#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ASPM	259266	genome.wustl.edu	37	1	197059075	197059075	+	Silent	SNP	C	C	T			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr1:197059075C>T	ENST00000367409.4	-	25	10225	c.9969G>A	c.(9967-9969)ttG>ttA	p.L3323L	ASPM_ENST00000294732.7_Silent_p.L1738L|ASPM_ENST00000367408.1_Silent_p.L988L	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	3323					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.L3323L(1)		breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						ATACATTAAGCAAGACTTGCA	0.363																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											64.0	68.0	67.0					1																	197059075		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.9969G>A	1.37:g.197059075C>T			Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	pfam_IQ_motif_EF-hand-BS,pfam_CAMSAP_CH,pfam_CH-domain,superfamily_CH-domain,superfamily_ARM-type_fold,smart_CH-domain,smart_IQ_motif_EF-hand-BS,pfscan_CH-domain,pfscan_IQ_motif_EF-hand-BS	p.L3323	ENST00000367409.4	37	c.9969	CCDS1389.1	1																																																																																			ASPM	-	superfamily_ARM-type_fold	ENSG00000066279		0.363	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ASPM	HGNC	protein_coding	OTTHUMT00000088256.1	74	0.00	0	C	NM_018136		197059075	197059075	-1	no_errors	ENST00000367409	ensembl	human	known	69_37n	silent	77	42.11	56	SNP	1.000	T
BTNL9	153579	genome.wustl.edu	37	5	180486582	180486582	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr5:180486582G>A	ENST00000327705.9	+	11	1559	c.1328G>A	c.(1327-1329)cGc>cAc	p.R443H	BTNL9_ENST00000376842.3_Missense_Mutation_p.R444H	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	443	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					integral component of membrane (GO:0016021)		p.R443H(1)		breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-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)			CTCACCCTGCGCGTGCCCCCG	0.701																																						dbGAP											1	Substitution - Missense(1)	breast(1)											29.0	30.0	30.0					5																	180486582		2200	4296	6496	-	-	-	SO:0001583	missense	0			AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.1328G>A	5.37:g.180486582G>A	ENSP00000330200:p.Arg443His		A6NL42|Q6P660|Q96DM5	Missense_Mutation	SNP	pfam_SPRY_rcpt,pfam_Ig_V-set,superfamily_ConA-like_lec_gl,smart_Ig_sub,smart_Ig_V-set_subgr,smart_PRY,smart_SPla/RYanodine_receptor_subgr,prints_Butyrophylin,pfscan_B30.2/SPRY,pfscan_Ig-like	p.R444H	ENST00000327705.9	37	c.1331	CCDS4460.2	5	.	.	.	.	.	.	.	.	.	.	g	10.11	1.259176	0.23051	.	.	ENSG00000165810	ENST00000327705;ENST00000376842	T;T	0.69306	-0.39;-0.39	4.43	3.48	0.39840	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.66257	0.2771	M	0.70842	2.15	0.09310	N	1	B	0.17465	0.022	B	0.24269	0.052	T	0.60250	-0.7300	9	0.51188	T	0.08	.	11.8533	0.52423	0.0:0.1784:0.8216:0.0	.	443	Q6UXG8	BTNL9_HUMAN	H	443;444	ENSP00000330200:R443H;ENSP00000366038:R444H	ENSP00000330200:R443H	R	+	2	0	BTNL9	180419188	0.000000	0.05858	0.833000	0.33012	0.059000	0.15707	0.415000	0.21181	2.211000	0.71520	0.449000	0.29647	CGC	BTNL9	-	pfam_SPRY_rcpt,superfamily_ConA-like_lec_gl,smart_SPla/RYanodine_receptor_subgr,prints_Butyrophylin,pfscan_B30.2/SPRY	ENSG00000165810		0.701	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	BTNL9	HGNC	protein_coding	OTTHUMT00000157342.3	16	0.00	0	G	NM_152547		180486582	180486582	+1	no_errors	ENST00000376842	ensembl	human	known	69_37n	missense	17	29.17	7	SNP	0.001	A
