#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
BTNL8	79908	genome.wustl.edu	37	5	180376957	180376957	+	Missense_Mutation	SNP	C	C	A			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr5:180376957C>A	ENST00000340184.4	+	8	1122	c.916C>A	c.(916-918)Ctg>Atg	p.L306M	BTNL8_ENST00000505126.1_Missense_Mutation_p.L99M|BTNL8_ENST00000533815.2_Missense_Mutation_p.L122M|BTNL8_ENST00000400707.3_Missense_Mutation_p.L181M|BTNL8_ENST00000508408.1_3'UTR|BTNL8_ENST00000231229.4_3'UTR|BTNL8_ENST00000511704.1_Missense_Mutation_p.L190M	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	306	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CGTTTCTGATCTGAAAACTGT	0.527																																						dbGAP											0													33.0	33.0	33.0					5																	180376957		2117	3882	5999	-	-	-	SO:0001583	missense	0			AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.916C>A	5.37:g.180376957C>A	ENSP00000342197:p.Leu306Met	Somatic		WXS	Illumina GAIIx	Phase_IV	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Missense_Mutation	SNP	pfam_SPRY_rcpt,pfam_Ig_V-set,superfamily_ConA-like_lec_gl,smart_Ig_sub,smart_PRY,smart_SPla/RYanodine_receptor_subgr,prints_Butyrophylin,pfscan_B30.2/SPRY,pfscan_Ig-like	p.L306M	ENST00000340184.4	37	c.916	CCDS43413.1	5	.	.	.	.	.	.	.	.	.	.	C	11.42	1.632602	0.29068	.	.	ENSG00000113303	ENST00000340184;ENST00000400707;ENST00000511704;ENST00000505126;ENST00000533815	T;T;T;T;T	0.13089	2.62;2.62;2.62;2.62;2.62	1.77	1.77	0.24775	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.30479	0.0766	M	0.67625	2.065	0.09310	N	1	D;D;D	0.71674	0.995;0.985;0.998	D;D;D	0.71414	0.973;0.96;0.959	T	0.03898	-1.0994	9	0.46703	T	0.11	.	9.1171	0.36764	0.0:1.0:0.0:0.0	.	181;190;306	E9PG07;E9PEF6;Q6UX41	.;.;BTNL8_HUMAN	M	306;181;190;99;122	ENSP00000342197:L306M;ENSP00000383543:L181M;ENSP00000425207:L190M;ENSP00000427441:L99M;ENSP00000435098:L122M	ENSP00000342197:L306M	L	+	1	2	BTNL8	180309563	0.074000	0.21230	0.016000	0.15963	0.118000	0.20060	-0.155000	0.10115	0.994000	0.38892	0.430000	0.28490	CTG	BTNL8	-	superfamily_ConA-like_lec_gl,smart_PRY,pfscan_B30.2/SPRY	ENSG00000113303		0.527	BTNL8-002	KNOWN	basic|CCDS	protein_coding	BTNL8	HGNC	protein_coding	OTTHUMT00000368440.1	95	0.00	0	C	NM_024850		180376957	180376957	+1	no_errors	ENST00000340184	ensembl	human	known	69_37n	missense	89	31.54	41	SNP	0.485	A
C9orf114	51490	genome.wustl.edu	37	9	131587072	131587072	+	Silent	SNP	G	G	A			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr9:131587072G>A	ENST00000361256.5	-	9	829	c.789C>T	c.(787-789)acC>acT	p.T263T		NM_016390.3	NP_057474.2	Q5T280	CI114_HUMAN	chromosome 9 open reading frame 114	263							poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(4)|ovary(1)	7						CCAGTCGGACGGTGTAGCCCC	0.547																																						dbGAP											0													116.0	94.0	102.0					9																	131587072		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS6913.1	9q34.11	2014-05-29			ENSG00000198917	ENSG00000198917			26933	protein-coding gene	gene with protein product	"""centromere protein 32"""					20813266	Standard	NM_016390		Approved	HSPC109, CENP-32	uc004bwd.3	Q5T280	OTTHUMG00000020762	ENST00000361256.5:c.789C>T	9.37:g.131587072G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q0D2P6|Q6P469|Q6PGP9|Q6PIJ1|Q6PJV9	Silent	SNP	pfam_Put_MeTrfase,superfamily_NA-bd_OB-fold-like	p.T263	ENST00000361256.5	37	c.789	CCDS6913.1	9																																																																																			C9orf114	-	pfam_Put_MeTrfase	ENSG00000198917		0.547	C9orf114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C9orf114	HGNC	protein_coding	OTTHUMT00000054500.1	129	0.00	0	G	NM_016390		131587072	131587072	-1	no_errors	ENST00000361256	ensembl	human	known	69_37n	silent	84	41.26	59	SNP	0.014	A
COLEC10	10584	genome.wustl.edu	37	8	120103458	120103458	+	Splice_Site	SNP	G	G	C			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr8:120103458G>C	ENST00000332843.2	+	3	332	c.291G>C	c.(289-291)aaG>aaC	p.K97N	COLEC10_ENST00000521788.1_3'UTR	NM_006438.3	NP_006429.2	Q9Y6Z7	COL10_HUMAN	collectin sub-family member 10 (C-type lectin)	97	Collagen-like.					collagen trimer (GO:0005581)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)	mannose binding (GO:0005537)			endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21	all_cancers(13;4.13e-26)|Lung NSC(37;1.36e-07)|Ovarian(258;0.018)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00113)			TTGGGAAGAAGGGTAAGTTGC	0.448																																						dbGAP											0													131.0	124.0	126.0					8																	120103458		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			AB002631	CCDS6327.1	8q23-q24.1	2007-12-19				ENSG00000184374		"""Collectins"""	2220	protein-coding gene	gene with protein product		607620				10224141	Standard	NM_006438		Approved	CL-L1	uc003yoo.3	Q9Y6Z7		ENST00000332843.2:c.292+1G>C	8.37:g.120103458G>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q3SYH6|Q6UW19	Missense_Mutation	SNP	pfam_C-type_lectin,pfam_Collagen,superfamily_C-type_lectin_fold,smart_C-type_lectin,pfscan_C-type_lectin	p.K97N	ENST00000332843.2	37	c.291	CCDS6327.1	8	.	.	.	.	.	.	.	.	.	.	G	19.17	3.775641	0.70107	.	.	ENSG00000184374	ENST00000332843	D	0.93859	-3.3	6.03	3.3	0.37823	.	0.095803	0.64402	D	0.000001	D	0.95959	0.8684	M	0.84948	2.725	0.46798	D	0.999201	D	0.76494	0.999	D	0.69824	0.966	D	0.94398	0.7620	10	0.59425	D	0.04	-25.4599	8.0059	0.30325	0.2474:0.0:0.7526:0.0	.	97	Q9Y6Z7	COL10_HUMAN	N	97	ENSP00000332723:K97N	ENSP00000332723:K97N	K	+	3	2	COLEC10	120172639	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	0.856000	0.27818	0.450000	0.26774	0.655000	0.94253	AAG	COLEC10	-	pfam_Collagen	ENSG00000184374		0.448	COLEC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COLEC10	HGNC	protein_coding	OTTHUMT00000381225.1	135	0.00	0	G		Missense_Mutation	120103458	120103458	+1	no_errors	ENST00000332843	ensembl	human	known	69_37n	missense	127	29.05	52	SNP	1.000	C
