#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
POTEM	641455	broad.mit.edu	37	14	20010235	20010235	+	Missense_Mutation	SNP	A	A	G	rs113380635		TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr14:20010235A>G	ENST00000551509.1	-	5	974	c.923T>C	c.(922-924)gTt>gCt	p.V308A	RP11-244H18.1_ENST00000547584.1_lincRNA|RNU6-1268P_ENST00000391214.1_RNA	NM_001145442.1	NP_001138914.1	A6NI47	POTEM_HUMAN	POTE ankyrin domain family, member M	308										endometrium(4)|kidney(1)|lung(4)	9						AAGTATGAGAACAGTTCTAAA	0.368																																						ENST00000551509.1																			0				endometrium(4)|kidney(1)|lung(4)	9						c.(922-924)gTt>gCt		POTE ankyrin domain family, member M							42.0	37.0	39.0					14																	20010235		365	763	1128	SO:0001583	missense	641455							g.chr14:20010235A>G		CCDS73609.1	14q11.2	2013-01-10			ENSG00000187537	ENSG00000187537		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	37096	protein-coding gene	gene with protein product	"""prostate-specific P704P"""					16364570	Standard	NM_001145442		Approved	POTE14beta, P704P, ACT	uc001vwc.3	A6NI47		ENST00000551509.1:c.923T>C	14.37:g.20010235A>G	ENSP00000452296:p.Val308Ala					RP11-244H18.1_ENST00000547584.1_lincRNA	p.V308A	NM_001145442.1	NP_001138914.1	A6NI47	POTEM_HUMAN			5	974	-			308						Missense_Mutation	SNP	ENST00000551509.1	37	c.923T>C	CCDS45076.1	.	.	.	.	.	.	.	.	.	.	g	5.617	0.298596	0.10622	.	.	ENSG00000187537	ENST00000551509;ENST00000439503;ENST00000344684	T	0.60040	0.22	0.906	0.906	0.19314	Ankyrin repeat-containing domain (4);	0.000000	0.32655	N	0.005811	T	0.10723	0.0262	N	0.00039	-2.51	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25187	-1.0139	8	.	.	.	.	3.4158	0.07375	0.2955:0.0:0.7045:0.0	.	308	A6NI47	POTEM_HUMAN	A	308;393;308	ENSP00000452296:V308A	.	V	-	2	0	POTEM	19080235	0.621000	0.27077	0.813000	0.32504	0.042000	0.13812	0.922000	0.28734	-0.020000	0.14032	-1.160000	0.01791	GTT		0.368	POTEM-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409490.3	NM_001145442		3	37	0	0	0	1	0	3	37				
HPS4	89781	broad.mit.edu	37	22	26854435	26854435	+	Missense_Mutation	SNP	C	C	T			TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr22:26854435C>T	ENST00000398145.2	-	12	2438	c.1822G>A	c.(1822-1824)Gac>Aac	p.D608N	HPS4_ENST00000493455.2_5'UTR|HPS4_ENST00000398141.1_Missense_Mutation_p.D621N|HPS4_ENST00000336873.5_Missense_Mutation_p.D608N|HPS4_ENST00000402105.3_Missense_Mutation_p.D603N	NM_022081.5	NP_071364.4	Q9NQG7	HPS4_HUMAN	Hermansky-Pudlak syndrome 4	608					blood coagulation (GO:0007596)|hemostasis (GO:0007599)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of eye pigmentation (GO:0048075)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|platelet dense granule (GO:0042827)	protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(3)|kidney(5)|large_intestine(4)|lung(12)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	32						TGAATGCGGTCGTAATGTGTG	0.577									Hermansky-Pudlak syndrome																													ENST00000398145.2																			0				breast(2)|endometrium(3)|kidney(5)|large_intestine(4)|lung(12)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	32						c.(1822-1824)Gac>Aac		Hermansky-Pudlak syndrome 4							113.0	89.0	97.0					22																	26854435		2203	4300	6503	SO:0001583	missense	89781	Hermansky-Pudlak syndrome	Familial Cancer Database	HPS, HPS1-8	lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity	g.chr22:26854435C>T		CCDS13835.1, CCDS46677.1	22q12.1	2014-09-17			ENSG00000100099	ENSG00000100099			15844	protein-coding gene	gene with protein product		606682				11836498, 12663659	Standard	NM_022081		Approved	KIAA1667, LE	uc003aci.4	Q9NQG7	OTTHUMG00000030459	ENST00000398145.2:c.1822G>A	22.37:g.26854435C>T	ENSP00000381213:p.Asp608Asn					HPS4_ENST00000493455.2_5'UTR|HPS4_ENST00000402105.3_Missense_Mutation_p.D603N|HPS4_ENST00000398141.1_Missense_Mutation_p.D621N|HPS4_ENST00000336873.5_Missense_Mutation_p.D608N	p.D608N	NM_022081.4	NP_071364.4	Q9NQG7	HPS4_HUMAN			12	2438	-			608					B1AHQ4|Q5H8V6|Q96LX6|Q9BY93|Q9UH37|Q9UH38	Missense_Mutation	SNP	ENST00000398145.2	37	c.1822G>A	CCDS13835.1	.	.	.	.	.	.	.	.	.	.	C	32	5.155505	0.94686	.	.	ENSG00000100099	ENST00000398145;ENST00000398141;ENST00000402105;ENST00000336873	T;T;T;T	0.21191	2.02;2.02;2.02;2.02	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.48978	0.1530	M	0.77103	2.36	0.49582	D	0.9998	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.54516	-0.8282	10	0.87932	D	0	-36.7621	16.8245	0.85927	0.0:1.0:0.0:0.0	.	608;608;608;621;603	Q6P1K3;Q9NQG7;A8K2E6;Q9NQG7-4;Q9NQG7-3	.;HPS4_HUMAN;.;.;.	N	608;621;603;608	ENSP00000381213:D608N;ENSP00000381210:D621N;ENSP00000384185:D603N;ENSP00000338457:D608N	ENSP00000338457:D608N	D	-	1	0	HPS4	25184435	1.000000	0.71417	0.883000	0.34634	0.862000	0.49288	6.553000	0.73918	2.437000	0.82529	0.655000	0.94253	GAC		0.577	HPS4-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320778.1	NM_022081		4	43	0	0	0	1	0	4	43				
