11212						pyridoxal phosphate binding	g.chr8:37623065C>T	AB018566	CCDS6096.1	8p11.2	2008-01-07	2001-12-04		ENSG00000147471	ENSG00000147471			9457	protein-coding gene	gene with protein product		604436	"""proline synthetase co-transcribed (bacterial homolog)"""				Standard	NM_007198		Approved		uc003xkh.3	O94903	OTTHUMG00000164024	ENST00000328195.3:c.121C>T	8.37:g.37623065C>T	ENSP00000333551:p.Arg41Trp						p.R41W	NM_007198.3	NP_009129.1	O94903	PROSC_HUMAN	BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)		2	188	+		Lung NSC(58;0.174)	41					Q6FI94	Missense_Mutation	SNP	ENST00000328195.3	37	c.121C>T	CCDS6096.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.574427	0.86542	2.27E-4	0.0	ENSG00000147471	ENST00000328195;ENST00000523358	T;T	0.48201	0.82;0.82	5.6	5.6	0.85130	Alanine racemase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.78123	0.4234	H	0.96080	3.765	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.84572	0.0656	10	0.87932	D	0	-9.1054	14.1154	0.65149	0.1504:0.8496:0.0:0.0	.	41	O94903	PROSC_HUMAN	W	41	ENSP00000333551:R41W;ENSP00000427778:R41W	ENSP00000333551:R41W	R	+	1	2	PROSC	37742223	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.701000	0.54793	2.642000	0.89623	0.557000	0.71058	CGG		0.532	PROSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376796.1	NM_007198		6	473	0	0	0	1	0	6	473				
FOXP2	93986	broad.mit.edu	37	7	114269973	114269973	+	Silent	SNP	A	A	G	rs576887296|rs398124272	byFrequency	TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr7:114269973A>G	ENST00000393494.2	+	5	789	c.510A>G	c.(508-510)caA>caG	p.Q170Q	AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000393498.2_Silent_p.Q150Q|FOXP2_ENST00000408937.3_Silent_p.Q195Q|FOXP2_ENST00000360232.4_Silent_p.Q170Q|FOXP2_ENST00000393500.3_Silent_p.Q95Q|FOXP2_ENST00000393491.3_Silent_p.Q78Q|FOXP2_ENST00000403559.4_Silent_p.Q187Q|FOXP2_ENST00000350908.4_Silent_p.Q170Q|FOXP2_ENST00000393489.3_Silent_p.Q78Q|FOXP2_ENST00000378237.3_Silent_p.Q170Q|FOXP2_ENST00000390668.3_Silent_p.Q194Q			O15409	FOXP2_HUMAN	forkhead box P2	170	Gln-rich.				camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|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 negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q195Q(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						agcagcagcaacaacaacaac	0.502																																						ENST00000393500.3																			1	Substitution - coding silent(1)	p.Q195Q(1)	kidney(1)	breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						c.(283-285)caA>caG		forkhead box P2							37.0	35.0	35.0					7																	114269973		2203	4294	6497	SO:0001819	synonymous_variant	93986				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	g.chr7:114269973A>G	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"""Forkhead boxes"""	13875	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 10"", ""forkhead/winged-helix transcription factor"", ""speech and language disorder 1"", ""CAG repeat protein 44"""	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.510A>G	7.37:g.114269973A>G						FOXP2_ENST00000378237.3_Silent_p.Q170Q|FOXP2_ENST00000350908.4_Silent_p.Q170Q|FOXP2_ENST00000390668.3_Silent_p.Q194Q|FOXP2_ENST00000360232.4_Silent_p.Q170Q|FOXP2_ENST00000393491.3_Silent_p.Q78Q|FOXP2_ENST00000393498.2_Silent_p.Q150Q|FOXP2_ENST00000393494.2_Silent_p.Q170Q|FOXP2_ENST00000408937.3_Silent_p.Q195Q|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000393489.3_Silent_p.Q78Q|FOXP2_ENST00000403559.4_Silent_p.Q187Q	p.Q95Q			O15409	FOXP2_HUMAN			11	1105	+			170			Gln-rich.		A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Silent	SNP	ENST00000393494.2	37	c.285A>G	CCDS5760.1																																																																																				0.502	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		5	73	0	0	0	1	0	5	73				
ROCK1	6093	broad.mit.edu	37	18	18547728	18547728	+	Silent	SNP	C	C	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr18:18547728C>T	ENST00000399799.2	-	26	4117	c.3177G>A	c.(3175-3177)ctG>ctA	p.L1059L		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	1059					actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					GCATGTCATTCAGTTCCTTCT	0.338																																						ENST00000399799.1																			0				NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16						c.(3175-3177)ctG>ctA		Rho-associated, coiled-coil containing protein kinase 1							250.0	243.0	246.0					18																	18547728		2203	4300	6503	SO:0001819	synonymous_variant	6093				actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction	centriole|cytosol|Golgi membrane	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity	g.chr18:18547728C>T		CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.3177G>A	18.37:g.18547728C>T							p.L1059L	NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN			26	4117	-	Melanoma(1;0.165)		1059					B0YJ91|Q2KHM4|Q59GZ4	Silent	SNP	ENST00000399799.2	37	c.3177G>A	CCDS11870.2																																																																																				0.338	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		81	174	0	0	0	1	0	81	174				