CSF1	1435	genome.wustl.edu	37	1	110466401	110466401	+	Missense_Mutation	SNP	G	G	C			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr1:110466401G>C	ENST00000329608.6	+	6	1549	c.1158G>C	c.(1156-1158)aaG>aaC	p.K386N	CSF1_ENST00000369801.1_Intron|CSF1_ENST00000344188.5_Intron|CSF1_ENST00000369802.3_Missense_Mutation_p.K386N|CSF1_ENST00000420111.2_Intron	NM_000757.5|NM_172211.3	NP_000748|NP_757350.1	P09603	CSF1_HUMAN	colony stimulating factor 1 (macrophage)	386					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|developmental process involved in reproduction (GO:0003006)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary duct terminal end bud growth (GO:0060763)|mammary gland fat development (GO:0060611)|monocyte activation (GO:0042117)|odontogenesis (GO:0042476)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|osteoclast proliferation (GO:0002158)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of macrophage derived foam cell differentiation (GO:0010743)|regulation of ossification (GO:0030278)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|macrophage colony-stimulating factor receptor binding (GO:0005157)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Acute lymphoblastic leukemia(138;0.204)		Lung(183;0.0238)|Colorectal(144;0.112)|all cancers(265;0.117)|Epithelial(280;0.127)|LUSC - Lung squamous cell carcinoma(189;0.135)		CCCCCCAGAAGACAGACCATC	0.657											OREG0013645	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0													49.0	53.0	51.0					1																	110466401		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC021117	CCDS816.1, CCDS817.1, CCDS30797.1	1p13.3	2012-09-20			ENSG00000184371	ENSG00000184371			2432	protein-coding gene	gene with protein product		120420				1540160	Standard	NM_172210		Approved	M-CSF, MCSF, MGC31930	uc001dyw.4	P09603	OTTHUMG00000011646	ENST00000329608.6:c.1158G>C	1.37:g.110466401G>C	ENSP00000327513:p.Lys386Asn	Somatic	1427	WXS	Illumina GAIIx	Phase_IV	A8K6J5|Q13130|Q14086|Q14806|Q5VVF3|Q5VVF4|Q9UQR8	Missense_Mutation	SNP	pfam_MCSF-1,superfamily_4_helix_cytokine-like_core,pirsf_MCSF-1	p.K386N	ENST00000329608.6	37	c.1158	CCDS816.1	1	.	.	.	.	.	.	.	.	.	.	G	18.42	3.619868	0.66787	.	.	ENSG00000184371	ENST00000329608;ENST00000369802	T;T	0.14640	2.49;2.49	4.82	3.9	0.45041	.	0.376195	0.19267	U	0.118512	T	0.13243	0.0321	L	0.56769	1.78	0.80722	D	1	D	0.58268	0.982	P	0.59825	0.864	T	0.10086	-1.0645	10	0.18710	T	0.47	.	9.2055	0.37287	0.1027:0.0:0.8973:0.0	.	386	P09603	CSF1_HUMAN	N	386	ENSP00000327513:K386N;ENSP00000358817:K386N	ENSP00000327513:K386N	K	+	3	2	CSF1	110267924	0.938000	0.31826	0.952000	0.39060	0.093000	0.18481	2.020000	0.41010	1.163000	0.42636	0.467000	0.42956	AAG	CSF1	-	pfam_MCSF-1,pirsf_MCSF-1	ENSG00000184371		0.657	CSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CSF1	HGNC	protein_coding	OTTHUMT00000032208.1	52	0.00	0	G	NM_000757		110466401	110466401	+1	no_errors	ENST00000329608	ensembl	human	known	69_37n	missense	39	20.41	10	SNP	0.810	C
DDR2	4921	genome.wustl.edu	37	1	162746132	162746132	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr1:162746132G>A	ENST00000367922.3	+	17	2693	c.2255G>A	c.(2254-2256)cGc>cAc	p.R752H	DDR2_ENST00000367921.3_Missense_Mutation_p.R752H|RN7SL861P_ENST00000473793.2_RNA	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	752	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> C (in SEMD-SL; causes retention in an intracellular compartment and thereby abolishes signaling in response collagen binding). {ECO:0000269|PubMed:19110212}.		biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	CTCCCTATCCGCTGGATGTCT	0.498																																					NSCLC(161;314 2006 8283 19651 23192)	dbGAP											0													98.0	93.0	95.0					1																	162746132		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"""discoidin domain receptor family, member 2"""	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.2255G>A	1.37:g.162746132G>A	ENSP00000356899:p.Arg752His	Somatic		WXS	Illumina GAIIx	Phase_IV	Q7Z730	Missense_Mutation	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_Coagulation_fac_5/8-C_type_dom,superfamily_Kinase-like_dom,superfamily_Galactose-bd-like,smart_Coagulation_fac_5/8-C_type_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Coagulation_fac_5/8-C_type_dom,pfscan_Prot_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.R752H	ENST00000367922.3	37	c.2255	CCDS1241.1	1	.	.	.	.	.	.	.	.	.	.	G	33	5.250777	0.95305	.	.	ENSG00000162733	ENST00000367922;ENST00000367921	D;D	0.83591	-1.74;-1.74	5.18	5.18	0.71444	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91637	0.7357	M	0.88377	2.95	0.41423	D	0.987810	D	0.89917	1.0	D	0.79108	0.992	D	0.92920	0.6354	9	0.87932	D	0	.	17.6139	0.88063	0.0:0.0:1.0:0.0	.	752	Q16832	DDR2_HUMAN	H	752	ENSP00000356899:R752H;ENSP00000356898:R752H	ENSP00000356898:R752H	R	+	2	0	DDR2	161012756	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.662000	0.98603	2.541000	0.85698	0.637000	0.83480	CGC	DDR2	-	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	ENSG00000162733		0.498	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DDR2	HGNC	protein_coding	OTTHUMT00000083213.2	87	0.00	0	G	NM_006182		162746132	162746132	+1	no_errors	ENST00000367921	ensembl	human	known	69_37n	missense	94	23.58	29	SNP	1.000	A
FREM2	341640	genome.wustl.edu	37	13	39261792	39261792	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr13:39261792G>A	ENST00000280481.7	+	1	527	c.311G>A	c.(310-312)cGc>cAc	p.R104H		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	104					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CCCGGGGACCGCTGCGCGGTT	0.682																																						dbGAP											0													16.0	17.0	17.0					13																	39261792		2202	4298	6500	-	-	-	SO:0001583	missense	0			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.311G>A	13.37:g.39261792G>A	ENSP00000280481:p.Arg104His	Somatic		WXS	Illumina GAIIx	Phase_IV	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	pfam_Calx_beta,superfamily_Cadherin-like,smart_Calx_beta	p.R104H	ENST00000280481.7	37	c.311	CCDS31960.1	13	.	.	.	.	.	.	.	.	.	.	G	15.99	2.995156	0.54147	.	.	ENSG00000150893	ENST00000280481	T	0.19532	2.14	5.46	3.71	0.42584	.	0.538193	0.18929	N	0.127278	T	0.17408	0.0418	L	0.39147	1.195	0.41103	D	0.98568	B	0.10296	0.003	B	0.09377	0.004	T	0.04078	-1.0979	10	0.49607	T	0.09	.	9.5698	0.39420	0.2172:0.0:0.7828:0.0	.	104	Q5SZK8	FREM2_HUMAN	H	104	ENSP00000280481:R104H	ENSP00000280481:R104H	R	+	2	0	FREM2	38159792	0.992000	0.36948	1.000000	0.80357	0.998000	0.95712	3.349000	0.52217	1.295000	0.44724	0.655000	0.94253	CGC	FREM2	-	NULL	ENSG00000150893		0.682	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FREM2	HGNC	protein_coding	OTTHUMT00000044599.2	17	0.00	0	G	NM_207361		39261792	39261792	+1	no_errors	ENST00000280481	ensembl	human	known	69_37n	missense	11	54.17	13	SNP	1.000	A