CASC1	55259	genome.wustl.edu	37	12	25307302	25307302	+	Missense_Mutation	SNP	G	G	T			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr12:25307302G>T	ENST00000320267.9	-	5	452	c.371C>A	c.(370-372)aCa>aAa	p.T124K	CASC1_ENST00000537577.1_Missense_Mutation_p.T12K|CASC1_ENST00000354189.5_Missense_Mutation_p.T188K|CASC1_ENST00000395990.2_Missense_Mutation_p.T84K|CASC1_ENST00000557684.1_5'UTR|CASC1_ENST00000545133.1_Missense_Mutation_p.T65K|CASC1_ENST00000395987.3_Missense_Mutation_p.T130K	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1	124								p.T188K(1)|p.T130K(1)		breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(3)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Melanoma(3;0.0301)|Colorectal(261;0.11)		OV - Ovarian serous cystadenocarcinoma(3;7.42e-20)|Epithelial(3;7.58e-16)|all cancers(3;1.07e-13)			AGTCTCATTTGTTTTCTCTTT	0.353																																						dbGAP											2	Substitution - Missense(2)	breast(2)											174.0	158.0	163.0					12																	25307302		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK093102	CCDS31759.2, CCDS41762.1, CCDS41763.1, CCDS55810.1, CCDS55811.1	12p12.1	2012-04-17			ENSG00000118307	ENSG00000118307		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 54"""					14583591	Standard	NM_018272		Approved	LAS1, FLJ10921, PPP1R54	uc001rgk.3	Q6TDU7	OTTHUMG00000150195	ENST00000320267.9:c.371C>A	12.37:g.25307302G>T	ENSP00000313141:p.Thr124Lys		B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Missense_Mutation	SNP	pfam_Casc1_domain,prints_Casc1	p.T130K	ENST00000320267.9	37	c.389	CCDS41762.1	12	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.278|9.278	1.047374|1.047374	0.19827|0.19827	.|.	.|.	ENSG00000118307|ENSG00000118307	ENST00000556006|ENST00000354189;ENST00000395987;ENST00000320267;ENST00000395990;ENST00000537577;ENST00000395992;ENST00000545133;ENST00000554347	.|T;T;T;T;T;T;T	.|0.30981	.|2.59;2.59;2.59;2.59;1.51;2.59;2.59	5.27|5.27	2.23|2.23	0.28157|0.28157	.|.	.|0.508674	.|0.21729	.|N	.|0.069988	T|T	0.11367|0.11367	0.0277|0.0277	N|N	0.11201|0.11201	0.11|0.11	0.22620|0.22620	N|N	0.998927|0.998927	.|B;B;B;B;B	.|0.28350	.|0.021;0.021;0.208;0.024;0.084	.|B;B;B;B;B	.|0.22152	.|0.022;0.022;0.038;0.007;0.022	T|T	0.29488|0.29488	-1.0010|-1.0010	5|10	.|0.07482	.|T	.|0.82	-11.6219|-11.6219	6.0717|6.0717	0.19893|0.19893	0.0895:0.0:0.5693:0.3412|0.0895:0.0:0.5693:0.3412	.|.	.|12;65;188;124;130	.|F5H555;F5H6T6;Q6TDU7-3;Q6TDU7;F8W8F9	.|.;.;.;CASC1_HUMAN;.	K|K	99|188;130;124;84;12;130;65;84	.|ENSP00000346126:T188K;ENSP00000379310:T130K;ENSP00000313141:T124K;ENSP00000379313:T84K;ENSP00000444715:T12K;ENSP00000437373:T65K;ENSP00000451232:T84K	.|ENSP00000313141:T124K	N|T	-|-	3|2	2|0	CASC1|CASC1	25198569|25198569	0.996000|0.996000	0.38824|0.38824	0.939000|0.939000	0.37840|0.37840	0.979000|0.979000	0.70002|0.70002	0.113000|0.113000	0.15499|0.15499	0.740000|0.740000	0.32651|0.32651	0.643000|0.643000	0.83706|0.83706	AAC|ACA	CASC1	-	NULL	ENSG00000118307		0.353	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	CASC1	HGNC	protein_coding	OTTHUMT00000316761.1	316	0.00	0	G	NM_018272		25307302	25307302	-1	no_errors	ENST00000395987	ensembl	human	known	69_37n	missense	245	35.01	132	SNP	0.791	T
CBFB	865	genome.wustl.edu	37	16	67100598	67100598	+	Missense_Mutation	SNP	C	C	T			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr16:67100598C>T	ENST00000290858.6	+	4	557	c.296C>T	c.(295-297)gCt>gTt	p.A99V	CBFB_ENST00000412916.2_Missense_Mutation_p.A99V|CBFB_ENST00000561924.2_5'UTR	NM_001755.2|NM_022845.2	NP_001746.1|NP_074036.1	Q13951	PEBB_HUMAN	core-binding factor, beta subunit	99					cell maturation (GO:0048469)|definitive hemopoiesis (GO:0060216)|lymphocyte differentiation (GO:0030098)|myeloid cell differentiation (GO:0030099)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.A99V(1)		breast(3)|large_intestine(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066)		TATTTGAAGGCTCCCATGATT	0.383			T	MYH11	AML																																	dbGAP		Dom	yes		16	16q22	865	"""core-binding factor, beta subunit"""		L	1	Substitution - Missense(1)	breast(1)											140.0	128.0	132.0					16																	67100598		2200	4300	6500	-	-	-	SO:0001583	missense	0			BC018509	CCDS10827.1, CCDS45508.1	16q22.1	2008-02-05			ENSG00000067955	ENSG00000067955			1539	protein-coding gene	gene with protein product		121360				8351518, 7587111	Standard	NM_001755		Approved	PEBP2B	uc002erb.3	Q13951	OTTHUMG00000137520	ENST00000290858.6:c.296C>T	16.37:g.67100598C>T	ENSP00000290858:p.Ala99Val		A8K347|Q13124|Q9HCT2	Missense_Mutation	SNP	pfam_CBF_beta,superfamily_CBF_beta	p.A99V	ENST00000290858.6	37	c.296	CCDS10827.1	16	.	