MIR514A2	574517	broad.mit.edu	37	X	146360769	146360769	+	RNA	SNP	C	C	A	rs374152740		TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chrX:146360769C>A	ENST00000385131.1	-	0	88				MIR514A1_ENST00000385133.1_RNA	NR_030239.1|NR_030240.1				microRNA 514a-2																		GTCTGTCGTACGTGTCATGCG	0.408													C|||	35	0.00927152	0.0083	0.0058	3775	,	,		14407	0.004		0.006	False		,,,				2504	0.0102					ENST00000385133.1																			0																				84.0	70.0	75.0					X																	146360769		1566	3568	5134			574516							g.chrX:146360769C>A			Xq27.3	2011-11-14	2011-11-14	2011-11-14	ENSG00000207866	ENSG00000207866		"""ncRNAs / Micro RNAs"""	32149	non-coding RNA	RNA, micro			"""microRNA 514-2"""	MIRN514-2, MIR514-2			Standard	NR_030239		Approved	hsa-mir-514-2	uc011mww.2				X.37:g.146360769C>A								NR_030238.1						0	93	-									RNA	SNP	ENST00000385131.1	37																																																																																						0.408	MIR514A2-201	KNOWN	basic	miRNA	miRNA		NR_030239		3	40	1	0	0.004672	1	0.004672	3	40				
CYP4Z1	199974	broad.mit.edu	37	1	47548102	47548102	+	Missense_Mutation	SNP	C	C	A			TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr1:47548102C>A	ENST00000334194.3	+	4	464	c.461C>A	c.(460-462)aCc>aAc	p.T154N		NM_178134.2	NP_835235.1	Q86W10	CP4Z1_HUMAN	cytochrome P450, family 4, subfamily Z, polypeptide 1	154						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			cervix(1)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	11						ATATTCATCACCATGATGTCT	0.483																																						ENST00000334194.3																			0				cervix(1)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	11						c.(460-462)aCc>aAc		cytochrome P450, family 4, subfamily Z, polypeptide 1							81.0	74.0	77.0					1																	47548102		2203	4300	6503	SO:0001583	missense	199974					endoplasmic reticulum membrane|integral to membrane|microsome	aromatase activity|electron carrier activity|heme binding	g.chr1:47548102C>A	AY262056	CCDS545.1	1p33	2008-02-05			ENSG00000186160	ENSG00000186160		"""Cytochrome P450s"""	20583	protein-coding gene	gene with protein product						15059886	Standard	NM_178134		Approved	CYP4A20	uc001cqu.1	Q86W10	OTTHUMG00000008019	ENST00000334194.3:c.461C>A	1.37:g.47548102C>A	ENSP00000334246:p.Thr154Asn						p.T154N	NM_178134.2	NP_835235.1	Q86W10	CP4Z1_HUMAN			4	464	+			154					Q5VVE4	Missense_Mutation	SNP	ENST00000334194.3	37	c.461C>A	CCDS545.1	.	.	.	.	.	.	.	.	.	.	-	2.347	-0.349686	0.05173	.	.	ENSG00000186160	ENST00000334194	T	0.68025	-0.3	2.4	-4.81	0.03180	.	0.491893	0.15365	U	0.266147	T	0.41858	0.1177	N	0.19112	0.55	0.09310	N	1	B	0.32010	0.351	B	0.31390	0.129	T	0.24119	-1.0169	10	0.23891	T	0.37	.	7.4051	0.26985	0.4437:0.3711:0.1852:0.0	.	154	Q86W10	CP4Z1_HUMAN	N	154	ENSP00000334246:T154N	ENSP00000334246:T154N	T	+	2	0	CYP4Z1	47320689	0.000000	0.05858	0.000000	0.03702	0.322000	0.28314	-2.989000	0.00658	-2.843000	0.00334	0.427000	0.28365	ACC		0.483	CYP4Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022020.1	NM_178134		3	20	1	0	0.00024832	1	0.000260145	3	20				
KCNT2	343450	broad.mit.edu	37	1	196398825	196398825	+	Missense_Mutation	SNP	T	T	C			TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr1:196398825T>C	ENST00000294725.9	-	9	1616	c.701A>G	c.(700-702)tAt>tGt	p.Y234C	KCNT2_ENST00000367433.5_Missense_Mutation_p.Y234C|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000609185.1_Missense_Mutation_p.Y234C|KCNT2_ENST00000367431.4_Missense_Mutation_p.Y234C|KCNT2_ENST00000451324.2_Intron			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	234					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						AATGCAGAAATAAAGGGAGTC	0.388																																						ENST00000367433.5																			0				NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						c.(700-702)tAt>tGt		potassium channel, subfamily T, member 2							101.0	89.0	93.0					1																	196398825		2203	4300	6503	SO:0001583	missense	343450					voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity	g.chr1:196398825T>C	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18866	protein-coding gene	gene with protein product	"""sodium and chloride activated ATP sensitive potassium channel"""	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.701A>G	1.37:g.196398825T>C	ENSP00000294725:p.Tyr234Cys					KCNT2_ENST00000294725.8_Missense_Mutation_p.Y234C|KCNT2_ENST00000451324.2_Intron|KCNT2_ENST00000367431.4_Missense_Mutation_p.Y234C|KCNT2_ENST00000498426.1_5'UTR	p.Y234C			Q6UVM3	KCNT2_HUMAN			9	802	-			234					Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	37	c.701A>G	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.137057	0.77775	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000535608;ENST00000294725	T;T;T	0.48201	0.82;0.82;0.82	5.31	5.31	0.75309	Ion transport 2 (1);	0.000000	0.49305	D	0.000147	T	0.80433	0.4622	H	0.98238	4.18	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;0.999	D	0.88015	0.2765	10	0.87932	D	0	-19.7056	15.2557	0.73582	0.0:0.0:0.0:1.0	.	234;234;234;234	A9LNM6;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;KCNT2_HUMAN	C	234;234;55;234	ENSP00000356403:Y234C;ENSP00000356401:Y234C;ENSP00000294725:Y234C	ENSP00000294725:Y234C	Y	-	2	0	KCNT2	194665448	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	8.035000	0.88872	2.012000	0.59069	0.533000	0.62120	TAT		0.388	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		11	12	0	0	0	1	0	11	12				