GRIN2D	2906	genome.wustl.edu	37	19	48908478	48908478	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr19:48908478G>A	ENST00000263269.3	+	3	1041	c.953G>A	c.(952-954)cGg>cAg	p.R318Q		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	318					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GACCTGGCTCGGCGAGTGGCA	0.701																																						dbGAP											0													11.0	13.0	13.0					19																	48908478		2027	4013	6040	-	-	-	SO:0001583	missense	0			U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4588	protein-coding gene	gene with protein product	"""N-methyl-d-aspartate receptor subunit 2D"""	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.953G>A	19.37:g.48908478G>A	ENSP00000263269:p.Arg318Gln	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Iontro_glu_rcpt,pfam_SBP_bac_3,pfam_Glu_rcpt_Glu/Gly-bd,pfam_ANF_lig-bd_rcpt,smart_Iontro_glu_rcpt,smart_Glu_rcpt_Glu/Gly-bd,prints_NMDA_rcpt	p.R318Q	ENST00000263269.3	37	c.953	CCDS12719.1	19	.	.	.	.	.	.	.	.	.	.	G	11.75	1.730912	0.30684	.	.	ENSG00000105464	ENST00000263269	T	0.05258	3.47	4.45	3.17	0.36434	Extracellular ligand-binding receptor (1);	0.000000	0.64402	D	0.000001	T	0.02571	0.0078	N	0.14661	0.345	0.38023	D	0.934923	B	0.30511	0.282	B	0.22386	0.039	T	0.35475	-0.9787	10	0.02654	T	1	.	6.9253	0.24412	0.2168:0.0:0.7832:0.0	.	318	O15399	NMDE4_HUMAN	Q	318	ENSP00000263269:R318Q	ENSP00000263269:R318Q	R	+	2	0	GRIN2D	53600290	0.808000	0.29022	1.000000	0.80357	0.990000	0.78478	5.412000	0.66392	2.199000	0.70637	0.561000	0.74099	CGG	GRIN2D	-	pfam_ANF_lig-bd_rcpt	ENSG00000105464		0.701	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GRIN2D	HGNC	protein_coding	OTTHUMT00000466121.1	24	0.00	0	G			48908478	48908478	+1	no_errors	ENST00000263269	ensembl	human	known	69_37n	missense	14	44.00	11	SNP	1.000	A
MAST4	375449	genome.wustl.edu	37	5	66459337	66459337	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr5:66459337G>A	ENST00000403625.2	+	29	4625	c.4330G>A	c.(4330-4332)Gtg>Atg	p.V1444M	MAST4_ENST00000404260.3_Missense_Mutation_p.V1447M|MAST4_ENST00000405643.1_Missense_Mutation_p.V1265M|MAST4_ENST00000403666.1_Missense_Mutation_p.V1255M|MAST4_ENST00000261569.7_Missense_Mutation_p.V1250M	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	1447						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		GCTCAAGCGCGTGCAGTCCGA	0.642																																						dbGAP											0													18.0	24.0	22.0					5																	66459337		2071	4200	6271	-	-	-	SO:0001583	missense	0			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.4330G>A	5.37:g.66459337G>A	ENSP00000385727:p.Val1444Met	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	pfam_MA_Ser/Thr_Kinase_dom,pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_PDZ,superfamily_Kinase-like_dom,superfamily_MAST_pre-PK_dom,superfamily_PDZ,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_PDZ,pfscan_PDZ,pfscan_Prot_kinase_cat_dom	p.V1447M	ENST00000403625.2	37	c.4339	CCDS54861.1	5	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.273040|5.273040	0.95429|0.95429	.|.	.|.	ENSG00000069020|ENSG00000069020	ENST00000443808|ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569	T|T;T;T;T;T	0.38401|0.41065	1.14|1.01;1.01;1.01;1.01;1.01	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.70334|0.70334	0.3212|0.3212	M|M	0.83953|0.83953	2.67|2.67	0.51233|0.51233	D|D	0.999919|0.999919	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.83275	.|0.996;0.996	T|T	0.72802|0.72802	-0.4183|-0.4183	7|10	0.87932|0.87932	D|D	0|0	-18.7665|-18.7665	20.3248|20.3248	0.98698|0.98698	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1447;1255	.|O15021;O15021-3	.|MAST4_HUMAN;.	H|M	500|1447;1444;1255;1265;1265;1250	ENSP00000400551:R500H|ENSP00000385048:V1447M;ENSP00000385727:V1444M;ENSP00000384313:V1255M;ENSP00000384099:V1265M;ENSP00000261569:V1250M	ENSP00000400551:R500H|ENSP00000261569:V1250M	R|V	+|+	2|1	0|0	MAST4|MAST4	66495093|66495093	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.995000|0.995000	0.86356|0.86356	9.869000|9.869000	0.99810|0.99810	2.818000|2.818000	0.97014|0.97014	0.655000|0.655000	0.94253|0.94253	CGT|GTG	MAST4	-	NULL	ENSG00000069020		0.642	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	MAST4	HGNC	protein_coding	OTTHUMT00000326324.2	13	0.00	0	G			66459337	66459337	+1	no_errors	ENST00000404260	ensembl	human	known	69_37n	missense	10	47.37	9	SNP	1.000	A
MCOLN1	57192	genome.wustl.edu	37	19	7591479	7591479	+	Missense_Mutation	SNP	A	A	T			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr19:7591479A>T	ENST00000264079.6	+	3	517	c.392A>T	c.(391-393)cAt>cTt	p.H131L		NM_020533.2	NP_065394.1	Q9GZU1	MCLN1_HUMAN	mucolipin 1	131					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular iron ion homeostasis (GO:0006879)|ion transmembrane transport (GO:0034220)|release of sequestered calcium ion into cytosol (GO:0051209)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cation channel activity (GO:0005261)|NAADP-sensitive calcium-release channel activity (GO:0072345)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GCCATCTTCCATGCTGTGGAC	0.682																																						dbGAP											0													90.0	75.0	80.0					19																	7591479		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF249319	CCDS12180.1	19p13.2	2011-12-16				ENSG00000090674		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	13356	protein-coding gene	gene with protein product		605248				16382100	Standard	NM_020533		Approved	TRPML1, ML4, MLIV, MST080, MSTP080, TRPM-L1	uc002mgo.3	Q9GZU1		ENST00000264079.6:c.392A>T	19.37:g.7591479A>T	ENSP00000264079:p.His131Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	D6W647|Q7Z4F7|Q9H292|Q9H4B3|Q9H4B5	Missense_Mutation	SNP	pfam_PKD1_2_channel,superfamily_Glycoside_hydrolase_SF	p.H131L	ENST00000264079.6	37	c.392	CCDS12180.1	19	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.27|13.27	2.187696|2.187696	0.38609|0.38609	.|.	.|.	ENSG00000090674|ENSG00000090674	ENST00000264079|ENST00000394321	T|.	0.52295|.	0.67|.	5.24|5.24	2.91|2.91	0.33838|0.33838	.|.	0.452778|.	0.26203|.	N|.	0.025738|.	T|T	0.28200|0.28200	0.0696|0.0696	L|L	0.27053|0.27053	0.805|0.805	0.09310|0.09310	N|N	1|1	B|B	0.18968|0.06786	0.032|0.001	B|B	0.19946|0.08055	0.027|0.003	T|T	0.18178|0.18178	-1.0345|-1.0345	10|7	0.28530|.	T|.	0.3|.	.|.	9.7205|9.7205	0.40300|0.40300	0.711:0.0:0.0:0.2889|0.711:0.0:0.0:0.2889	.|.	131|18	Q9GZU1|Q9GZU1-2	MCLN1_HUMAN|.	L|L	131|18	ENSP00000264079:H131L|.	ENSP00000264079:H131L|.	H|M	+|+	2|1	0|0	MCOLN1|MCOLN1	7497479|7497479	0.896000|0.896000	0.30565|0.30565	0.011000|0.011000	0.14972|0.14972	0.925000|0.925000	0.55904|0.55904	2.622000|2.622000	0.46427|0.46427	0.810000|0.810000	0.34279|0.34279	0.533000|0.533000	0.62120|0.62120	CAT|ATG	MCOLN1	-	NULL	ENSG00000090674		0.682	MCOLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MCOLN1	HGNC	protein_coding	OTTHUMT00000458974.2	78	0.00	0	A	NM_020533		7591479	7591479	+1	no_errors	ENST00000264079	ensembl	human	known	69_37n	missense	41	50.00	41	SNP	0.123	T