.	.	.	.	.	.	.	.	.	C	31	5.091162	0.94149	.	.	ENSG00000067955	ENST00000290858;ENST00000412916	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.74481	0.3722	L	0.45581	1.43	0.80722	D	1	D;D	0.65815	0.994;0.995	D;D	0.74023	0.97;0.982	T	0.74061	-0.3786	9	0.51188	T	0.08	-2.409	18.1601	0.89705	0.0:1.0:0.0:0.0	.	99;99	Q13951-2;Q13951	.;PEBB_HUMAN	V	99	.	ENSP00000290858:A99V	A	+	2	0	CBFB	65658099	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.597000	0.82733	2.648000	0.89879	0.561000	0.74099	GCT	CBFB	-	pfam_CBF_beta,superfamily_CBF_beta	ENSG00000067955		0.383	CBFB-001	KNOWN	basic|CCDS	protein_coding	CBFB	HGNC	protein_coding	OTTHUMT00000268843.2	421	0.00	0	C	NM_001755		67100598	67100598	+1	no_errors	ENST00000290858	ensembl	human	known	69_37n	missense	112	63.55	197	SNP	1.000	T
CCNB3	85417	genome.wustl.edu	37	X	50094618	50094618	+	Missense_Mutation	SNP	A	A	T			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chrX:50094618A>T	ENST00000376042.1	+	13	4402	c.4104A>T	c.(4102-4104)gaA>gaT	p.E1368D	CCNB3_ENST00000348603.2_Missense_Mutation_p.E264D|CCNB3_ENST00000376038.1_Missense_Mutation_p.E264D|CCNB3_ENST00000276014.7_Missense_Mutation_p.E1368D			Q8WWL7	CCNB3_HUMAN	cyclin B3	1368					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)		p.E1368D(2)		breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					TCTTCTTTGAAGTCGCCAAAA	0.488																																						dbGAP											2	Substitution - Missense(2)	breast(2)											115.0	98.0	104.0					X																	50094618		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.4104A>T	X.37:g.50094618A>T	ENSP00000365210:p.Glu1368Asp		B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	pfam_Cyclin_N,pfam_Cyclin_C,superfamily_Cyclin-like,smart_Cyclin-like	p.E1368D	ENST00000376042.1	37	c.4104	CCDS14331.1	X	.	.	.	.	.	.	.	.	.	.	A	14.32	2.500283	0.44455	.	.	ENSG00000147082	ENST00000376042;ENST00000376038;ENST00000348603;ENST00000276014	T;T;T;T	0.23950	1.88;1.88;1.88;1.88	5.17	3.96	0.45880	Cyclin, C-terminal (1);Cyclin-like (2);	0.154293	0.56097	D	0.000029	T	0.44829	0.1312	M	0.80183	2.485	0.47621	D	0.999474	P;P;P	0.50156	0.932;0.929;0.932	P;P;P	0.61201	0.795;0.614;0.885	T	0.32640	-0.9899	9	.	.	.	.	5.8732	0.18814	0.7425:0.1672:0.0902:0.0	.	1368;264;1368	A8K8T9;Q8WWL7-2;Q8WWL7	.;.;CCNB3_HUMAN	D	1368;264;264;1368	ENSP00000365210:E1368D;ENSP00000365206:E264D;ENSP00000338682:E264D;ENSP00000276014:E1368D	.	E	+	3	2	CCNB3	50111358	1.000000	0.71417	0.789000	0.31954	0.139000	0.21198	1.291000	0.33330	0.680000	0.31366	0.430000	0.28490	GAA	CCNB3	-	pfam_Cyclin_C,superfamily_Cyclin-like	ENSG00000147082		0.488	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CCNB3	HGNC	protein_coding	OTTHUMT00000056558.1	290	0.00	0	A			50094618	50094618	+1	no_errors	ENST00000276014	ensembl	human	known	69_37n	missense	227	42.39	167	SNP	1.000	T