RSBN1L	222194	broad.mit.edu	37	7	77326163	77326163	+	Missense_Mutation	SNP	G	G	A			TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr7:77326163G>A	ENST00000334955.8	+	1	404	c.377G>A	c.(376-378)cGc>cAc	p.R126H	RSBN1L_ENST00000445288.1_5'Flank|RSBN1L-AS1_ENST00000440088.1_lincRNA	NM_198467.2	NP_940869.2	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	126						nucleus (GO:0005634)				central_nervous_system(1)|endometrium(12)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CCGGTGCCGCGCAAACTGCTG	0.677																																						ENST00000334955.7																			0				central_nervous_system(1)|endometrium(12)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						c.(376-378)cGc>cAc		round spermatid basic protein 1-like							18.0	23.0	22.0					7																	77326163		2150	4241	6391	SO:0001583	missense	222194					nucleus		g.chr7:77326163G>A	AK124517	CCDS43607.1	7q21.11	2004-08-11			ENSG00000187257	ENSG00000187257			24765	protein-coding gene	gene with protein product						12477932	Standard	NM_198467		Approved	FLJ42526, FLJ45813, MGC71764	uc010ldt.1	Q6PCB5	OTTHUMG00000155517	ENST00000334955.8:c.377G>A	7.37:g.77326163G>A	ENSP00000334040:p.Arg126His						p.R126H	NM_198467.2	NP_940869.2	Q6PCB5	RSBNL_HUMAN			1	404	+			126					C9K0P1|Q6ZS58|Q6ZVI9|Q86X48	Missense_Mutation	SNP	ENST00000334955.8	37	c.377G>A	CCDS43607.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.550493	0.65311	.	.	ENSG00000187257	ENST00000334955	T	0.07444	3.19	3.52	3.52	0.40303	.	0.504809	0.18273	N	0.146255	T	0.15912	0.0383	L	0.27053	0.805	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.03673	-1.1014	10	0.46703	T	0.11	-5.4532	12.2417	0.54546	0.0:0.0:1.0:0.0	.	126	Q6PCB5	RSBNL_HUMAN	H	126	ENSP00000334040:R126H	ENSP00000334040:R126H	R	+	2	0	RSBN1L	77164099	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	3.044000	0.49830	1.948000	0.56530	0.313000	0.20887	CGC		0.677	RSBN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340455.3	NM_198467		3	27	0	0	0	1	0	3	27				
HAP1	9001	broad.mit.edu	37	17	39884515	39884515	+	Nonsense_Mutation	SNP	G	G	A			TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr17:39884515G>A	ENST00000310778.5	-	7	1147	c.1138C>T	c.(1138-1140)Cag>Tag	p.Q380*	HAP1_ENST00000393939.2_Nonsense_Mutation_p.Q380*|HAP1_ENST00000341193.5_Nonsense_Mutation_p.Q388*|RN7SL399P_ENST00000471648.2_RNA|JUP_ENST00000540235.1_Intron|HAP1_ENST00000347901.4_Nonsense_Mutation_p.Q380*			P54257	HAP1_HUMAN	huntingtin-associated protein 1	380	Glu-rich.|HAP1 N-terminal.				anterograde axon cargo transport (GO:0008089)|autophagy (GO:0006914)|brain development (GO:0007420)|cell projection organization (GO:0030030)|exocytosis (GO:0006887)|negative regulation of beta-amyloid formation (GO:1902430)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|positive regulation of neurotrophin production (GO:0032901)|positive regulation of nonmotile primary cilium assembly (GO:1902857)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|protein localization (GO:0008104)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of organelle transport along microtubule (GO:1902513)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)|vesicle transport along microtubule (GO:0047496)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synapse (GO:0045202)	brain-derived neurotrophic factor binding (GO:0048403)|ion channel binding (GO:0044325)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			TCCTGCTGCTGCCGTTCATAG	0.657																																						ENST00000393939.2																			0				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21						c.(1138-1140)Cag>Tag		huntingtin-associated protein 1							48.0	42.0	44.0					17																	39884515		2203	4300	6503	SO:0001587	stop_gained	9001				brain development|protein localization|synaptic transmission	actin cytoskeleton	protein binding	g.chr17:39884515G>A	AF040723	CCDS11406.1, CCDS42338.1, CCDS42339.1	17q21.2-q21.3	2008-04-23	2008-04-23		ENSG00000173805	ENSG00000173805			4812	protein-coding gene	gene with protein product	"""neuroan 1"""	600947		HAP2		7477378, 9668110	Standard	NM_177977		Approved	HLP, hHLP1, HIP5	uc002hxn.1	P54257	OTTHUMG00000133498	ENST00000310778.5:c.1138C>T	17.37:g.39884515G>A	ENSP00000309392:p.Gln380*					HAP1_ENST00000341193.5_Nonsense_Mutation_p.Q388*|HAP1_ENST00000310778.5_Nonsense_Mutation_p.Q380*|JUP_ENST00000540235.1_Intron|HAP1_ENST00000347901.4_Nonsense_Mutation_p.Q380*	p.Q380*			P54257	HAP1_HUMAN	BRCA - Breast invasive adenocarcinoma(4;0.0677)		7	1147	-		Breast(137;0.000162)	380			Glu-rich.|HAP1 N-terminal.		A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Nonsense_Mutation	SNP	ENST00000310778.5	37	c.1138C>T		.	.	.	.	.	.	.	.	.	.	G	24.9	4.582033	0.86748	.	.	ENSG00000173805	ENST00000393939;ENST00000310778;ENST00000347901;ENST00000341193	.	.	.	4.14	3.16	0.36331	.	0.000000	0.39687	N	0.001299	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-29.6099	7.9593	0.30062	0.1125:0.0:0.8875:0.0	.	.	.	.	X	380;380;380;388	.	ENSP00000309392:Q380X	Q	-	1	0	HAP1	37138041	1.000000	0.71417	0.978000	0.43139	0.580000	0.36256	2.546000	0.45778	0.989000	0.38761	0.549000	0.68633	CAG		0.657	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949		4	42	0	0	0	1	0	4	42				