HRH3	11255	broad.mit.edu	37	20	60791509	60791509	+	Silent	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr20:60791509G>A	ENST00000340177.5	-	3	1175	c.891C>T	c.(889-891)ggC>ggT	p.G297G	HRH3_ENST00000317393.6_Silent_p.G297G	NM_007232.2	NP_009163.2	Q9Y5N1	HRH3_HUMAN	histamine receptor H3	297	Poly-Gly.				brain development (GO:0007420)|drinking behavior (GO:0042756)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of serotonin secretion (GO:0014063)|neurotransmitter secretion (GO:0007269)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of norepinephrine secretion (GO:0014061)|response to organic cyclic compound (GO:0014070)	integral component of plasma membrane (GO:0005887)|myelin sheath (GO:0043209)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|histamine receptor activity (GO:0004969)			breast(1)|endometrium(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;7.08e-07)		Betahistine(DB06698)|Histamine Phosphate(DB00667)|Mirtazapine(DB00370)	CCACGGAGCCGCCCCCACCGC	0.741																																						ENST00000340177.5																			0				breast(1)|endometrium(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9						c.(889-891)ggC>ggT		histamine receptor H3	Histamine Phosphate(DB00667)						3.0	4.0	4.0					20																	60791509		1911	3832	5743	SO:0001819	synonymous_variant	11255				G-protein signaling, coupled to cyclic nucleotide second messenger|neurotransmitter secretion	integral to plasma membrane	histamine receptor activity	g.chr20:60791509G>A	AF140538	CCDS13493.1	20q13.33	2013-09-19			ENSG00000101180	ENSG00000101180		"""GPCR / Class A : Histamine receptors"""	5184	protein-coding gene	gene with protein product		604525				10347254	Standard	NM_007232		Approved	GPCR97	uc002ycf.2	Q9Y5N1	OTTHUMG00000032899	ENST00000340177.5:c.891C>T	20.37:g.60791509G>A						HRH3_ENST00000317393.6_Silent_p.G297G	p.G297G	NM_007232.2	NP_009163.2	Q9Y5N1	HRH3_HUMAN	BRCA - Breast invasive adenocarcinoma(19;7.08e-07)		3	1175	-	Breast(26;7.76e-09)		297			Poly-Gly.		Q4QRI7|Q9GZX2|Q9H4K8	Silent	SNP	ENST00000340177.5	37	c.891C>T	CCDS13493.1																																																																																				0.741	HRH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079994.1	NM_007232		8	1	0	0	0	1	0	8	1				
SMC1A	8243	broad.mit.edu	37	X	53423264	53423264	+	Silent	SNP	A	A	G			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chrX:53423264A>G	ENST00000322213.4	-	18	2872	c.2745T>C	c.(2743-2745)atT>atC	p.I915I		NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	915					DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						GCTTGGTCTCAATGGCTGTCA	0.507																																						ENST00000322213.4																			0				NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						c.(2743-2745)atT>atC		structural maintenance of chromosomes 1A							161.0	122.0	135.0					X																	53423264		2203	4300	6503	SO:0001819	synonymous_variant	8243				cell cycle checkpoint|cell division|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic sister chromatid cohesion|mitotic spindle organization|negative regulation of DNA endoreduplication|nuclear mRNA splicing, via spliceosome|response to radiation|signal transduction in response to DNA damage	cohesin core heterodimer|condensed chromosome kinetochore|condensed nuclear chromosome|cytoplasm|meiotic cohesin complex|nucleoplasm	ATP binding|chromatin binding|microtubule motor activity|protein heterodimerization activity	g.chrX:53423264A>G	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"""Structural maintenance of chromosomes proteins"""	11111	protein-coding gene	gene with protein product		300040	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"""	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.2745T>C	X.37:g.53423264A>G							p.I915I	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN			18	2872	-			915					O14995|Q16351|Q2M228	Silent	SNP	ENST00000322213.4	37	c.2745T>C	CCDS14352.1																																																																																				0.507	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306		67	6	0	0	0	1	0	67	6				