MEX3C	51320	genome.wustl.edu	37	18	48702727	48702727	+	5'Flank	SNP	G	G	A			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr18:48702727G>A	ENST00000591040.1	-	0	799							Q5U5Q3	MEX3C_HUMAN	mex-3 RNA binding family member C						chondrocyte hypertrophy (GO:0003415)|energy homeostasis (GO:0097009)|regulation of fat cell differentiation (GO:0045598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|skin(1)	17		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)		ATAGTTAAGAGTGAATTTGGA	0.383																																						dbGAP											0													49.0	47.0	48.0					18																	48702727		2203	4300	6503	-	-	-	SO:0001631	upstream_gene_variant	0			BC041122	CCDS11951.2	18q21.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000176624	ENSG00000176624		"""RING-type (C3HC4) zinc fingers"", ""Mex-3 homologs"""	28040	protein-coding gene	gene with protein product		611005	"""ring finger and KH domain containing 2"", ""mex-3 homolog C (C. elegans)"""	RKHD2		17267406	Standard	NM_016626		Approved	FLJ38871, RNF194	uc002lfc.4	Q5U5Q3	OTTHUMG00000132693		18.37:g.48702727G>A	Exception_encountered	Somatic		WXS	Illumina GAIIx	Phase_IV	A1L022|Q9NZE3	Silent	SNP	pfam_KH_dom_type_1,smart_KH_dom,smart_Znf_RING,pfscan_Znf_RING,pfscan_KH_dom_type_1	p.H658	ENST00000591040.1	37	c.1974		18																																																																																			MEX3C	-	NULL	ENSG00000176624		0.383	MEX3C-003	KNOWN	mRNA_end_NF|basic	processed_transcript	MEX3C	HGNC	protein_coding	OTTHUMT00000449559.1	26	0.00	0	G	NM_016626		48702727	48702727	-1	no_errors	ENST00000406189	ensembl	human	known	69_37n	silent	15	46.43	13	SNP	1.000	A
MSRB2	22921	genome.wustl.edu	37	10	23393167	23393167	+	Silent	SNP	G	G	A			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr10:23393167G>A	ENST00000376510.3	+	2	316	c.213G>A	c.(211-213)acG>acA	p.T71T		NM_012228.3	NP_036360.3	Q9Y3D2	MSRB2_HUMAN	methionine sulfoxide reductase B2	71					actin filament polymerization (GO:0030041)|protein repair (GO:0030091)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)	actin binding (GO:0003779)|peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	9					L-Methionine(DB00134)	AAAAGGGAACGGAACCGGTAA	0.507																																					Esophageal Squamous(89;1240 1363 4973 30188 42299)	dbGAP											0													75.0	73.0	74.0					10																	23393167		1954	4149	6103	-	-	-	SO:0001819	synonymous_variant	0			AF122004	CCDS41495.1	10p12	2004-12-07	2004-12-06	2004-12-07	ENSG00000148450	ENSG00000148450			17061	protein-coding gene	gene with protein product		613782	"""methionine sulfoxide reductase B"""	MSRB		8749308, 10375640	Standard	NM_012228		Approved	PILB, CGI-131, CBS1, CBS-1	uc001iro.3	Q9Y3D2	OTTHUMG00000017812	ENST00000376510.3:c.213G>A	10.37:g.23393167G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q17R44|Q4G1C7|Q9Y5W6	Missense_Mutation	SNP	pfam_Methionine_sulphoxide_MsrB,superfamily_Mss4-like	p.R32Q	ENST00000376510.3	37	c.95	CCDS41495.1	10																																																																																			MSRB2	-	pfam_Methionine_sulphoxide_MsrB,superfamily_Mss4-like	ENSG00000148450		0.507	MSRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MSRB2	HGNC	protein_coding	OTTHUMT00000047205.1	76	0.00	0	G	NM_012228		23393167	23393167	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000472663	ensembl	human	known	69_37n	missense	71	36.61	41	SNP	0.563	A
NHSL2	340527	genome.wustl.edu	37	X	71359229	71359229	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chrX:71359229C>T	ENST00000373677.1	+	2	1995	c.733C>T	c.(733-735)Cac>Tac	p.H245Y	NHSL2_ENST00000510661.1_Missense_Mutation_p.H380Y|NHSL2_ENST00000535692.1_Missense_Mutation_p.H245Y|NHSL2_ENST00000540800.1_Missense_Mutation_p.H611Y			Q5HYW2	NHSL2_HUMAN	NHS-like 2	245										NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					TCAAGGACATCACTCGTCCCA	0.527																																						dbGAP											0													125.0	92.0	103.0					X																	71359229		2203	4300	6503	-	-	-	SO:0001583	missense	0					Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.733C>T	X.37:g.71359229C>T	ENSP00000362781:p.His245Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RN94	Missense_Mutation	SNP	NULL	p.H611Y	ENST00000373677.1	37	c.1831		X	.	.	.	.	.	.	.	.	.	.	C	11.41	1.630536	0.28978	.	.	ENSG00000204131	ENST00000540800;ENST00000373677;ENST00000510661;ENST00000535692	T;T;T;T	0.44881	1.51;0.93;0.91;0.93	5.68	3.85	0.44370	.	0.760641	0.13027	N	0.419599	T	0.34454	0.0898	L	0.43152	1.355	0.21897	N	0.999484	B;B;B	0.32620	0.255;0.378;0.378	B;B;B	0.34931	0.145;0.192;0.192	T	0.17531	-1.0366	10	0.11794	T	0.64	-0.1107	11.1014	0.48177	0.4872:0.5128:0.0:0.0	.	611;380;245	F5H593;D6RBM4;Q5HYW2	.;.;NHSL2_HUMAN	Y	611;245;380;245	ENSP00000444617:H611Y;ENSP00000362781:H245Y;ENSP00000424079:H380Y;ENSP00000444914:H245Y	ENSP00000362781:H245Y	H	+	1	0	NHSL2	71275954	0.000000	0.05858	0.196000	0.23383	0.984000	0.73092	0.345000	0.19979	0.512000	0.28257	0.600000	0.82982	CAC	NHSL2	-	NULL	ENSG00000204131		0.527	NHSL2-001	KNOWN	basic	protein_coding	NHSL2	HGNC	protein_coding	OTTHUMT00000057170.1	81	0.00	0	C	NM_001013627		71359229	71359229	+1	no_errors	ENST00000540800	ensembl	human	known	69_37n	missense	75	38.02	46	SNP	0.410	T
NR5A2	2494	genome.wustl.edu	37	1	200012952	200012952	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr1:200012952C>T	ENST00000367362.3	+	3	499	c.253C>T	c.(253-255)Ctt>Ttt	p.L85F	NR5A2_ENST00000544748.1_Missense_Mutation_p.L13F|NR5A2_ENST00000236914.3_Missense_Mutation_p.L39F	NM_001276464.1|NM_205860.1	NP_001263393.1|NP_995582.1	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	85					bile acid metabolic process (GO:0008206)|cholesterol homeostasis (GO:0042632)|embryo development (GO:0009790)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|homeostatic process (GO:0042592)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral genome replication (GO:0045070)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31	Prostate(682;0.19)					TCTGGAAGAGCTTTGTCCCGT	0.373																																					Melanoma(179;1138 2773 15678 26136)	dbGAP											0													120.0	112.0	115.0					1																	200012952		2203	4300	6503	-	-	-	SO:0001583	missense	0			U93553	CCDS1400.1, CCDS1401.1, CCDS60383.1	1q32.11	2013-01-16			ENSG00000116833	ENSG00000116833		"""Nuclear hormone receptors"""	7984	protein-coding gene	gene with protein product	"""liver receptor homolog-1"""	604453		FTF		9858833, 7680097	Standard	NM_205860		Approved	FTZ-F1beta, hB1F, LRH-1, FTZ-F1, hB1F-2, B1F2	uc001gvb.4	O00482	OTTHUMG00000035635	ENST00000367362.3:c.253C>T	1.37:g.200012952C>T	ENSP00000356331:p.Leu85Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	B4E2P3|O95642|Q147U3	Missense_Mutation	SNP	pfam_Nucl_hrmn_rcpt_lig-bd_core,pfam_Znf_hrmn_rcpt,superfamily_Nucl_hormone_rcpt_ligand-bd,smart_Znf_hrmn_rcpt,smart_Nucl_hrmn_rcpt_lig-bd_core,pirsf_Steroidogenic_factor_1,pfscan_Znf_hrmn_rcpt,prints_Str_hrmn_rcpt,prints_Znf_hrmn_rcpt	p.L85F	ENST00000367362.3	37	c.253	CCDS1401.1	1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.413908	0.62511	.	