CEP170	9859	genome.wustl.edu	37	1	243289876	243289876	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr1:243289876G>A	ENST00000366542.1	-	20	4681	c.4630C>T	c.(4630-4632)Ctt>Ttt	p.L1544F	CEP170_ENST00000481987.1_Missense_Mutation_p.L280F|CEP170_ENST00000468254.1_5'UTR|CEP170_ENST00000490813.1_Missense_Mutation_p.L253F|CEP170_ENST00000366543.1_Missense_Mutation_p.L1420F|CEP170_ENST00000366544.1_Missense_Mutation_p.L1446F	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	1544	Targeting to centrosomes.|Targeting to microtubules.					centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)		p.L1544F(1)		NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			GCAGGATGAAGAGCCCTAGCT	0.498																																						dbGAP											1	Substitution - Missense(1)	breast(1)											14.0	13.0	13.0					1																	243289876		1814	4039	5853	-	-	-	SO:0001583	missense	0			AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.4630C>T	1.37:g.243289876G>A	ENSP00000355500:p.Leu1544Phe		O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	pfam_FHA_dom,superfamily_SMAD_FHA_domain,superfamily_Fibronectin_type3,smart_FHA_dom,pfscan_FHA_dom	p.L1544F	ENST00000366542.1	37	c.4630	CCDS44339.1	1	.	.	.	.	.	.	.	.	.	.	G	14.06	2.423412	0.43020	.	.	ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543;ENST00000481987;ENST00000490813	T;T;T	0.46819	0.88;0.87;0.86	4.84	4.84	0.62591	.	0.377687	0.23411	N	0.048465	T	0.31136	0.0787	N	0.08118	0	0.28187	N	0.927916	B;B;B	0.26081	0.141;0.141;0.108	B;B;B	0.31547	0.132;0.132;0.122	T	0.32428	-0.9907	10	0.52906	T	0.07	-4.5608	12.961	0.58458	0.0:0.1623:0.8377:0.0	.	1446;1420;1544	Q5SW79-3;Q5SW79-2;Q5SW79	.;.;CE170_HUMAN	F	1544;1446;1420;280;253	ENSP00000355500:L1544F;ENSP00000355502:L1446F;ENSP00000355501:L1420F	ENSP00000355500:L1544F	L	-	1	0	CEP170	241356499	0.003000	0.15002	1.000000	0.80357	0.932000	0.56968	0.337000	0.19841	2.403000	0.81681	0.455000	0.32223	CTT	CEP170	-	NULL	ENSG00000143702		0.498	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	CEP170	HGNC	protein_coding	OTTHUMT00000096178.2	70	0.00	0	G	NM_014812		243289876	243289876	-1	no_errors	ENST00000366542	ensembl	human	known	69_37n	missense	90	19.64	22	SNP	0.998	A
MT-ND2	4536	genome.wustl.edu	37	M	2499	2499	+	5'Flank	SNP	T	T	C			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chrM:2499T>C	ENST00000361453.3	+	0	0				MT-TM_ENST00000387377.1_RNA|MT-ND1_ENST00000361390.2_5'Flank|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TF_ENST00000387314.1_RNA|MT-TV_ENST00000387342.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TQ_ENST00000387372.1_RNA			P03891	NU2M_HUMAN	mitochondrially encoded NADH dehydrogenase 2						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|lung(1)	3						ACCCCGCCTGTTTACCAAAAA	0.478																																						dbGAP											0																																										-	-	-	SO:0001631	upstream_gene_variant	0					mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198763	ENSG00000198763	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7456	protein-coding gene	gene with protein product	"""complex I ND2 subunit"", ""NADH-ubiquinone oxidoreductase chain 2"""	516001	"""NADH dehydrogenase 2"""	MTND2			Standard			Approved	ND2, NAD2		P03891			M.37:g.2499T>C	Exception_encountered		Q34769|Q9TGI0|Q9TGI1|Q9TGI2|Q9TGI3|Q9TGI4	RNA	SNP	-	NULL	ENST00000361453.3	37	NULL		MT																																																																																			J01415.4	-	-	ENSG00000210082		0.478	MT-ND2-201	KNOWN	basic|appris_principal	protein_coding	ENSG00000210082	Clone_based_ensembl_gene	protein_coding		154	0.00	0	T	YP_003024027		2499	2499	+1	no_errors	ENST00000387347	ensembl	human	known	69_37n	rna	108	20.59	28	SNP	NULL	C
EVI5	7813	genome.wustl.edu	37	1	93131496	93131496	+	Splice_Site	DEL	T	T	-			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr1:93131496delT	ENST00000370331.1	-	11	1353	c.1344delA	c.(1342-1344)aaa>aa	p.K448fs	EVI5_ENST00000543509.1_Splice_Site_p.K448fs|EVI5_ENST00000540033.1_Splice_Site_p.K448fs|EVI5_ENST00000491940.1_5'UTR	NM_005665.4	NP_005656.4	O60447	EVI5_HUMAN	ecotropic viral integration site 5	448	Dimerization.|Interaction with alpha-tubulin, gamma- tubulin, BIRC5 and FBXO5.|Targeting to the centrosomes.