ZFHX3	463	broad.mit.edu	37	16	72991587	72991587	+	Missense_Mutation	SNP	G	G	A			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr16:72991587G>A	ENST00000268489.5	-	2	3130	c.2458C>T	c.(2458-2460)Cgc>Tgc	p.R820C	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	820					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				ATGTGAATGCGGAGGTTCCTG	0.567																																						ENST00000268489.5																			0				NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153						c.(2458-2460)Cgc>Tgc		zinc finger homeobox 3							215.0	181.0	193.0					16																	72991587		2198	4300	6498	SO:0001583	missense	463				muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding	g.chr16:72991587G>A	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.2458C>T	16.37:g.72991587G>A	ENSP00000268489:p.Arg820Cys					ZFHX3_ENST00000397992.5_Intron	p.R820C	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN			2	3130	-		Ovarian(137;0.13)	820					D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	c.2458C>T	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	G	13.97	2.395064	0.42512	.	.	ENSG00000140836	ENST00000268489	T	0.45668	0.89	5.52	5.52	0.82312	Zinc finger, C2H2-like (1);	0.000000	0.51477	D	0.000098	T	0.67287	0.2877	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.70178	-0.4943	10	0.87932	D	0	.	19.4741	0.94979	0.0:0.0:1.0:0.0	.	820	Q15911	ZFHX3_HUMAN	C	820	ENSP00000268489:R820C	ENSP00000268489:R820C	R	-	1	0	ZFHX3	71549088	1.000000	0.71417	0.990000	0.47175	0.979000	0.70002	9.807000	0.99171	2.595000	0.87683	0.655000	0.94253	CGC		0.567	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		79	118	0	0	0	1	0	79	118				
ALG1L2	644974	broad.mit.edu	37	3	129817127	129817127	+	RNA	SNP	A	A	C			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr3:129817127A>C	ENST00000507643.1	+	0	709				AC083906.2_ENST00000578837.1_RNA			C9J202	AG1L2_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like 2								transferase activity, transferring glycosyl groups (GO:0016757)										CCAGTTCCGGAAGAACCTGCG	0.522																																						ENST00000507643.1																			0																																																			644974				biosynthetic process		transferase activity, transferring glycosyl groups	g.chr3:129817127A>C	BC127756		3q22.1	2013-02-22	2013-02-22		ENSG00000251287	ENSG00000251287		"""Glycosyltransferase group 1 domain containing"""	37258	other	unknown			"""asparagine-linked glycosylation 1-like 2"""				Standard	NM_001136152		Approved		uc011bld.2	C9J202	OTTHUMG00000159782		3.37:g.129817127A>C										C9J202	AG1L2_HUMAN			0	709	+									RNA	SNP	ENST00000507643.1	37																																																																																						0.522	ALG1L2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000357289.1	NM_001136152		4	76	0	0	0	1	0	4	76				
GRK5	2869	broad.mit.edu	37	10	121196183	121196183	+	Silent	SNP	C	C	T	rs534305178		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr10:121196183C>T	ENST00000392870.2	+	9	1088	c.759C>T	c.(757-759)taC>taT	p.Y253Y	GRK5_ENST00000369108.3_Silent_p.Y148Y	NM_005308.2	NP_005299.1	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5	253	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein autophosphorylation (GO:0046777)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|phospholipid binding (GO:0005543)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(5)|lung(15)|skin(3)|stomach(1)|urinary_tract(1)	27		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		CCTATGCCTACGAGACCAAGG	0.562													C|||	1	0.000199681	0.0	0.0	5008	,	,		24241	0.001		0.0	False		,,,				2504	0.0					ENST00000392870.2																			0				endometrium(2)|large_intestine(5)|lung(15)|skin(3)|stomach(1)|urinary_tract(1)	27						c.(757-759)taC>taT		G protein-coupled receptor kinase 5							123.0	97.0	106.0					10																	121196183		2203	4300	6503	SO:0001819	synonymous_variant	2869				G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity	g.chr10:121196183C>T	L15388	CCDS7612.1	10q26.11	2013-09-19	2004-02-04	2004-02-06	ENSG00000198873	ENSG00000198873			4544	protein-coding gene	gene with protein product		600870		GPRK5		7685906	Standard	NM_005308		Approved		uc001led.3	P34947	OTTHUMG00000019149	ENST00000392870.2:c.759C>T	10.37:g.121196183C>T						GRK5_ENST00000369108.3_Silent_p.Y148Y	p.Y253Y	NM_005308.2	NP_005299.1	P34947	GRK5_HUMAN		all cancers(201;0.0227)	9	1088	+		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)	253			Protein kinase.		D3DRD0|Q5T059	Silent	SNP	ENST00000392870.2	37	c.759C>T	CCDS7612.1																																																																																				0.562	GRK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050652.2	NM_005308		5	48	0	0	0	1	0	5	48				