KCNH6	81033	broad.mit.edu	37	17	61619703	61619703	+	Nonsense_Mutation	SNP	C	C	T			TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr17:61619703C>T	ENST00000583023.1	+	9	2067	c.2056C>T	c.(2056-2058)Cag>Tag	p.Q686*	KCNH6_ENST00000314672.5_Nonsense_Mutation_p.Q686*|KCNH6_ENST00000456941.2_Nonsense_Mutation_p.Q633*|KCNH6_ENST00000581784.1_Nonsense_Mutation_p.Q633*	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	686					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	GCACAAGATCCAGCGGGCAGA	0.592																																						ENST00000583023.1																			0				breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						c.(2056-2058)Cag>Tag		potassium voltage-gated channel, subfamily H (eag-related), member 6	Ibutilide(DB00308)						103.0	87.0	92.0					17																	61619703		2203	4300	6503	SO:0001587	stop_gained	81033				regulation of transcription, DNA-dependent|signal transduction			g.chr17:61619703C>T	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.2056C>T	17.37:g.61619703C>T	ENSP00000463533:p.Gln686*					KCNH6_ENST00000314672.5_Nonsense_Mutation_p.Q686*|KCNH6_ENST00000456941.2_Nonsense_Mutation_p.Q633*|KCNH6_ENST00000581784.1_Nonsense_Mutation_p.Q633*	p.Q686*	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN			9	2067	+			686					Q9BRD7	Nonsense_Mutation	SNP	ENST00000583023.1	37	c.2056C>T	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	C	38	6.698726	0.97772	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	.	.	.	4.73	4.73	0.59995	.	0.256304	0.32204	N	0.006431	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	.	17.687	0.88258	0.0:1.0:0.0:0.0	.	.	.	.	X	686;633	.	ENSP00000318212:Q686X	Q	+	1	0	KCNH6	58973435	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.999000	0.70665	2.148000	0.66965	0.467000	0.42956	CAG		0.592	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		16	23	0	0	0	1	0	16	23				
DAK	26007	broad.mit.edu	37	11	61110893	61110893	+	Silent	SNP	C	C	A			TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr11:61110893C>A	ENST00000394900.3	+	11	1174	c.945C>A	c.(943-945)acC>acA	p.T315T		NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2 homolog (S. cerevisiae)	315	DhaK. {ECO:0000255|PROSITE- ProRule:PRU00814}.				carbohydrate phosphorylation (GO:0046835)|cellular carbohydrate metabolic process (GO:0044262)|glycerol metabolic process (GO:0006071)|innate immune response (GO:0045087)|regulation of innate immune response (GO:0045088)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|FAD-AMP lyase (cyclizing) activity (GO:0034012)|glycerone kinase activity (GO:0004371)|metal ion binding (GO:0046872)|triokinase activity (GO:0050354)			NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						TTTCTCTCACCCTCCTGCTGG	0.592																																						ENST00000394900.3																			0				NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						c.(943-945)acC>acA		dihydroxyacetone kinase 2 homolog (S. cerevisiae)							107.0	104.0	105.0					11																	61110893		2203	4299	6502	SO:0001819	synonymous_variant	26007				glycerol metabolic process	cytosol	ATP binding|FAD-AMP lyase (cyclizing) activity|glycerone kinase activity|metal ion binding	g.chr11:61110893C>A		CCDS8003.1	11q12.2	2009-11-06	2006-04-04		ENSG00000149476	ENSG00000149476			24552	protein-coding gene	gene with protein product		615844	"""dihydroxyacetone kinase 2 homolog (yeast)"""				Standard	XM_005273898		Approved	DKFZP586B1621, NET45	uc001nre.3	Q3LXA3	OTTHUMG00000168076	ENST00000394900.3:c.945C>A	11.37:g.61110893C>A							p.T315T	NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN			11	1174	+			315			DhaK.		Q2L9C1|Q53EQ9|Q9BVA7|Q9H895	Silent	SNP	ENST00000394900.3	37	c.945C>A	CCDS8003.1																																																																																				0.592	DAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394425.4	NM_015533		5	54	1	0	1.06961e-07	1	1.17657e-07	5	54				
PSG5	5673	broad.mit.edu	37	19	43690622	43690622	+	De_novo_Start_OutOfFrame	SNP	C	C	T	rs138160369	byFrequency	TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr19:43690622C>T	ENST00000366175.3	-	0	66				PSG5_ENST00000407356.1_De_novo_Start_OutOfFrame|PSG5_ENST00000404580.1_De_novo_Start_OutOfFrame|PSG5_ENST00000407568.1_De_novo_Start_OutOfFrame|PSG5_ENST00000401992.1_5'UTR|PSG5_ENST00000342951.6_De_novo_Start_OutOfFrame|PSG5_ENST00000599812.1_De_novo_Start_OutOfFrame			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5						female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				TTCCTGAGCACGGCTGTAGGC	0.627													C|||	177	0.0353435	0.0862	0.0144	5008	,	,		17765	0.004		0.006	False		,,,				2504	0.044					ENST00000404580.1																			0				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35								pregnancy specific beta-1-glycoprotein 5		C	,	94,1290		4,86,602	41.0	45.0	44.0		,	0.2	0.0	19	dbSNP_134	44	11,3169		0,11,1579	no	utr-5,utr-5	PSG5	NM_001130014.1,NM_002781.3	,	4,97,2181	TT,TC,CC		0.3459,6.7919,2.3006	,	,	43690622	105,4459	692	1590	2282			5673				female pregnancy	extracellular region		g.chr19:43690622C>T		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9522	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta 1 glycoprotein"""	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.-65G>A	19.37:g.43690622C>T						PSG5_ENST00000599812.1_De_novo_Start_OutOfFrame|PSG5_ENST00000407356.1_De_novo_Start_OutOfFrame|PSG5_ENST00000366175.3_De_novo_Start_OutOfFrame|PSG5_ENST00000401992.1_5'UTR|PSG5_ENST00000342951.6_De_novo_Start_OutOfFrame|PSG5_ENST00000407568.1_De_novo_Start_OutOfFrame				Q15238	PSG5_HUMAN			0	24	-		Prostate(69;0.00899)						Q15239|Q96QJ1|Q9UQ75	Translation_Start_Site	SNP	ENST00000366175.3	37		CCDS12617.1																																																																																				0.627	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781		7	35	0	0	0	1	0	7	35				