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|retrograde transport, endosome to Golgi (GO:0042147)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|skin(1)	38		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		ACTTACTTACTTTTTCTAATG	0.333																																						dbGAP											0													125.0	122.0	123.0					1																	93131496		2203	4298	6501	-	-	-	SO:0001630	splice_region_variant	0			AF008915	CCDS30774.1	1p22	2013-07-09			ENSG00000067208	ENSG00000067208			3501	protein-coding gene	gene with protein product	"""neuroblastoma stage 4S gene"""	602942				9618176	Standard	XM_005271180		Approved	NB4S	uc001dox.3	O60447	OTTHUMG00000010895	ENST00000370331.1:c.1344+1A>-	1.37:g.93131496delT			A6NKX8|B9A6J0|Q9H1Y9	Frame_Shift_Del	DEL	pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Rab-GTPase-TBC_dom,pfscan_Rab-GTPase-TBC_dom	p.E449fs	ENST00000370331.1	37	c.1344	CCDS30774.1	1																																																																																			EVI5	-	NULL	ENSG00000067208		0.333	EVI5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EVI5	HGNC	protein_coding	OTTHUMT00000030047.1	398	0.00	0	T	NM_005665	Frame_Shift_Del	93131496	93131496	-1	no_errors	ENST00000543509	ensembl	human	known	69_37n	frame_shift_del	276	36.77	164	DEL	1.000	-
FBXW12	285231	genome.wustl.edu	37	3	48416853	48416853	+	Missense_Mutation	SNP	C	C	T	rs148596796		TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr3:48416853C>T	ENST00000296438.5	+	5	482	c.296C>T	c.(295-297)aCg>aTg	p.T99M	FBXW12_ENST00000436231.1_5'UTR|FBXW12_ENST00000415155.1_Missense_Mutation_p.T99M|FBXW12_ENST00000445170.1_Missense_Mutation_p.T80M	NM_207102.2	NP_996985.2	Q6X9E4	FBW12_HUMAN	F-box and WD repeat domain containing 12	99								p.T99M(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GCATTTGAGACGGAGTTGGCT	0.388													C|||	1	0.000199681	0.0	0.0	5008	,	,		19994	0.0		0.001	False		,,,				2504	0.0					dbGAP											1	Substitution - Missense(1)	breast(1)											112.0	106.0	108.0					3																	48416853		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK097594, AY247969	CCDS2764.1, CCDS54577.1, CCDS54578.1	3p21.31	2011-07-01	2007-02-08	2004-07-21	ENSG00000164049	ENSG00000164049		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	20729	protein-coding gene	gene with protein product		609075	"""F-box only protein 35"", ""F-box and WD-40 domain protein 12"""	FBXO35		15040455	Standard	NM_207102		Approved	Fbw12	uc010hjv.3	Q6X9E4	OTTHUMG00000133530	ENST00000296438.5:c.296C>T	3.37:g.48416853C>T	ENSP00000296438:p.Thr99Met		E9PG36|Q494Y9|Q494Z0	Missense_Mutation	SNP	pfam_F-box_dom_cyclin-like,superfamily_Quino_amine_DH_bsu,superfamily_F-box_dom_cyclin-like,smart_F-box_dom_cyclin-like,pfscan_F-box_dom_cyclin-like	p.T99M	ENST00000296438.5	37	c.296	CCDS2764.1	3	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	3.965	-0.009587	0.07727	.	.	ENSG00000164049	ENST00000458736;ENST00000296438;ENST00000445170;ENST00000415155	T;T;T	0.31510	1.91;1.51;1.49	3.86	-3.76	0.04359	F-box domain, Skp2-like (1);	6.341150	0.00357	N	0.000021	T	0.14184	0.0343	N	0.08118	0	0.09310	N	1	B;B;B;B	0.22003	0.063;0.063;0.038;0.038	B;B;B;B	0.19666	0.026;0.016;0.007;0.011	T	0.11299	-1.0593	10	0.54805	T	0.06	-16.3636	0.7794	0.01038	0.2531:0.3413:0.1252:0.2804	.	20;80;99;99	E9PCA2;E9PG36;Q494Z0;Q6X9E4	.;.;.;FBW12_HUMAN	M	20;99;80;99	ENSP00000296438:T99M;ENSP00000406139:T80M;ENSP00000414683:T99M	ENSP00000296438:T99M	T	+	2	0	FBXW12	48391857	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.214000	0.02988	-0.951000	0.03654	-1.842000	0.00583	ACG	FBXW12	-	superfamily_F-box_dom_cyclin-like	ENSG00000164049		0.388	FBXW12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	FBXW12	HGNC	protein_coding	OTTHUMT00000257505.1	191	0.00	0	C	NM_207102		48416853	48416853	+1	no_errors	ENST00000296438	ensembl	human	known	69_37n	missense	227	19.50	55	SNP	0.000	T