USH2A	7399	broad.mit.edu	37	1	216258155	216258155	+	Silent	SNP	C	C	T			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr1:216258155C>T	ENST00000307340.3	-	25	5438	c.5052G>A	c.(5050-5052)ccG>ccA	p.P1684P	RP11-22M7.2_ENST00000445619.1_RNA|RP11-22M7.2_ENST00000446411.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA|USH2A_ENST00000366943.2_Silent_p.P1684P|RP11-22M7.2_ENST00000430890.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1684	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		AAATAGCTGACGGATTGTAAT	0.393										HNSCC(13;0.011)																												ENST00000366943.2																			0				NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527						c.(5050-5052)ccG>ccA		Usher syndrome 2A (autosomal recessive, mild)							113.0	113.0	113.0					1																	216258155		2203	4300	6503	SO:0001819	synonymous_variant	7399				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding	g.chr1:216258155C>T	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.5052G>A	1.37:g.216258155C>T		HNSCC(13;0.011)				RP11-22M7.2_ENST00000446411.1_RNA|USH2A_ENST00000307340.3_Silent_p.P1684P|RP11-22M7.2_ENST00000445619.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA	p.P1684P			O75445	USH2A_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)	25	5438	-			1684			Laminin G-like 1.		Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	c.5052G>A	CCDS31025.1																																																																																				0.393	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		15	77	0	0	0	1	0	15	77				
ZNF98	148198	broad.mit.edu	37	19	22604998	22604998	+	Splice_Site	SNP	A	A	G			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr19:22604998A>G	ENST00000357774.5	-	1	150	c.29T>C	c.(28-30)aTg>aCg	p.M10T	ZNF98_ENST00000601553.1_Splice_Site_p.M10T|AC011516.1_ENST00000599129.1_lincRNA	NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	10					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				CACTCTCACCATTTCTAGGCT	0.607																																						ENST00000357774.5																			0				central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37						c.e1+1		zinc finger protein 98							113.0	114.0	113.0					19																	22604998		2203	4300	6503	SO:0001630	splice_region_variant	148198				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:22604998A>G		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"""Zinc fingers, C2H2-type"", ""-"""	13174	protein-coding gene	gene with protein product	"""zinc finger protein 739"""	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.30+1T>C	19.37:g.22604998A>G						ZNF98_ENST00000601553.1_Splice_Site_p.M10_splice	p.M10_splice	NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN			1	150	-		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)	10						Splice_Site	SNP	ENST00000357774.5	37	c.30_splice	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	5.481	0.273782	0.10403	.	.	ENSG00000197360	ENST00000357774	T	0.00753	5.74	0.185	0.185	0.15096	Krueppel-associated box (1);	.	.	.	.	T	0.00815	0.0027	L	0.39898	1.24	0.09310	N	1	B	0.26195	0.144	B	0.23716	0.048	T	0.44772	-0.9306	8	0.39692	T	0.17	.	.	.	.	.	10	A6NK75	ZNF98_HUMAN	T	10	ENSP00000350418:M10T	ENSP00000350418:M10T	M	-	2	0	ZNF98	22396838	0.041000	0.20044	0.226000	0.23910	0.231000	0.25187	0.335000	0.19806	0.251000	0.21505	0.248000	0.18094	ATG		0.607	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	Missense_Mutation	53	134	0	0	0	1	0	53	134				
CEP89	84902	broad.mit.edu	37	19	33444543	33444543	+	Missense_Mutation	SNP	T	T	C			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr19:33444543T>C	ENST00000305768.5	-	4	558	c.470A>G	c.(469-471)tAc>tGc	p.Y157C	CEP89_ENST00000590597.2_Missense_Mutation_p.Y157C	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	157					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						TGGCACAGCGTACAGGTCATC	0.488																																						ENST00000305768.4																			0				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						c.(469-471)tAc>tGc		centrosomal protein 89kDa							428.0	460.0	449.0					19																	33444543		2203	4300	6503	SO:0001583	missense	84902					centrosome|spindle pole		g.chr19:33444543T>C	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.470A>G	19.37:g.33444543T>C	ENSP00000306105:p.Tyr157Cys					CEP89_ENST00000590597.1_Missense_Mutation_p.Y157C	p.Y157C	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN			4	558	-			157					B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	c.470A>G	CCDS32987.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.814000	0.50527	.	.	ENSG00000121289	ENST00000305768	T	0.55413	0.52	5.12	5.12	0.69794	.	0.520993	0.19936	N	0.102748	T	0.69611	0.3130	M	0.72894	2.215	0.19575	N	0.999967	D;D;D	0.89917	1.0;1.0;0.997	D;D;P	0.76575	0.988;0.976;0.897	T	0.63024	-0.6729	10	0.72032	D	0.01	-3.3811	11.5924	0.50953	0.0:0.0:0.0:1.0	.	128;157;157	Q8WUL5;Q96ST8-3;Q96ST8	.;.;CEP89_HUMAN	C	157	ENSP00000306105:Y157C	ENSP00000306105:Y157C	Y	-	2	0	CEP89	38136383	0.853000	0.29707	0.062000	0.19696	0.014000	0.08584	2.480000	0.45206	2.048000	0.60808	0.482000	0.46254	TAC		0.488	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816		13	693	0	0	0	1	0	13	693				