LOC220729	220729	broad.mit.edu	37	3	197348674	197348674	+	RNA	SNP	A	A	G	rs376114863		TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr3:197348674A>G	ENST00000418868.1	-	0	585					NR_003266.2																						GGCTCTGTCCACCAAATGCAC	0.478																																						ENST00000418868.1																			0																																																			220729							g.chr3:197348674A>G																													3.37:g.197348674A>G								NR_003266.2						0	585	-									RNA	SNP	ENST00000418868.1	37																																																																																						0.478	AC024560.3-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000340283.1			3	64	0	0	0	1	0	3	64				
SEPT8	23176	broad.mit.edu	37	5	132099470	132099470	+	Silent	SNP	G	G	C			TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr5:132099470G>C	ENST00000378719.2	-	4	699	c.462C>G	c.(460-462)ctC>ctG	p.L154L	SEPT8_ENST00000378699.2_Silent_p.L94L|SEPT8_ENST00000448933.1_Silent_p.L94L|SEPT8_ENST00000378701.1_Silent_p.L152L|SEPT8_ENST00000481030.1_5'Flank|SEPT8_ENST00000378721.4_Silent_p.L152L|SEPT8_ENST00000296873.7_Silent_p.L154L|SEPT8_ENST00000378706.1_Silent_p.L154L|SEPT8_ENST00000458488.2_Silent_p.L154L	NM_001098811.1	NP_001092281.1	Q92599	SEPT8_HUMAN	septin 8	154	Septin-type G.				cell cycle (GO:0007049)	septin complex (GO:0031105)	GTP binding (GO:0005525)		SEPT8/AFF4(2)	kidney(2)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGATGAAGTAGAGGCAAACGT	0.512																																						ENST00000296873.7																		SEPT8/AFF4(2)	0				kidney(2)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	11						c.(460-462)ctC>ctG		septin 8							193.0	196.0	195.0					5																	132099470		2038	4202	6240	SO:0001819	synonymous_variant	23176				cell cycle	septin complex	GTP binding|protein binding	g.chr5:132099470G>C	AF179995	CCDS43358.1, CCDS43359.1, CCDS43360.1, CCDS47262.1, CCDS75298.1	5q31	2013-01-21			ENSG00000164402	ENSG00000164402		"""Septins"""	16511	protein-coding gene	gene with protein product		608418				9039502, 9149945	Standard	NM_001098812		Approved	KIAA0202, SEP2	uc003kxr.2	Q92599	OTTHUMG00000059735	ENST00000378719.2:c.462C>G	5.37:g.132099470G>C						SEPT8_ENST00000448933.1_Silent_p.L94L|SEPT8_ENST00000378699.2_Silent_p.L94L|SEPT8_ENST00000378701.1_Silent_p.L152L|SEPT8_ENST00000458488.2_Silent_p.L154L|SEPT8_ENST00000378706.1_Silent_p.L154L|SEPT8_ENST00000378719.2_Silent_p.L154L|SEPT8_ENST00000378721.4_Silent_p.L152L	p.L154L	NM_001098812.1|NM_015146.1	NP_001092282.1|NP_055961.1	Q92599	SEPT8_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		4	745	-		all_cancers(142;0.0751)|Breast(839;0.198)	154					A6NC65|A6NKP6|F6W7K9|Q8IX36|Q8IX37|Q9BVB3	Silent	SNP	ENST00000378719.2	37	c.462C>G	CCDS43358.1																																																																																				0.512	SEPT8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132827.2	XM_034872		7	137	0	0	0	1	0	7	137				
HLA-A	3105	broad.mit.edu	37	6	29910693	29910693	+	Missense_Mutation	SNP	A	A	G	rs41559716	byFrequency	TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr6:29910693A>G	ENST00000396634.1	+	4	574	c.233A>G	c.(232-234)cAg>cGg	p.Q78R	HLA-A_ENST00000376802.2_Missense_Mutation_p.Q78R|HLA-A_ENST00000376809.5_Missense_Mutation_p.Q78R|HLA-A_ENST00000376806.5_Missense_Mutation_p.Q78R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	78	Alpha-1.				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 exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.Q78R(2)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TGGATAGAGCAGGAGGGGCCG	0.657									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																												ENST00000396634.1																			2	Substitution - Missense(2)	p.Q78R(2)	lung(1)|endometrium(1)	central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						c.(232-234)cAg>cGg		major histocompatibility complex, class I, A							54.0	57.0	56.0					6																	29910693		2203	4299	6502	SO:0001583	missense	3105	Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity	g.chr6:29910693A>G	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.233A>G	6.37:g.29910693A>G	ENSP00000379873:p.Gln78Arg	Multiple Myeloma(9;0.094)				HLA-A_ENST00000376806.5_Missense_Mutation_p.Q78R|HLA-A_ENST00000376802.2_Missense_Mutation_p.Q78R|HLA-A_ENST00000376809.5_Missense_Mutation_p.Q78R	p.Q78R			P30443	1A01_HUMAN			4	574	+			78			Alpha-1.		O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	c.233A>G	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	9.798	1.179669	0.21787	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00784	5.7;5.7;5.7;5.7	3.72	-4.39	0.03611	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	1.398580	0.06189	N	0.681068	T	0.00815	0.0027	L	0.56280	1.765	0.09310	N	1	B;P;B;P;B	0.42483	0.0;0.781;0.0;0.781;0.0	B;D;B;D;B	0.71184	0.006;0.972;0.01;0.972;0.01	T	0.44952	-0.9294	10	0.87932	D	0	.	0.9552	0.01384	0.3504:0.1689:0.3159:0.1647	rs41559716	78;78;78;78;78	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	R	78	ENSP00000379873:Q78R;ENSP00000366002:Q78R;ENSP00000366005:Q78R;ENSP00000365998:Q78R	ENSP00000348012:Q78R	Q	+	2	0	HLA-A	30018672	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	-0.990000	0.03732	-0.910000	0.03847	-0.450000	0.05554	CAG		0.657	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		3	10	0	0	0	1	0	3	10				