.	ENSG00000116833	ENST00000367362;ENST00000236914;ENST00000544748;ENST00000235480	D;D;D	0.96651	-4.08;-4.08;-4.08	5.91	5.01	0.66863	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (3);	0.044997	0.85682	D	0.000000	D	0.96150	0.8745	L	0.55481	1.735	0.49915	D	0.999839	B;B	0.29188	0.236;0.14	B;P	0.47891	0.182;0.56	D	0.93707	0.7020	9	.	.	.	.	9.8057	0.40792	0.1392:0.7911:0.0:0.0697	.	39;85	F1D8R9;O00482	.;NR5A2_HUMAN	F	85;39;13;5	ENSP00000356331:L85F;ENSP00000236914:L39F;ENSP00000439116:L13F	.	L	+	1	0	NR5A2	198279575	1.000000	0.71417	0.990000	0.47175	0.977000	0.68977	4.509000	0.60448	1.517000	0.48917	0.650000	0.86243	CTT	NR5A2	-	pfam_Znf_hrmn_rcpt,smart_Znf_hrmn_rcpt,pirsf_Steroidogenic_factor_1,pfscan_Znf_hrmn_rcpt	ENSG00000116833		0.373	NR5A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NR5A2	HGNC	protein_coding	OTTHUMT00000086497.2	209	0.00	0	C			200012952	200012952	+1	no_errors	ENST00000367362	ensembl	human	known	69_37n	missense	218	33.84	112	SNP	1.000	T
NRXN2	9379	genome.wustl.edu	37	11	64435947	64435947	+	Missense_Mutation	SNP	C	C	T	rs557104010		TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr11:64435947C>T	ENST00000377551.1	-	7	1538	c.1327G>A	c.(1327-1329)Gtc>Atc	p.V443I	NRXN2_ENST00000377559.3_Missense_Mutation_p.V412I|NRXN2_ENST00000265459.6_Missense_Mutation_p.V443I|NRXN2_ENST00000409571.1_Missense_Mutation_p.V436I			Q9P2S2	NRX2A_HUMAN	neurexin 2	443	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						TTGTTGCTGACGGGCGAGCCC	0.592																																						dbGAP											0													73.0	66.0	69.0					11																	64435947		2201	4297	6498	-	-	-	SO:0001583	missense	0				CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"""neurexin II"""	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.1327G>A	11.37:g.64435947C>T	ENSP00000366774:p.Val443Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	pfam_Laminin_G,superfamily_ConA-like_lec_gl,smart_Laminin_G,smart_EGF-like,smart_Neurexin-like,pfscan_EG-like_dom,pfscan_Laminin_G	p.V443I	ENST00000377551.1	37	c.1327	CCDS8077.1	11	.	.	.	.	.	.	.	.	.	.	C	22.9	4.355260	0.82243	.	.	ENSG00000110076	ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571;ENST00000442300	T;T;T;T;T	0.79940	-1.32;-1.24;-1.32;-1.32;-1.32	4.78	4.78	0.61160	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.38217	U	0.001768	T	0.81725	0.4883	N	0.20357	0.565	0.53688	D	0.99997	D;P;D	0.67145	0.996;0.937;0.991	D;P;D	0.80764	0.994;0.497;0.959	T	0.81026	-0.1119	10	0.33940	T	0.23	.	15.3313	0.74215	0.0:1.0:0.0:0.0	.	412;443;189	Q9P2S2-2;Q9P2S2;E7EV67	.;NRX2A_HUMAN;.	I	443;412;443;412;436;199	ENSP00000366774:V443I;ENSP00000366782:V412I;ENSP00000265459:V443I;ENSP00000386416:V436I;ENSP00000388971:V199I	ENSP00000265459:V443I	V	-	1	0	NRXN2	64192523	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	5.883000	0.69721	2.462000	0.83206	0.555000	0.69702	GTC	NRXN2	-	pfam_Laminin_G,superfamily_ConA-like_lec_gl,smart_Laminin_G,pfscan_Laminin_G	ENSG00000110076		0.592	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NRXN2	HGNC	protein_coding	OTTHUMT00000104967.3	53	0.00	0	C	NM_015080		64435947	64435947	-1	no_errors	ENST00000265459	ensembl	human	known	69_37n	missense	49	38.75	31	SNP	1.000	T
OTOF	9381	genome.wustl.edu	37	2	26688892	26688892	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr2:26688892G>A	ENST00000272371.2	-	37	4679	c.4553C>T	c.(4552-4554)gCc>gTc	p.A1518V	OTOF_ENST00000402415.3_Missense_Mutation_p.A828V|OTOF_ENST00000338581.6_Missense_Mutation_p.A751V|OTOF_ENST00000403946.3_Missense_Mutation_p.A1518V|OTOF_ENST00000339598.3_Missense_Mutation_p.A751V	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1518	C2 4. {ECO:0000255|PROSITE- ProRule:PRU00041}.				membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAGCCGGATGGCGATGTAGGG	0.592																																					GBM(102;732 1451 20652 24062 31372)	dbGAP											0													242.0	190.0	208.0					2																	26688892		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.4553C>T	2.37:g.26688892G>A	ENSP00000272371:p.Ala1518Val	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	pfam_C2_Ca-dep,pfam_Ferlin_B-domain,pfam_FerIin-domain,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_C2_Ca-dep,pfscan_C2_membr_targeting	p.A1518V	ENST00000272371.2	37	c.4553	CCDS1725.1	2	.	.	.	.	.	.	.	.	.	.	G	6.999	0.554489	0.13374	.	.	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	5.58	4.71	0.59529	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.110704	0.64402	D	0.000005	T	0.23249	0.0562	N	0.00122	-2.065	0.37681	D	0.923479	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.09377	0.004;0.001;0.002;0.0	T	0.22661	-1.0210	10	0.10377	T	0.69	-20.778	8.8659	0.35286	0.2274:0.0:0.7726:0.0	.	1518;751;828;751	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	V	751;751;828;1518;1518	ENSP00000345137:A751V;ENSP00000344521:A751V;ENSP00000383906:A828V;ENSP00000272371:A1518V;ENSP00000385255:A1518V	ENSP00000272371:A1518V	A	-	2	0	OTOF	26542396	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.807000	0.55591	1.387000	0.46486	0.555000	0.69702	GCC	OTOF	-	pfam_C2_Ca-dep,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_C2_Ca-dep,pfscan_C2_membr_targeting	ENSG00000115155		0.592	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	OTOF	HGNC	protein_coding	OTTHUMT00000214047.3	360	0.00	0	G			26688892	26688892	-1	no_errors	ENST00000272371	ensembl	human	known	69_37n	missense	268	40.84	185	SNP	1.000	A