PLA2G4A	5321	broad.mit.edu	37	1	186823502	186823502	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr1:186823502delC	ENST00000367466.3	+	2	168	c.16delC	c.(16-18)cctfs	p.P6fs	PLA2G4A_ENST00000442353.2_Frame_Shift_Del_p.P6fs|PLA2G4A_ENST00000466600.1_3'UTR	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	6	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000305}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	ATTTATAGATCCTTACCAGCA	0.343																																						ENST00000367466.3																			0				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53						c.(16-18)ctfs		phospholipase A2, group IVA (cytosolic, calcium-dependent)	Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Medrysone(DB00253)|Quinacrine(DB01103)						133.0	135.0	134.0					1																	186823502		2202	4298	6500	SO:0001589	frameshift_variant	5321				phospholipid catabolic process|platelet activating factor biosynthetic process|platelet activation	cytosol|endoplasmic reticulum membrane	calcium ion binding|calcium-dependent phospholipid binding|lysophospholipase activity	g.chr1:186823502delC	M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.16delC	1.37:g.186823502delC	ENSP00000356436:p.Pro6fs					PLA2G4A_ENST00000442353.2_Frame_Shift_Del_p.P6fs|PLA2G4A_ENST00000466600.1_3'UTR	p.P6fs	NM_024420.2	NP_077734.1	P47712	PA24A_HUMAN			2	168	+			6			C2.|Phospholipid binding (Probable).		B1AKG4|Q29R80	Frame_Shift_Del	DEL	ENST00000367466.3	37	c.16delC	CCDS1372.1																																																																																				0.343	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		29	34						29	34	---	---	---	---
GFPT1	2673	broad.mit.edu	37	2	69614196	69614196	+	Splice_Site	DEL	C	C	-			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr2:69614196delC	ENST00000357308.4	-	1	186		c.e1+1		GFPT1_ENST00000494201.1_Splice_Site|GFPT1_ENST00000361060.5_Splice_Site	NM_001244710.1	NP_001231639.1	Q06210	GFPT1_HUMAN	glutamine--fructose-6-phosphate transaminase 1						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|circadian regulation of gene expression (GO:0032922)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|endoplasmic reticulum unfolded protein response (GO:0030968)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glucosamine biosynthetic process (GO:0006042)|glutamine metabolic process (GO:0006541)|negative regulation of glycogen biosynthetic process (GO:0045719)|post-translational protein modification (GO:0043687)|protein homotetramerization (GO:0051289)|protein N-linked glycosylation via asparagine (GO:0018279)|response to sucrose (GO:0009744)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)			endometrium(1)|large_intestine(3)|lung(5)|skin(3)	12						GGCCCCCTTACCACACATGAT	0.736																																						ENST00000357308.4																			0				endometrium(1)|large_intestine(3)|lung(5)|skin(3)	12						c.e1+1		glutamine--fructose-6-phosphate transaminase 1							3.0	4.0	4.0					2																	69614196		1831	3786	5617	SO:0001630	splice_region_variant	2673				dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding	g.chr2:69614196delC		CCDS33216.1, CCDS58713.1	2p13	2014-09-17	2010-05-11		ENSG00000198380	ENSG00000198380	2.6.1.16		4241	protein-coding gene	gene with protein product		138292	"""glutamine-fructose-6-phosphate transaminase 1"""	GFPT		1460020	Standard	NM_002056		Approved	GFAT, GFA, GFAT1	uc002sfi.2	Q06210	OTTHUMG00000152666	ENST00000357308.4:c.7+1G>-	2.37:g.69614196delC						GFPT1_ENST00000494201.1_Splice_Site|GFPT1_ENST00000361060.4_Splice_Site		NM_001244710.1	NP_001231639.1	Q06210	GFPT1_HUMAN			1	186	-								Q53QE6|Q9BXF8	Splice_Site	DEL	ENST00000357308.4	37		CCDS58713.1																																																																																				0.736	GFPT1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			Intron	2	4						2	4	---	---	---	---
SYN2	6854	broad.mit.edu	37	3	12046124	12046126	+	RNA	DEL	AGC	AGC	-	rs76272937|rs74800608|rs375843790|rs74185804|rs202010288	byFrequency	TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr3:12046124_12046126delAGC	ENST00000432424.2	+	0	245_247							Q92777	SYN2_HUMAN	synapsin II						neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)			breast(5)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	18						AGCCCCAGCAAGCGCCGAcgccg	0.764														5004	0.999201	0.9992	1.0	5008	,	,		2724	1.0		0.999	False		,,,				2504	0.998					ENST00000432424.2																			0				breast(5)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	18								synapsin II																																						6854				neurotransmitter secretion	synaptic vesicle	ATP binding|ligase activity	