GABRG2	2566	genome.wustl.edu	37	5	161522529	161522529	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr5:161522529G>A	ENST00000361925.4	+	3	508	c.288G>A	c.(286-288)atG>atA	p.M96I	GABRG2_ENST00000414552.2_Missense_Mutation_p.M96I|GABRG2_ENST00000393933.4_Start_Codon_SNP_p.M1I|GABRG2_ENST00000356592.3_Missense_Mutation_p.M96I			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	96					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.M96I(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	ACACAGACATGTATGTGAATA	0.333																																						dbGAP											1	Substitution - Missense(1)	breast(1)											160.0	149.0	153.0					5																	161522529		2202	4299	6501	-	-	-	SO:0001583	missense	0				CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4087	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma 2"""	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.288G>A	5.37:g.161522529G>A	ENSP00000354651:p.Met96Ile		F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	pfam_Neur_chan_lig-bd,pfam_Neurotrans-gated_channel_TM,superfamily_Neur_chan_lig-bd,superfamily_Neurotrans-gated_channel_TM,prints_GABBAg_rcpt,prints_GABAA_rcpt,prints_GABBAg2_rcpt,prints_GABAAa_rcpt,prints_Neur_channel,tigrfam_Neur_channel	p.M96I	ENST00000361925.4	37	c.288	CCDS4358.1	5	.	.	.	.	.	.	.	.	.	.	G	10.54	1.379519	0.24944	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933;ENST00000522053	T;T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1;-1.1	6.07	6.07	0.98685	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.53094	0.1775	N	0.01656	-0.775	0.80722	D	1	B;B;B	0.12630	0.006;0.0;0.001	B;B;B	0.14023	0.01;0.004;0.002	T	0.59091	-0.7519	10	0.02654	T	1	.	20.6439	0.99570	0.0:0.0:1.0:0.0	.	96;96;96	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	I	96;96;96;1;1	ENSP00000349000:M96I;ENSP00000410732:M96I;ENSP00000354651:M96I;ENSP00000377510:M1I;ENSP00000430182:M1I	ENSP00000349000:M96I	M	+	3	0	GABRG2	161455107	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.167000	0.64972	2.890000	0.99128	0.650000	0.86243	ATG	GABRG2	-	pfam_Neur_chan_lig-bd,superfamily_Neur_chan_lig-bd,prints_GABBAg_rcpt,prints_GABAAa_rcpt,tigrfam_Neur_channel	ENSG00000113327		0.333	GABRG2-002	KNOWN	basic|CCDS	protein_coding	GABRG2	HGNC	protein_coding	OTTHUMT00000252706.1	325	0.00	0	G			161522529	161522529	+1	no_errors	ENST00000356592	ensembl	human	known	69_37n	missense	296	31.32	135	SNP	1.000	A
GBP1	2633	genome.wustl.edu	37	1	89521803	89521805	+	In_Frame_Del	DEL	CTT	CTT	-			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	CTT	CTT					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr1:89521803_89521805delCTT	ENST00000370473.4	-	8	1481_1483	c.1262_1264delAAG	c.(1261-1266)gaagtg>gtg	p.E421del	GBP1_ENST00000484970.1_5'Flank	NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN	guanylate binding protein 1, interferon-inducible	421					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)	cytosol (GO:0005829)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	30		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		CCCGCCTTCACTTCTTCTTCTAG	0.429																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0			BC002666	CCDS718.1	1p22.2	2011-03-09	2011-03-09		ENSG00000117228	ENSG00000117228			4182	protein-coding gene	gene with protein product		600411	"""guanylate binding protein 1, interferon-inducible, 67kDa"""			7518790	Standard	NM_002053		Approved		uc001dmx.2	P32455	OTTHUMG00000010614	ENST00000370473.4:c.1262_1264delAAG	1.37:g.89521809_89521811delCTT	ENSP00000359504:p.Glu421del		D3DT26|Q5T8M1	In_Frame_Del	DEL	pfam_Guanylate-bd_C,pfam_Guanylate-bd_N,superfamily_Guanylate-bd_C	p.E421in_frame_del	ENST00000370473.4	37	c.1264_1262	CCDS718.1	1																																																																																			GBP1	-	pfam_Guanylate-bd_C,superfamily_Guanylate-bd_C	ENSG00000117228		0.429	GBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GBP1	HGNC	protein_coding	OTTHUMT00000029289.3	266	0.00	0	CTT	NM_002053		89521803	89521805	-1	no_errors	ENST00000370473	ensembl	human	known	69_37n	in_frame_del	294	23.77	92	DEL	0.012:0.000:0.000	-