PAXIP1	22976	genome.wustl.edu	37	7	154752763	154752763	+	Missense_Mutation	SNP	T	T	A			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr7:154752763T>A	ENST00000404141.1	-	12	2428	c.2274A>T	c.(2272-2274)aaA>aaT	p.K758N	PAXIP1_ENST00000397192.1_Missense_Mutation_p.K758N|PAXIP1_ENST00000473219.1_5'UTR			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	758	BRCT 4. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Interaction with TP53BP1.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		ACTCTTTGGCTTTTTCATACT	0.388																																						dbGAP											0													80.0	76.0	77.0					7																	154752763		1864	4088	5952	-	-	-	SO:0001583	missense	0			U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"""PAX transcription activation domain interacting protein 1 like"""	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.2274A>T	7.37:g.154752763T>A	ENSP00000384048:p.Lys758Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	pfam_BRCT_dom,superfamily_BRCT_dom,smart_BRCT_dom,pfscan_BRCT_dom	p.K758N	ENST00000404141.1	37	c.2274	CCDS47753.1	7	.	.	.	.	.	.	.	.	.	.	T	18.13	3.556027	0.65425	.	.	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000357094;ENST00000323199	D;D	0.84146	-1.81;-1.81	5.51	-6.23	0.02052	BRCT (3);	0.000000	0.64402	U	0.000020	D	0.91503	0.7317	M	0.84433	2.695	0.39501	D	0.968208	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.998	D	0.90990	0.4834	10	0.72032	D	0.01	-36.2153	19.3202	0.94236	0.0:0.6848:0.0:0.3152	.	711;724;758	B4DEQ6;Q6ZW49-1;Q6ZW49	.;.;PAXI1_HUMAN	N	758;758;582;711	ENSP00000384048:K758N;ENSP00000380376:K758N	ENSP00000319149:K711N	K	-	3	2	PAXIP1	154383696	0.909000	0.30893	0.697000	0.30258	0.909000	0.53808	0.020000	0.13466	-1.153000	0.02829	-0.297000	0.09499	AAA	PAXIP1	-	pfam_BRCT_dom,superfamily_BRCT_dom,smart_BRCT_dom,pfscan_BRCT_dom	ENSG00000157212		0.388	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	PAXIP1	HGNC	protein_coding	OTTHUMT00000322223.1	199	0.00	0	T	NM_007349		154752763	154752763	-1	no_errors	ENST00000397192	ensembl	human	known	69_37n	missense	175	13.37	27	SNP	0.979	A
PCDHGA1	56114	genome.wustl.edu	37	5	140711179	140711179	+	Missense_Mutation	SNP	G	G	A	rs201338329		TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr5:140711179G>A	ENST00000517417.1	+	1	928	c.928G>A	c.(928-930)Gaa>Aaa	p.E310K	PCDHGA1_ENST00000378105.3_Missense_Mutation_p.E310K|AC005618.6_ENST00000606901.1_lincRNA	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	310	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(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTAGATTTCGAAGAATACAA	0.373																																						dbGAP											0													55.0	57.0	56.0					5																	140711179		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"""Cadherins / Protocadherins : Clustered"""	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.928G>A	5.37:g.140711179G>A	ENSP00000431083:p.Glu310Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2M273|Q9Y5D6	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.E310K	ENST00000517417.1	37	c.928	CCDS54922.1	5	.	.	.	.	.	.	.	.	.	.	G	24.5	4.542865	0.86022	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.72394	-0.65;-0.65	3.99	3.99	0.46301	Cadherin (4);Cadherin-like (1);	0.136800	0.32671	N	0.005784	D	0.90061	0.6896	H	0.98314	4.2	0.39624	D	0.970074	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.969	D	0.94618	0.7810	10	0.87932	D	0	.	16.2627	0.82553	0.0:0.0:1.0:0.0	.	310;310	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	K	310	ENSP00000431083:E310K;ENSP00000367345:E310K	ENSP00000367345:E310K	E	+	1	0	PCDHGA1	140691363	1.000000	0.71417	0.993000	0.49108	0.980000	0.70556	9.601000	0.98297	2.237000	0.73441	0.650000	0.86243	GAA	PCDHGA1	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000204956		0.373	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PCDHGA1	HGNC	protein_coding	OTTHUMT00000374737.1	46	0.00	0	G	NM_018912		140711179	140711179	+1	no_errors	ENST00000517417	ensembl	human	known	69_37n	missense	27	35.71	15	SNP	1.000	A
PIGA	5277	genome.wustl.edu	37	X	15339870	15339870	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chrX:15339870C>T	ENST00000333590.4	-	6	1297	c.1213G>A	c.(1213-1215)Gct>Act	p.A405T	PIGA_ENST00000542278.1_Missense_Mutation_p.A171T|PIGA_ENST00000482148.1_5'UTR|PIGA_ENST00000428964.1_Missense_Mutation_p.A90T	NM_002641.3	NP_002632.1	P37287	PIGA_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class A	405					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|positive regulation of metabolic process (GO:0009893)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)|UDP-glycosyltransferase activity (GO:0008194)			endometrium(2)|kidney(2)|large_intestine(2)|ovary(1)|prostate(2)|urinary_tract(1)	10	Hepatocellular(33;0.183)					GGCAACACAGCTTCCACTGAT	0.488																																						dbGAP											0													94.0	97.0	96.0					X																	15339870		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC038236	CCDS14165.1, CCDS48086.1, CCDS48086.2	Xp22.1	2014-09-17	2008-07-31		ENSG00000165195	ENSG00000165195	2.4.1.198	"""Glycosyltransferase group 1 domain containing"", ""Phosphatidylinositol glycan anchor biosynthesis"""	8957	protein-coding gene	gene with protein product	"""paroxysmal nocturnal hemoglobinuria"", ""phosphatidylinositol N-acetylglucosaminyltransferase"""	311770	"""phosphatidylinositol glycan, class A (paroxysmal nocturnal hemoglobinuria)"""			8500164	Standard	NM_002641		Approved	GPI3	uc004cwr.3	P37287	OTTHUMG00000021174	ENST00000333590.4:c.1213G>A	X.37:g.15339870C>T	ENSP00000369820:p.Ala405Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	B4E0V2|Q16025|Q16250	Missense_Mutation	SNP	pfam_PIGA_GPI_anchor_biosynthesis,pfam_Glyco_trans_1	p.A405T	ENST00000333590.4	37	c.1213	CCDS14165.1	X	.	.	.	.	.	.	.	.	.	.	C	9.489	1.100107	0.20552	.	.	ENSG00000165195	ENST00000542278;ENST00000333590;ENST00000428964	.	.	.	5.79	3.07	0.35406	.	0.575652	0.19554	N	0.111498	T	0.12817	0.0311	N	0.02011	-0.69	0.24630	N	0.993629	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.06405	0.001;0.002;0.001;0.0	T	0.27365	-1.0076	9	0.20519	T	0.43	-2.5323	7.195	0.25847	0.1387:0.7125:0.0:0.1489	.	171;236;405;405	B4E0V2;P37287-2;B2RCE0;P37287	.;.;.;PIGA_HUMAN	T	171;405;90	.	ENSP00000369820:A405T	A	-	1	0	PIGA	15249791	0.307000	0.24500	0.019000	0.16419	0.605000	0.37080	0.906000	0.28517	0.224000	0.20940	0.523000	0.50628	GCT	PIGA	-	NULL	ENSG00000165195		0.488	PIGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PIGA	HGNC	protein_coding	OTTHUMT00000055854.1	60	0.00	0	C	NM_002641		15339870	15339870	-1	no_errors	ENST00000333590	ensembl	human	known	69_37n	missense	57	43.00	43	SNP	0.876	T