g.chr3:12046124_12046126delAGC		CCDS74900.1, CCDS74901.1	3p25.2	2013-09-20			ENSG00000157152	ENSG00000157152			11495	protein-coding gene	gene with protein product		600755				8530057	Standard	XM_006713311		Approved	SYNII, SYNIIa, SYNIIb	uc003bwm.3	Q92777	OTTHUMG00000155335		3.37:g.12046124_12046126delAGC										Q86VA8	Q86VA8_HUMAN			0	245_247	+								A8MY98	RNA	DEL	ENST00000432424.2	37																																																																																						0.764	SYN2-002	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000339528.3	NM_133625		4	9						4	9	---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94377041	94377041	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr4:94377041delC	ENST00000282020.4	+	11	2032	c.1774delC	c.(1774-1776)cccfs	p.P593fs	GRID2_ENST00000510992.1_Frame_Shift_Del_p.P498fs	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	593					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		CTGGCTTAATCCCCCACGATT	0.453																																						ENST00000282020.4																			0				NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100						c.(1774-1776)ccfs		glutamate receptor, ionotropic, delta 2	L-Glutamic Acid(DB00142)						223.0	197.0	206.0					4																	94377041		2203	4300	6503	SO:0001589	frameshift_variant	2895				glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity	g.chr4:94377041delC	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.1774delC	4.37:g.94377041delC	ENSP00000282020:p.Pro593fs					GRID2_ENST00000510992.1_Frame_Shift_Del_p.P498fs	p.P593fs	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	11	2032	+		Hepatocellular(203;0.114)|all_hematologic(202;0.177)	593					E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Frame_Shift_Del	DEL	ENST00000282020.4	37	c.1774delC	CCDS3637.1																																																																																				0.453	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			40	73						40	73	---	---	---	---
CLINT1	9685	broad.mit.edu	37	5	157216481	157216485	+	Frame_Shift_Del	DEL	GGCAA	GGCAA	-			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr5:157216481_157216485delGGCAA	ENST00000411809.2	-	11	1621_1625	c.1417_1421delTTGCC	c.(1417-1422)ttgcccfs	p.LP473fs	CLINT1_ENST00000523908.1_Frame_Shift_Del_p.LP491fs|CLINT1_ENST00000523094.1_Frame_Shift_Del_p.LP473fs|CLINT1_ENST00000296951.5_Frame_Shift_Del_p.LP473fs|CLINT1_ENST00000530742.1_Frame_Shift_Del_p.LP473fs	NM_014666.3	NP_055481.1	Q14677	EPN4_HUMAN	clathrin interactor 1	473					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|lipid binding (GO:0008289)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|urinary_tract(1)	21	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCAAGTAGAGGGCAAGGTTTTGCTG	0.439																																					Colon(22;427 587 2170 6147 14291)	ENST00000523094.1																			0				breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|urinary_tract(1)	21						c.(1417-1422)cfs		clathrin interactor 1																																				SO:0001589	frameshift_variant	9685				endocytosis|post-Golgi vesicle-mediated transport	clathrin-coated vesicle|cytosol|Golgi apparatus|membrane|perinuclear region of cytoplasm	clathrin binding|lipid binding	g.chr5:157216481_157216485delGGCAA	AF434813	CCDS47330.1, CCDS56388.1, CCDS56389.1	5q33.3	2006-06-13			ENSG00000113282	ENSG00000113282			23186	protein-coding gene	gene with protein product		607265				12213833, 12429846	Standard	NM_014666		Approved	ENTH, KIAA0171, EPNR, CLINT	uc011ddv.2	Q14677	OTTHUMG00000163527	ENST00000411809.2:c.1417_1421delTTGCC	5.37:g.157216481_157216485delGGCAA	ENSP00000388340:p.Leu473fs					CLINT1_ENST00000411809.2_Frame_Shift_Del_p.LP473fs|CLINT1_ENST00000296951.5_Frame_Shift_Del_p.LP473fs|CLINT1_ENST00000530742.1_Frame_Shift_Del_p.LP473fs|CLINT1_ENST00000523908.1_Frame_Shift_Del_p.LP491fs	p.LP473fs	NM_001195555.1|NM_001195556.1	NP_001182484.1|NP_001182485.1	Q14677	EPN4_HUMAN	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		11	1622_1626	-	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	473					B7Z6F8|D3DQJ6|Q8NAF1|Q96E05	Frame_Shift_Del	DEL	ENST00000411809.2	37	c.1417_1421delTTGCC	CCDS47330.1																																																																																				0.439	CLINT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374001.1	NM_014666		52	105						52	105	---	---	---	---