MIR514A2	574517	broad.mit.edu	37	X	146360813	146360813	+	RNA	SNP	A	A	G	rs148964961		TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chrX:146360813A>G	ENST00000385131.1	-	0	88				MIR514A1_ENST00000385133.1_RNA	NR_030239.1|NR_030240.1				microRNA 514a-2																		ATCAAATTTAATTATACATGA	0.433													A|||	26	0.00688742	0.0083	0.0072	3775	,	,		14217	0.0		0.006	False		,,,				2504	0.0041					ENST00000385133.1																			0															A		12,2613		0,11,1,1048,506	83.0	71.0	75.0			-1.4	0.0	X	dbSNP_134	75	18,5470		0,3,15,1913,1641	no	intergenic				0,14,16,2961,2147	GG,GA,G,AA,A		0.328,0.4571,0.3698			146360813	30,8083	1566	3572	5138			574516							g.chrX:146360813A>G			Xq27.3	2011-11-14	2011-11-14	2011-11-14	ENSG00000207866	ENSG00000207866		"""ncRNAs / Micro RNAs"""	32149	non-coding RNA	RNA, micro			"""microRNA 514-2"""	MIRN514-2, MIR514-2			Standard	NR_030239		Approved	hsa-mir-514-2	uc011mww.2				X.37:g.146360813A>G								NR_030238.1						0	49	-									RNA	SNP	ENST00000385131.1	37																																																																																						0.433	MIR514A2-201	KNOWN	basic	miRNA	miRNA		NR_030239		4	54	0	0	0	1	0	4	54				
FRG1B	284802	broad.mit.edu	37	20	29628283	29628283	+	Silent	SNP	G	G	C	rs200164543		TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr20:29628283G>C	ENST00000278882.3	+	6	665	c.285G>C	c.(283-285)ggG>ggC	p.G95G	FRG1B_ENST00000358464.4_Silent_p.G95G|FRG1B_ENST00000439954.2_Silent_p.G100G			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	95								p.G95G(4)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						ATGAAGCAGGGGACATAGAAG	0.378																																						ENST00000278882.3																			4	Substitution - coding silent(4)	p.G95G(4)	urinary_tract(2)|kidney(2)	endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(283-285)ggG>ggC																																						SO:0001819	synonymous_variant	284802							g.chr20:29628283G>C			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.285G>C	20.37:g.29628283G>C						FRG1B_ENST00000439954.2_Silent_p.G100G|FRG1B_ENST00000358464.4_Silent_p.G95G	p.G95G							6	665	+								C4AME5	Silent	SNP	ENST00000278882.3	37	c.285G>C																																																																																					0.378	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		4	59	0	0	0	1	0	4	59				
IGHA2	3494	broad.mit.edu	37	14	106054030	106054030	+	RNA	SNP	C	C	G	rs374247139		TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr14:106054030C>G	ENST00000390539.2	-	0	488				AL928742.1_ENST00000581377.1_RNA			P01877	IGHA2_HUMAN	immunoglobulin heavy constant alpha 2 (A2m marker)						antibacterial humoral response (GO:0019731)|glomerular filtration (GO:0003094)|immune response (GO:0006955)|positive regulation of respiratory burst (GO:0060267)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|monomeric IgA immunoglobulin complex (GO:0071748)|secretory dimeric IgA immunoglobulin complex (GO:0071752)|secretory IgA immunoglobulin complex (GO:0071751)	antigen binding (GO:0003823)										AGAGGTCACGCTCAGGTGGTC	0.632																																						ENST00000390539.2																			0															C		0,4258		0,0,2129	32.0	39.0	37.0			3.3	0.0	14		37	2,8464		0,2,4231	no	intergenic				0,2,6360	GG,GC,CC		0.0236,0.0,0.0157			106054030	2,12722	2129	4233	6362			3494							g.chr14:106054030C>G	J00221		14q32.33	2012-10-02			ENSG00000211890	ENSG00000211890		"""Immunoglobulins / IGH locus"""	5479	other	immunoglobulin gene		147000					Standard	NG_001019		Approved			P01877	OTTHUMG00000152472		14.37:g.106054030C>G														0	488	-									RNA	SNP	ENST00000390539.2	37																																																																																						0.632	IGHA2-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	IG_C_gene	OTTHUMT00000326338.1	NG_001019		3	16	0	0	0	1	0	3	16				
FXR1	8087	broad.mit.edu	37	3	180630496	180630496	+	Missense_Mutation	SNP	T	T	G			TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr3:180630496T>G	ENST00000357559.4	+	1	407	c.23T>G	c.(22-24)gTt>gGt	p.V8G	FXR1_ENST00000305586.7_5'UTR|FXR1_ENST00000445140.2_Missense_Mutation_p.V8G|FXR1_ENST00000491062.1_Missense_Mutation_p.V8G|FXR1_ENST00000491674.1_Missense_Mutation_p.V8G|FXR1_ENST00000480918.1_5'Flank|FXR1_ENST00000468861.1_5'UTR	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	8	Agenet-like 1.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of translation (GO:0017148)	costamere (GO:0043034)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysome (GO:0005844)	G-quadruplex RNA binding (GO:0002151)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|large_intestine(5)|lung(12)|skin(2)	26	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			ACGGTGGAGGTTCGCGGCTCT	0.592											OREG0015934	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000357559.4																			0				breast(3)|endometrium(4)|large_intestine(5)|lung(12)|skin(2)	26						c.