GSPT2	23708	genome.wustl.edu	37	X	51488514	51488514	+	Missense_Mutation	SNP	A	A	G			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chrX:51488514A>G	ENST00000340438.4	+	1	2034	c.1792A>G	c.(1792-1794)Aaa>Gaa	p.K598E		NM_018094.4	NP_060564.2	Q8IYD1	ERF3B_HUMAN	G1 to S phase transition 2	598					cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational termination (GO:0006415)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)	p.K598E(1)		breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Ovarian(276;0.236)					CGAGACGTTCAAAGATTTTCC	0.428																																						dbGAP											1	Substitution - Missense(1)	breast(1)											83.0	74.0	77.0					X																	51488514		2203	4300	6503	-	-	-	SO:0001583	missense	0			AI285711	CCDS14336.1	Xp11.22	2008-05-14			ENSG00000189369	ENSG00000189369			4622	protein-coding gene	gene with protein product		300418				10575220	Standard	NM_018094		Approved	eRF3b, FLJ10441	uc004dpl.3	Q8IYD1	OTTHUMG00000021538	ENST00000340438.4:c.1792A>G	X.37:g.51488514A>G	ENSP00000341247:p.Lys598Glu		Q9H909|Q9NVY0|Q9NY44	Missense_Mutation	SNP	pfam_ProtSyn_GTP-bd,pfam_Transl_elong_EFTu/EF1A_C,pfam_Transl_elong_EFTu/EF1A_2,pfam_Ataxin-2_C,superfamily_Transl_elong_EF1A/Init_IF2_C,superfamily_Transl_elong_init/rib_B-barrel,prints_ProtSyn_GTP-bd	p.K598E	ENST00000340438.4	37	c.1792	CCDS14336.1	X	.	.	.	.	.	.	.	.	.	.	A	12.44	1.939901	0.34283	.	.	ENSG00000189369	ENST00000340438;ENST00000502175	T	0.32023	1.47	4.54	4.54	0.55810	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (1);Translation elongation factor EFTu/EF1A, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.33000	0.0848	L	0.31845	0.965	0.80722	D	1	P	0.48407	0.91	P	0.52710	0.707	T	0.02553	-1.1142	10	0.31617	T	0.26	-11.3429	11.2136	0.48813	1.0:0.0:0.0:0.0	.	598	Q8IYD1	ERF3B_HUMAN	E	598;515	ENSP00000341247:K598E	ENSP00000341247:K598E	K	+	1	0	GSPT2	51505254	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.637000	0.74304	2.012000	0.59069	0.483000	0.47432	AAA	GSPT2	-	pfam_Transl_elong_EFTu/EF1A_C,superfamily_Transl_elong_EF1A/Init_IF2_C	ENSG00000189369		0.428	GSPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GSPT2	HGNC	protein_coding	OTTHUMT00000056587.1	127	0.78	1	A			51488514	51488514	+1	no_errors	ENST00000340438	ensembl	human	known	69_37n	missense	87	33.08	43	SNP	1.000	G
HFM1	164045	genome.wustl.edu	37	1	91727807	91727807	+	Missense_Mutation	SNP	A	A	G			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr1:91727807A>G	ENST00000370425.3	-	38	4327	c.4229T>C	c.(4228-4230)gTt>gCt	p.V1410A	Y_RNA_ENST00000384090.1_RNA|HFM1_ENST00000370424.3_Missense_Mutation_p.V1089A|HFM1_ENST00000294696.5_3'UTR|HFM1_ENST00000462405.1_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	1410					resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.V1410A(1)		breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		CCTGAAATCAACTTCCTTTTT	0.264																																						dbGAP											1	Substitution - Missense(1)	breast(1)											35.0	33.0	33.0					1																	91727807		1794	4051	5845	-	-	-	SO:0001583	missense	0			AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.4229T>C	1.37:g.91727807A>G	ENSP00000359454:p.Val1410Ala		B1B0B6|Q8N9Q0	Missense_Mutation	SNP	pfam_Sec63-dom,pfam_DNA/RNA_helicase_DEAD/DEAH_N,pfam_Helicase_C,pfam_Helicase/UvrB_dom,smart_Helicase_ATP-bd,smart_Helicase_C,smart_Sec63-dom,pfscan_Helicase_ATP-bd,pfscan_Helicase_C	p.V1410A	ENST00000370425.3	37	c.4229	CCDS30769.2	1	.	.	.	.	.	.	.	.	.	.	A	9.758	1.169242	0.21621	.	.	