GTF2IRD1P1	729156	broad.mit.edu	37	7	66304731	66304731	+	RNA	DEL	T	T	-			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr7:66304731delT	ENST00000457166.1	-	0	189					NR_003934.1				GTF2I repeat domain containing 1 pseusogene 1																		TTTCTTTCCCttttttttttt	0.512																																						ENST00000457166.1																			0																																																			729156							g.chr7:66304731delT			7q11.21	2012-06-29			ENSG00000230583	ENSG00000230583			44136	pseudogene	pseudogene							Standard	NR_003934		Approved		uc003tvj.1		OTTHUMG00000156927		7.37:g.66304731delT								NR_003934.1						0	189	-									RNA	DEL	ENST00000457166.1	37																																																																																						0.512	GTF2IRD1P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000346561.1	NR_003934		4	8						4	8	---	---	---	---
UBXN8	7993	broad.mit.edu	37	8	30612473	30612474	+	RNA	INS	-	-	T	rs549841322|rs34741520		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr8:30612473_30612474insT	ENST00000519246.1	+	0	604							O00124	UBXN8_HUMAN	UBX domain protein 8						ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|single fertilization (GO:0007338)	integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(1)|lung(2)	3						GGGGTTGGTCGttttttttttt	0.391																																					Colon(169;855 1943 17895 39459 47884)	ENST00000519246.1																			0				central_nervous_system(1)|lung(2)	3								UBX domain protein 8																																						7993				single fertilization			g.chr8:30612473_30612474insT	D83767	CCDS75723.1, CCDS75724.1, CCDS75725.1	8p12-p11.2	2012-07-06	2008-07-25	2008-07-25		ENSG00000104691		"""UBX domain containing"""	30307	protein-coding gene	gene with protein product		602155	"""UBX domain containing 6"""	UBXD6		9027507, 21949850	Standard	NM_005671		Approved	D8S2298E, REP8	uc003xii.3	O00124			8.37:g.30612484_30612484dupT										O00124	UBXN8_HUMAN			0	604	+								Q7Z6F2	RNA	INS	ENST00000519246.1	37																																																																																						0.391	UBXN8-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000375957.1	NM_005671		2	4						2	4	---	---	---	---
C8orf37-AS1	100616530	broad.mit.edu	37	8	96415908	96415918	+	lincRNA	DEL	TTTTTTTTTTT	TTTTTTTTTTT	-	rs547474951|rs140735178		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr8:96415908_96415918delTTTTTTTTTTT	ENST00000521905.1	+	0	126																											aataaaAGACttttttttttttttttttttt	0.322																																						ENST00000521905.1																			0																																																			100616530							g.chr8:96415908_96415918delTTTTTTTTTTT																													8.37:g.96415908_96415918delTTTTTTTTTTT														0	126	+									RNA	DEL	ENST00000521905.1	37																																																																																						0.322	KB-1047C11.2-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000379669.1			3	6						3	6	---	---	---	---
NLRP6	171389	broad.mit.edu	37	11	281553	281555	+	In_Frame_Del	DEL	GAG	GAG	-	rs377505007		TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr11:281553_281555delGAG	ENST00000312165.5	+	4	1819_1821	c.1819_1821delGAG	c.(1819-1821)gagdel	p.E611del	NLRP6_ENST00000534750.1_In_Frame_Del_p.E611del	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	611	Poly-Glu.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		CGAAGAGCCAGAGGAGGAGGAGG	0.67																																						ENST00000534750.1																			0				breast(1)|skin(1)|upper_aerodigestive_tract(2)	4						c.(1819-1821)del		NLR family, pyrin domain containing 6																																				SO:0001651	inframe_deletion	171389					cytoplasm	ATP binding	g.chr11:281553_281555delGAG	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"""Nucleotide-binding domain and leucine rich repeat containing"""	22944	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"""	609650	"""NACHT, leucine rich repeat and PYD containing 6"""	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.1819_1821delGAG	11.37:g.281562_281564delGAG	ENSP00000309767:p.Glu611del					NLRP6_ENST00000312165.5_In_Frame_Del_p.E611del	p.E611del	NM_001276700.1	NP_001263629.1	P59044	NALP6_HUMAN		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)	4	2024_2026	+		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)	611			Poly-Glu.		A8K9F3|E9PJZ8	In_Frame_Del	DEL	ENST00000312165.5	37	c.1819_1821delGAG	CCDS7693.1																																																																																				0.670	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		7	173						7	173	---	---	---	---
RP11-160C18.2	0	broad.mit.edu	37	15	79023175	79023175	+	RNA	DEL	C	C	-			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr15:79023175delC	ENST00000568337.1	+	0	31																											GGTGCAGTGACCCTGCAGGCC	0.537																																						ENST00000568337.1																			0																																																			0							g.chr15:79023175delC																													15.37:g.79023175delC														0	31	+									RNA	DEL	ENST00000568337.1	37																																																																																						0.537	RP11-160C18.2-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000421327.1			2	4						2	4	---	---	---	---