PRICKLE3	4007	genome.wustl.edu	37	X	49040116	49040117	+	Intron	DEL	GT	GT	-			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	GT	GT					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chrX:49040116_49040117delGT	ENST00000376317.3	-	3	407				PRICKLE3_ENST00000536904.1_Frame_Shift_Del_p.T60fs|PRICKLE3_ENST00000538114.1_Frame_Shift_Del_p.T128fs|PRICKLE3_ENST00000376310.3_Intron|PRICKLE3_ENST00000540849.1_Intron	NM_006150.3	NP_006141.2	O43900	PRIC3_HUMAN	prickle homolog 3 (Drosophila)								zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|skin(2)	22						TCCCACCTGAGTGTGTGTGTGT	0.604																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			BC016856	CCDS14320.1	Xp11.23	2008-02-05	2007-09-18	2007-09-18	ENSG00000012211	ENSG00000012211			6645	protein-coding gene	gene with protein product		300111	"""LIM domain only 6"""	LMO6		9344658	Standard	XM_005272605		Approved		uc004dmy.1	O43900	OTTHUMG00000024134	ENST00000376317.3:c.312+69AC>-	X.37:g.49040126_49040127delGT		Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z8F2|O76007|Q53XR5	Frame_Shift_Del	DEL	pfam_Znf_LIM,pfam_PET_domain,smart_Znf_LIM,pfscan_Znf_LIM	p.T60fs	ENST00000376317.3	37	c.179_178	CCDS14320.1	X																																																																																			PRICKLE3	-	NULL	ENSG00000012211		0.604	PRICKLE3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PRICKLE3	HGNC	protein_coding	OTTHUMT00000060811.1	24	0.00	0	GT	NM_006150		49040116	49040117	-1	no_errors	ENST00000536904	ensembl	human	known	69_37n	frame_shift_del	21	16.00	4	DEL	0.149:0.119	-
PLS3	5358	genome.wustl.edu	37	X	114883857	114883857	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chrX:114883857G>A	ENST00000420625.2	+	16	2003	c.1869G>A	c.(1867-1869)atG>atA	p.M623I	PLS3_ENST00000537301.1_Missense_Mutation_p.M610I|PLS3_ENST00000289290.3_Missense_Mutation_p.M587I|PLS3_ENST00000355899.3_Missense_Mutation_p.M623I|PLS3_ENST00000543070.1_Missense_Mutation_p.M217I|PLS3_ENST00000539310.1_Missense_Mutation_p.M578I	NM_001136025.3|NM_001172335.1|NM_001282338.1	NP_001129497.1|NP_001165806.1|NP_001269267.1	P13797	PLST_HUMAN	plastin 3	623	Actin-binding 2.|CH 4. {ECO:0000255|PROSITE- ProRule:PRU00044}.				bone development (GO:0060348)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)	26						CATGTTTGATGGGCAGGGGAA	0.463																																					Colon(160;1047 1864 8490 12969 29601)	dbGAP											0													179.0	158.0	165.0					X																	114883857		2203	4300	6503	-	-	-	SO:0001583	missense	0			L05491	CCDS14568.1, CCDS65312.1	Xq23	2013-01-10	2010-02-10		ENSG00000102024	ENSG00000102024		"""EF-hand domain containing"""	9091	protein-coding gene	gene with protein product		300131	"""plastin 3 (T isoform)"""			8428952	Standard	NM_005032		Approved	T-plastin	uc004eqe.3	P13797	OTTHUMG00000022237	ENST00000420625.2:c.1869G>A	X.37:g.114883857G>A	ENSP00000398945:p.Met623Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K579|B1AQ09|B4DGB4|B7Z6M1|Q86YI6	Missense_Mutation	SNP	pfam_CH-domain,pfam_CAMSAP_CH,superfamily_CH-domain,smart_EF_hand_Ca-bd,smart_CH-domain,pfscan_CH-domain,pfscan_EF_HAND_2	p.M623I	ENST00000420625.2	37	c.1869	CCDS14568.1	X	.	.	.	.	.	.	.	.	.	.	g	24.9	4.581156	0.86748	.	.	ENSG00000102024	ENST00000355899;ENST00000537301;ENST00000289290;ENST00000420625;ENST00000539310;ENST00000543070	D;D;D;D;D;D	0.95724	-3.79;-3.79;-3.79;-3.79;-3.79;-3.79	5.87	5.87	0.94306	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.98086	0.9369	M	0.88775	2.98	0.80722	D	1	D;P;P	0.69078	0.997;0.863;0.863	D;P;P	0.83275	0.996;0.76;0.76	D	0.98839	1.0754	10	0.72032	D	0.01	-22.4669	17.6529	0.88170	0.0:0.0:1.0:0.0	.	596;610;623	B4DPW9;B4DGB4;P13797	.;.;PLST_HUMAN	I	623;610;587;623;578;217	ENSP00000348163:M623I;ENSP00000445105:M610I;ENSP00000289290:M587I;ENSP00000398945:M623I;ENSP00000445339:M578I;ENSP00000439260:M217I	ENSP00000289290:M587I	M	+	3	0	PLS3	114790113	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.678000	0.98647	2.491000	0.84063	0.591000	0.81541	ATG	PLS3	-	pfam_CH-domain,superfamily_CH-domain,smart_CH-domain,pfscan_CH-domain	ENSG00000102024		0.463	PLS3-201	KNOWN	basic|CCDS	protein_coding	PLS3	HGNC	protein_coding	OTTHUMT00000057976.2	146	0.00	0	G			114883857	114883857	+1	no_errors	ENST00000355899	ensembl	human	known	69_37n	missense	119	24.20	38	SNP	1.000	A
RALGPS2	55103	genome.wustl.edu	37	1	178780488	178780488	+	Silent	SNP	A	A	G			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr1:178780488A>G	ENST00000367635.3	+	6	674	c.336A>G	c.(334-336)caA>caG	p.Q112Q	RALGPS2_ENST00000367634.2_Silent_p.Q112Q	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	112	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						TTCATGCTCAAACATTAAAAA	0.259																																						dbGAP											0													60.0	70.0	67.0					1																	178780488		2201	4283	6484	-	-	-	SO:0001819	synonymous_variant	0			AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"""Pleckstrin homology (PH) domain containing"""	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.336A>G	1.37:g.178780488A>G		Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Silent	SNP	pfam_RasGRF_CDC25,superfamily_Ras_GEF_dom,smart_RasGRF_CDC25,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology,pfscan_RasGRF_CDC25	p.Q112	ENST00000367635.3	37	c.336	CCDS1325.1	1																																																																																			RALGPS2	-	pfam_RasGRF_CDC25,superfamily_Ras_GEF_dom,smart_RasGRF_CDC25,pfscan_RasGRF_CDC25	ENSG00000116191		0.259	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	RALGPS2	HGNC	protein_coding	OTTHUMT00000084926.2	41	0.00	0	A	NM_152663		178780488	178780488	+1	no_errors	ENST00000367635	ensembl	human	known	69_37n	silent	48	54.29	57	SNP	0.991	G
TG	7038	genome.wustl.edu	37	8	133948004	133948004	+	Nonsense_Mutation	SNP	C	C	T	rs555316512		TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr8:133948004C>T	ENST00000220616.4	+	25	4976	c.4936C>T	c.(4936-4938)Cga>Tga	p.R1646*	TG_ENST00000377869.1_Nonsense_Mutation_p.R1589*|TG_ENST00000542445.1_Nonsense_Mutation_p.R80*	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1646					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		TCTCCAGAAACGAGATGCACT	0.463													C|||	1	0.000199681	0.0	0.0	5008	,	,		21117	0.001		0.0	False		,,,				2504	0.0					dbGAP											0													86.0	77.0	80.0					8																	133948004		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.4936C>T	8.37:g.133948004C>T	ENSP00000220616:p.Arg1646*	Somatic		WXS	Illumina GAIIx	Phase_IV	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Nonsense_Mutation	SNP	pfam_Thyroglobulin_1,pfam_CarbesteraseB,pfam_Tyr-kin_ephrin_A/B_rcpt-like,superfamily_Thyroglobulin_1,smart_Thyroglobulin_1,pirsf_Thyroglobulin,pfscan_Thyroglobulin_1	p.R1646*	ENST00000220616.4	37	c.4936	CCDS34944.1	8	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	42|42	9.247169|9.247169	0.99113|0.99113	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445|ENST00000519178	.|.	.|.	.|.	6.16|6.16	3.38|3.38	0.38709|0.38709	.|.	0.512916|.	0.19833|.	N|.	0.105045|.	.|T	.|0.65647	.|0.2711	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69815	.|-0.5043	.|3	0.48119|.	T|.	0.1|.	.|.	15.0189|15.0189	0.71613|0.71613	0.0:0.5099:0.4901:0.0|0.0:0.5099:0.4901:0.0	.|.	.|.	.|.	.|.	X|M	1589;452;1646;80|165	.|.	ENSP00000220616:R1646X|.	R|T	+|+	1|2	2|0	TG|TG	134017186|134017186	0.009000|0.009000	0.17119|0.17119	0.001000|0.001000	0.08648|0.08648	0.014000|0.014000	0.08584|0.08584	0.619000|0.619000	0.24388|0.24388	0.444000|0.444000	0.26612|0.26612	0.650000|0.650000	0.86243|0.86243	CGA|ACG	TG	-	pirsf_Thyroglobulin	ENSG00000042832		0.463	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TG	HGNC	protein_coding	OTTHUMT00000379606.1	96	0.00	0	C	NM_003235		133948004	133948004	+1	no_errors	ENST00000220616	ensembl	human	known	69_37n	nonsense	69	38.39	43	SNP	0.004	T