(22-24)gTt>gGt		fragile X mental retardation, autosomal homolog 1							146.0	145.0	146.0					3																	180630496		2203	4300	6503	SO:0001583	missense	8087				apoptosis|cell differentiation|muscle organ development	nucleolus|polysome		g.chr3:180630496T>G	M67468	CCDS3238.1, CCDS33894.1, CCDS46965.1	3q28	2014-01-28			ENSG00000114416	ENSG00000114416			4023	protein-coding gene	gene with protein product		600819				7781595, 9642279	Standard	NM_005087		Approved		uc003fkq.3	P51114	OTTHUMG00000158138	ENST00000357559.4:c.23T>G	3.37:g.180630496T>G	ENSP00000350170:p.Val8Gly		OREG0015934	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1963	FXR1_ENST00000491674.1_Missense_Mutation_p.V8G|FXR1_ENST00000491062.1_Missense_Mutation_p.V8G|FXR1_ENST00000468861.1_5'UTR|FXR1_ENST00000445140.2_Missense_Mutation_p.V8G|FXR1_ENST00000305586.7_5'UTR	p.V8G	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)		1	407	+	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		8					A8K9B8|Q7Z450|Q8N6R8	Missense_Mutation	SNP	ENST00000357559.4	37	c.23T>G	CCDS3238.1	.	.	.	.	.	.	.	.	.	.	T	11.59	1.685380	0.29872	.	.	ENSG00000114416	ENST00000357559;ENST00000491674;ENST00000491062;ENST00000445140	T;T;T	0.59906	0.89;0.48;0.23	3.93	2.78	0.32641	.	0.292430	0.31246	N	0.007986	T	0.70176	0.3194	M	0.71036	2.16	0.80722	D	1	D;B;B	0.89917	1.0;0.019;0.007	D;B;B	0.91635	0.999;0.156;0.026	T	0.70389	-0.4885	10	0.87932	D	0	-2.4011	7.6175	0.28167	0.0:0.1043:0.0:0.8957	.	8;8;8	E9PFF5;P51114-2;P51114	.;.;FXR1_HUMAN	G	8	ENSP00000350170:V8G;ENSP00000420643:V8G;ENSP00000388828:V8G	ENSP00000350170:V8G	V	+	2	0	FXR1	182113190	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	4.941000	0.63540	0.867000	0.35654	0.459000	0.35465	GTT		0.592	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350265.5			22	65	0	0	0	1	0	22	65				
FOXP2	93986	broad.mit.edu	37	7	114269973	114269973	+	Silent	SNP	A	A	G	rs576887296|rs398124272	byFrequency	TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr7:114269973A>G	ENST00000393494.2	+	5	789	c.510A>G	c.(508-510)caA>caG	p.Q170Q	FOXP2_ENST00000408937.3_Silent_p.Q195Q|FOXP2_ENST00000393498.2_Silent_p.Q150Q|FOXP2_ENST00000393491.3_Silent_p.Q78Q|FOXP2_ENST00000403559.4_Silent_p.Q187Q|FOXP2_ENST00000393500.3_Silent_p.Q95Q|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000393489.3_Silent_p.Q78Q|FOXP2_ENST00000378237.3_Silent_p.Q170Q|FOXP2_ENST00000350908.4_Silent_p.Q170Q|FOXP2_ENST00000360232.4_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_ENST00000360232.4_Silent_p.Q170Q|FOXP2_ENST00000403559.4_Silent_p.Q187Q|FOXP2_ENST00000393498.2_Silent_p.Q150Q|FOXP2_ENST00000393491.3_Silent_p.Q78Q|FOXP2_ENST00000378237.3_Silent_p.Q170Q|FOXP2_ENST00000393494.2_Silent_p.Q170Q|FOXP2_ENST00000390668.3_Silent_p.Q194Q|FOXP2_ENST00000408937.3_Silent_p.Q195Q|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000393489.3_Silent_p.Q78Q|FOXP2_ENST00000350908.4_Silent_p.Q170Q	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		3	58	0	0	0	1	0	3	58				
TCF23	150921	broad.mit.edu	37	2	27372135	27372135	+	Frame_Shift_Del	DEL	G	G	-			TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr2:27372135delG	ENST00000296096.5	+	1	264	c.134delG	c.(133-135)tggfs	p.W45fs	TCF23_ENST00000407815.3_3'UTR	NM_175769.2	NP_786951.1	Q7RTU1	TCF23_HUMAN	transcription factor 23	45					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	nucleus (GO:0005634)				large_intestine(2)|lung(11)|prostate(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGGACCCGTGGGAAGAAAGA	0.637																																						ENST00000296096.5																			0				large_intestine(2)|lung(11)|prostate(1)	14						c.(133-135)tgfs		transcription factor 23							36.0	30.0	32.0					2																	27372135		2178	4289	6467	SO:0001589	frameshift_variant	150921				cell differentiation|muscle organ development|regulation of transcription, DNA-dependent	nucleus		g.chr2:27372135delG	AC013403	CCDS33163.1	2p23.3	2013-05-21			ENSG00000163792	ENSG00000163792		"""Basic helix-loop-helix proteins"""	18602	protein-coding gene	gene with protein product		609635				11701948, 10652346	Standard	NM_175769		Approved	OUT, bHLHa24	uc010ylg.2	Q7RTU1	OTTHUMG00000152031	ENST00000296096.5:c.134delG	2.37:g.27372135delG	ENSP00000296096:p.Trp45fs					TCF23_ENST00000407815.3_3'UTR	p.W45fs	NM_175769.2	NP_786951.1	Q7RTU1	TCF23_HUMAN			1	264	+	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)		45					B2RNZ3	Frame_Shift_Del	DEL	ENST00000296096.5	37	c.134delG	CCDS33163.1																																																																																				0.637	TCF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324980.1	NM_175769		2	4						2	4	---	---	---	---
SOX4	6659	broad.mit.edu	37	6	21595016	21595016	+	Frame_Shift_Del	DEL	T	T	-			TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr6:21595016delT	ENST00000244745.1	+	1	1045	c.251delT	c.(250-252)atgfs	p.M84fs	SOX4_ENST00000543472.1_Frame_Shift_Del_p.M84fs	NM_003107.2	NP_003098.1	Q06945	SOX4_HUMAN	SRY (sex determining region Y)-box 4	84					ascending aorta morphogenesis (GO:0035910)|atrial septum primum morphogenesis (GO:0003289)|canonical Wnt signaling pathway (GO:0060070)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle formation (GO:0003211)|cellular response to glucose stimulus (GO:0071333)|DNA damage response, detection of DNA damage (GO:0042769)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endocrine pancreas development (GO:0031018)|glial cell development (GO:0021782)|glial cell proliferation (GO:0014009)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|kidney morphogenesis (GO:0060993)|limb bud formation (GO:0060174)|mitral valve morphogenesis (GO:0003183)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of protein ubiquitination (GO:0031397)|neural tube formation (GO:0001841)|neuroepithelial cell differentiation (GO:0060563)|noradrenergic neuron differentiation (GO:0003357)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin secretion (GO:0032024)|positive regulation of N-terminal peptidyl-lysine acetylation (GO:2000761)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of Wnt signaling pathway (GO:0030177)|pro-B cell differentiation (GO:0002328)|protein stabilization (GO:0050821)|regulation of protein stability (GO:0031647)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spinal cord development (GO:0021510)|spinal cord motor neuron differentiation (GO:0021522)|sympathetic nervous system development (GO:0048485)|T cell differentiation (GO:0030217)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			kidney(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	6	Ovarian(93;0.163)		all cancers(50;0.0751)|Epithelial(50;0.155)			TCGCCCGACATGCACAACGCC	0.607																																						ENST00000244745.1																			0				kidney(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	6						c.(250-252)agfs		SRY (sex determining region Y)-box 4							39.0	35.0	37.0					6																	21595016		2203	4300	6503	SO:0001589	frameshift_variant	6659				canonical Wnt receptor signaling pathway|cardiac ventricle formation|cellular response to glucose stimulus|DNA damage response, detection of DNA damage|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|glial cell development|glial cell proliferation|limb bud formation|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein export from nucleus|negative regulation of protein ubiquitination|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|positive regulation of apoptosis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell proliferation|positive regulation of insulin secretion|positive regulation of N-terminal peptidyl-lysine acetylation|positive regulation of translation|pro-B cell differentiation|protein stabilization|skeletal system development|spinal cord motor neuron differentiation|sympathetic nervous system development|T cell differentiation	mitochondrion|nucleus	core promoter sequence-specific DNA binding|protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity	g.chr6:21595016delT	AF070669	CCDS4547.1	6p22.3	2008-02-05			ENSG00000124766	ENSG00000124766		"""SRY (sex determining region Y)-boxes"""	11200	protein-coding gene	gene with protein product		184430				8268656, 9730625	Standard	NM_003107		Approved		uc003ndi.3	Q06945	OTTHUMG00000016101	ENST00000244745.1:c.251delT	6.37:g.21595016delT	ENSP00000244745:p.Met84fs					SOX4_ENST00000543472.1_Frame_Shift_Del_p.M84fs	p.M84fs	NM_003107.2	NP_003098.1	Q06945	SOX4_HUMAN	all cancers(50;0.0751)|Epithelial(50;0.155)		1	1045	+	Ovarian(93;0.163)		84						Frame_Shift_Del	DEL	ENST00000244745.1	37	c.251delT	CCDS4547.1																																																																																				0.607	SOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043301.1	NM_003107		2	4						2	4	---	---	---	---
PMS2P4	5382	broad.mit.edu	37	7	66762432	66762432	+	RNA	DEL	G	G	-	rs530279026|rs201332789|rs370991247	byFrequency	TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr7:66762432delG	ENST00000414507.1	-	0	184				Y_RNA_ENST00000364695.1_RNA					postmeiotic segregation increased 2 pseudogene 4																		gtctcaaaaagaaaaaaaaaa	0.408																																						ENST00000414507.1																			0																																																			5382							g.chr7:66762432delG	D38438		7q11.22	2010-10-26	2010-10-26	2010-10-26	ENSG00000067601	ENSG00000067601			9129	pseudogene	pseudogene	"""PMS2 pseudogene"""		"""postmeiotic segregation increased 2-like 4"", ""postmeiotic segregation increased 2-like 4 pseudogene"""	PMS2L4		8586419	Standard	NR_046297		Approved	PMS6	uc003tvo.3		OTTHUMG00000156923		7.37:g.66762432delG														0	184	-									RNA	DEL	ENST00000414507.1	37																																																																																						0.408	PMS2P4-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000346632.1	NR_022007		3	6						3	6	---	---	---	---
REXO1L1P	254958	broad.mit.edu	37	8	86574438	86574439	+	Frame_Shift_Del	DEL	AC	AC	-	rs560943870		TCGA-SR-A6MT-01A-11D-A35I-08	TCGA-SR-A6MT-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dcacf523-f3c2-4869-a508-495c63961c4b	035aa651-02f7-48c3-b98b-23baf22ea71d	g.chr8:86574438_86574439delAC	ENST00000379010.2	-	1	1287_1288	c.1288_1289delGT	c.(1288-1290)gtafs	p.V430fs		NM_172239.4	NP_758439.4														endometrium(1)|lung(4)	5						CTGGTCGCGTACACAGCGGCCC	0.658																																						ENST00000379010.2																			0				endometrium(1)|lung(4)	5						c.(1288-1290)afs		REX1, RNA exonuclease 1 homolog (S. cerevisiae)-like 1				0,246		0,0,123						-0.8	0.0			1	8,990		3,2,494	no	frameshift	REXO1L1	NM_172239.4		3,2,617	A1A1,A1R,RR		0.8016,0.0,0.6431				8,1236				SO:0001589	frameshift_variant	254958					cytoplasm|nucleus	exonuclease activity|nucleic acid binding	g.chr8:86574438_86574439delAC																												ENST00000379010.2:c.1288_1289delGT	8.37:g.86574440_86574441delAC	ENSP00000368295:p.Val430fs						p.V430fs	NM_172239.4	NP_758439.4	Q8IX06	GOR_HUMAN			1	1287_1288	-			430			GOR1-125 epitope.			Frame_Shift_Del	DEL	ENST00000379010.2	37	c.1288_1289delGT																																																																																					0.658	REXO1L1-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000381106.1			4	6						4	6	---	---	---	---