CCNF	899	broad.mit.edu	37	16	2481177	2481177	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr16:2481177delA	ENST00000397066.4	+	2	151	c.63delA	c.(61-63)cgafs	p.R22fs		NM_001761.2	NP_001752.2	P41002	CCNF_HUMAN	cyclin F	22					mitotic nuclear division (GO:0007067)|negative regulation of centrosome duplication (GO:0010826)|placenta development (GO:0001890)|protein ubiquitination (GO:0016567)|re-entry into mitotic cell cycle (GO:0000320)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	centriole (GO:0005814)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(2)|lung(5)|prostate(4)|skin(1)	20		Ovarian(90;0.17)				CTACAAAGCGAAGAATAAGGA	0.443																																						ENST00000397066.4																			0				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(2)|lung(5)|prostate(4)|skin(1)	20						c.(61-63)cgfs		cyclin F							135.0	131.0	132.0					16																	2481177		2198	4300	6498	SO:0001589	frameshift_variant	899				cell division|mitosis|negative regulation of centrosome duplication|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	centriole|nucleus|SCF ubiquitin ligase complex	protein binding	g.chr16:2481177delA	Z36714	CCDS10467.1	16p13.3	2008-02-05			ENSG00000162063	ENSG00000162063		"""F-boxes /  ""other"""""	1591	protein-coding gene	gene with protein product		600227				7896286	Standard	NM_001761		Approved	FBX1, FBXO1	uc002cqd.1	P41002	OTTHUMG00000128858	ENST00000397066.4:c.63delA	16.37:g.2481177delA	ENSP00000380256:p.Arg22fs						p.R22fs	NM_001761.2	NP_001752.2	P41002	CCNF_HUMAN			2	151	+		Ovarian(90;0.17)	22					B2R8H3|Q96EG9	Frame_Shift_Del	DEL	ENST00000397066.4	37	c.63delA	CCDS10467.1																																																																																				0.443	CCNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250801.1	NM_001761		46	80						46	80	---	---	---	---
LYPD3	27076	broad.mit.edu	37	19	43969653	43969655	+	In_Frame_Del	DEL	AGC	AGC	-	rs141441894	byFrequency	TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chr19:43969653_43969655delAGC	ENST00000244333.3	-	1	157_159	c.69_71delGCT	c.(67-72)ctgctt>ctt	p.23_24LL>L		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	23					cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				ACCTCCGCGAAGCAGCAGCAGCA	0.675																																						ENST00000244333.3																			0				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11						c.(67-72)ctt>ct		LY6/PLAUR domain containing 3																																				SO:0001651	inframe_deletion	27076					anchored to plasma membrane		g.chr19:43969653_43969655delAGC	AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.69_71delGCT	19.37:g.43969662_43969664delAGC	ENSP00000244333:p.Leu24del						p.LL23del	NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN			1	157_159	-		Prostate(69;0.0153)	23					Q9UJ74	In_Frame_Del	DEL	ENST00000244333.3	37	c.69_71delGCT	CCDS12620.1																																																																																				0.675	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400		7	235						7	235	---	---	---	---
USP9X	8239	broad.mit.edu	37	X	41060380	41060380	+	Frame_Shift_Del	DEL	G	G	-			TCGA-HD-A634-01A-11D-A28R-08	TCGA-HD-A634-10A-01D-A28U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8e12e6ab-b2a4-4bcc-bc70-f0432bd57b86	cb781355-b159-46e4-9f27-c4a3e5113845	g.chrX:41060380delG	ENST00000324545.8	+	31	5304	c.4671delG	c.(4669-4671)gtgfs	p.V1557fs	USP9X_ENST00000378308.2_Frame_Shift_Del_p.V1557fs	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1557	USP.				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)			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						AAGGATTCGTGGGGCTGAAAA	0.463																																					Ovarian(172;1807 2695 35459 49286)	ENST00000324545.7																			0				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						c.(4669-4671)gtfs		ubiquitin specific peptidase 9, X-linked							96.0	89.0	91.0					X																	41060380		2203	4299	6502	SO:0001589	frameshift_variant	8239				BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity	g.chrX:41060380delG	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.4671delG	X.37:g.41060380delG	ENSP00000316357:p.Val1557fs					USP9X_ENST00000378308.2_Frame_Shift_Del_p.V1557fs	p.V1557fs	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN			31	5304	+			1557					O75550|Q8WWT3|Q8WX12	Frame_Shift_Del	DEL	ENST00000324545.8	37	c.4671delG	CCDS43930.1																																																																																				0.463	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		51	10						51	10	---	---	---	---