TTN	7273	genome.wustl.edu	37	2	179650417	179650417	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr2:179650417C>T	ENST00000591111.1	-	15	2647	c.2423G>A	c.(2422-2424)cGc>cAc	p.R808H	TTN_ENST00000359218.5_Missense_Mutation_p.R762H|TTN_ENST00000460472.2_Missense_Mutation_p.R762H|TTN_ENST00000342992.6_Missense_Mutation_p.R808H|TTN_ENST00000589042.1_Missense_Mutation_p.R808H|TTN_ENST00000360870.5_Missense_Mutation_p.R808H|TTN_ENST00000342175.6_Missense_Mutation_p.R762H			Q8WZ42	TITIN_HUMAN	titin	33639					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTGCGGGGGCGTTTATCCAC	0.398																																						dbGAP											0													209.0	200.0	203.0					2																	179650417		2203	4300	6503	-	-	-	SO:0001583	missense	0			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.2423G>A	2.37:g.179650417C>T	ENSP00000465570:p.Arg808His	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	pfam_Ig_I-set,pfam_Fibronectin_type3,pfam_Immunoglobulin,pfam_Ig_V-set,pfam_Titin_Z,pfam_PPAK_motif,pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,superfamily_Calpain_domain_III,superfamily_RNaseH-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_Prot_kinase_cat_dom,pfscan_Ig-like	p.R808H	ENST00000591111.1	37	c.2423		2	.	.	.	.	.	.	.	.	.	.	C	14.12	2.441191	0.43326	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.63913	-0.07;0.18;0.17;0.16;0.26	5.51	5.51	0.81932	Ribonuclease H-like (1);	.	.	.	.	T	0.46444	0.1393	N	0.17082	0.46	0.25491	N	0.987642	B;B;B;B;P	0.38110	0.032;0.032;0.032;0.032;0.618	B;B;B;B;B	0.33521	0.007;0.007;0.007;0.007;0.165	T	0.49532	-0.8930	9	0.87932	D	0	.	13.0533	0.58966	0.0:0.9263:0.0:0.0737	.	762;762;762;808;808	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	H	808;762;762;762;762;808	ENSP00000343764:R808H;ENSP00000434586:R762H;ENSP00000340554:R762H;ENSP00000352154:R762H;ENSP00000354117:R808H	ENSP00000340554:R762H	R	-	2	0	TTN	179358662	0.995000	0.38212	1.000000	0.80357	0.998000	0.95712	2.800000	0.47900	2.738000	0.93877	0.655000	0.94253	CGC	TTN	-	superfamily_RNaseH-like_dom	ENSG00000155657		0.398	TTN-019	PUTATIVE	basic	protein_coding	TTN	HGNC	protein_coding	OTTHUMT00000460310.1	300	0.00	0	C	NM_133378		179650417	179650417	-1	no_errors	ENST00000342992	ensembl	human	known	69_37n	missense	221	35.19	120	SNP	1.000	T
USP40	55230	genome.wustl.edu	37	2	234428319	234428319	+	Splice_Site	SNP	T	T	C			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr2:234428319T>C	ENST00000427112.2	-	17	2358		c.e17-2		USP40_ENST00000251722.6_Splice_Site|USP40_ENST00000450966.1_Splice_Site			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40						ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		AAACACCATCTAAAACAGAGA	0.274																																						dbGAP											0													25.0	22.0	23.0					2																	234428319		1703	3861	5564	-	-	-	SO:0001630	splice_region_variant	0			AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.2323-2A>G	2.37:g.234428319T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q6NX38|Q70EL0	Splice_Site	SNP	-	e17-2	ENST00000427112.2	37	c.2359-2	CCDS46547.1	2	.	.	.	.	.	.	.	.	.	.	T	15.47	2.842279	0.51057	.	.	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112;ENST00000452724	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2271	0.59921	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	USP40	234093058	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	4.337000	0.59310	2.105000	0.64084	0.383000	0.25322	.	USP40	-	-	ENSG00000085982		0.274	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	USP40	HGNC	protein_coding	OTTHUMT00000397235.1	96	0.00	0	T	XM_114294	Intron	234428319	234428319	-1	no_errors	ENST00000450966	ensembl	human	known	69_37n	splice_site	70	39.66	46	SNP	1.000	C
ZCCHC2	54877	genome.wustl.edu	37	18	60191460	60191460	+	Missense_Mutation	SNP	T	T	A			TCGA-E2-A10E-01A-21D-A10M-09	TCGA-E2-A10E-10A-01D-A10M-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	1bb66f02-3977-4ab2-8800-beb75513385b	d81fe1bd-0628-4d43-bcd3-81ac3e939331	g.chr18:60191460T>A	ENST00000269499.5	+	1	1221	c.803T>A	c.(802-804)cTg>cAg	p.L268Q		NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	268						cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25						ATGGCCTCGCTGCACCCGGCT	0.721																																						dbGAP											0													15.0	21.0	19.0					18																	60191460		692	1591	2283	-	-	-	SO:0001583	missense	0			AB051531	CCDS45880.1	18q21.33	2012-04-19			ENSG00000141664	ENSG00000141664		"""Zinc fingers, CCHC domain containing"""	22916	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 49"""	C18orf49		11214970	Standard	NM_017742		Approved	FLJ20281, KIAA1744, FLJ20222	uc002lip.4	Q9C0B9		ENST00000269499.5:c.803T>A	18.37:g.60191460T>A	ENSP00000269499:p.Leu268Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RPG6|Q8N3S1|Q9NXF6	Missense_Mutation	SNP	pfam_Znf_CCHC,superfamily_Phox,superfamily_Znf_CCHC,smart_Znf_CCHC,pfscan_Znf_CCHC	p.L268Q	ENST00000269499.5	37	c.803	CCDS45880.1	18	.	.	.	.	.	.	.	.	.	.	T	16.60	3.167770	0.57476	.	.	ENSG00000141664	ENST00000269499	T	0.04360	3.64	4.0	4.0	0.46444	.	.	.	.	.	T	0.13927	0.0337	L	0.50333	1.59	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.10613	-1.0622	9	0.22706	T	0.39	.	12.9236	0.58247	0.0:0.0:0.0:1.0	.	268	Q9C0B9	ZCHC2_HUMAN	Q	268	ENSP00000269499:L268Q	ENSP00000269499:L268Q	L	+	2	0	ZCCHC2	58342440	1.000000	0.71417	0.996000	0.52242	0.729000	0.41735	2.322000	0.43814	1.437000	0.47472	0.448000	0.29417	CTG	ZCCHC2	-	NULL	ENSG00000141664		0.721	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	ZCCHC2	HGNC	protein_coding	OTTHUMT00000450083.1	11	0.00	0	T	NM_017742		60191460	60191460	+1	no_errors	ENST00000269499	ensembl	human	known	69_37n	missense	8	42.86	6	SNP	0.998	A