ENSG00000162669	ENST00000370425;ENST00000370424	T;T	0.63417	0.39;-0.04	4.85	1.35	0.21983	.	.	.	.	.	T	0.15219	0.0367	N	0.08118	0	0.51767	D	0.999937	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.12116	-1.0560	9	0.11485	T	0.65	.	6.2085	0.20615	0.6218:0.0:0.3782:0.0	.	621;1410	B1B0B5;A2PYH4	.;HFM1_HUMAN	A	1410;1089	ENSP00000359454:V1410A;ENSP00000359453:V1089A	ENSP00000359453:V1089A	V	-	2	0	HFM1	91500395	0.349000	0.24870	0.926000	0.36857	0.611000	0.37282	0.535000	0.23114	0.428000	0.26173	0.455000	0.32223	GTT	HFM1	-	NULL	ENSG00000162669		0.264	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	HFM1	HGNC	protein_coding	OTTHUMT00000316716.2	107	0.00	0	A	NM_001017975		91727807	91727807	-1	no_errors	ENST00000370425	ensembl	human	known	69_37n	missense	66	34.65	35	SNP	0.832	G
IL33	90865	genome.wustl.edu	37	9	6252949	6252949	+	Missense_Mutation	SNP	T	T	G			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr9:6252949T>G	ENST00000381434.3	+	4	440	c.427T>G	c.(427-429)Tat>Gat	p.Y143D	IL33_ENST00000417746.2_Intron|IL33_ENST00000456383.2_Intron	NM_033439.3	NP_254274.1	O95760	IL33_HUMAN	interleukin 33	143					extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of immunoglobulin secretion (GO:0051025)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type 2 immune response (GO:0002830)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|nucleus (GO:0005634)	cytokine activity (GO:0005125)	p.Y143D(1)		breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)		GGATGAAAGTTATGAGATATA	0.269																																						dbGAP											1	Substitution - Missense(1)	breast(1)											60.0	61.0	61.0					9																	6252949		2203	4299	6502	-	-	-	SO:0001583	missense	0			AB024518	CCDS6468.1, CCDS56563.1, CCDS56564.1	9p24.1	2014-01-28	2006-11-20	2006-11-20	ENSG00000137033	ENSG00000137033		"""Interleukins and interleukin receptors"""	16028	protein-coding gene	gene with protein product	"""DVS27-related protein"", ""nuclear factor for high endothelial venules"", ""interleukin-1 family, member 11"""	608678	"""chromosome 9 open reading frame 26 (NF-HEV)"""	C9orf26		10566975, 12819012	Standard	NM_033439		Approved	DVS27, DKFZp586H0523, NF-HEV, IL1F11	uc003zjt.3	O95760	OTTHUMG00000019516	ENST00000381434.3:c.427T>G	9.37:g.6252949T>G	ENSP00000370842:p.Tyr143Asp		B2R8L1|B4DJ35|B4E1Q9|D3DRI5|E7EAX4|Q2YEJ5	Missense_Mutation	SNP	NULL	p.Y143D	ENST00000381434.3	37	c.427	CCDS6468.1	9	.	.	.	.	.	.	.	.	.	.	T	13.43	2.234762	0.39498	.	.	ENSG00000137033	ENST00000381434	T	0.60548	0.18	5.15	4.0	0.46444	.	0.330144	0.22396	N	0.060603	T	0.64616	0.2614	L	0.47190	1.495	0.18873	N	0.999981	D	0.67145	0.996	D	0.63381	0.914	T	0.56098	-0.8035	10	0.87932	D	0	-9.1335	9.2612	0.37614	0.0:0.0:0.1817:0.8183	.	143	O95760	IL33_HUMAN	D	143	ENSP00000370842:Y143D	ENSP00000370842:Y143D	Y	+	1	0	IL33	6242949	0.785000	0.28726	0.008000	0.14137	0.509000	0.34042	1.924000	0.40065	1.067000	0.40740	0.528000	0.53228	TAT	IL33	-	NULL	ENSG00000137033		0.269	IL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IL33	HGNC	protein_coding	OTTHUMT00000051655.1	159	0.00	0	T	NM_033439		6252949	6252949	+1	no_errors	ENST00000381434	ensembl	human	known	69_37n	missense	93	45.29	77	SNP	0.078	G
JUN	3725	genome.wustl.edu	37	1	59248498	59248498	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr1:59248498delT	ENST00000371222.2	-	1	1287	c.245delA	c.(244-246)cagfs	p.Q82fs	RP4-794H19.2_ENST00000419531.2_lincRNA	NM_002228.3	NP_002219.1	P05412	JUN_HUMAN	jun proto-oncogene	82					aging (GO:0007568)|angiogenesis (GO:0001525)|axon regeneration (GO:0031103)|cellular response to calcium ion (GO:0071277)|cellular response to potassium ion starvation (GO:0051365)|circadian rhythm (GO:0007623)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|leading edge cell differentiation (GO:0035026)|learning (GO:0007612)|liver development (GO:0001889)|membrane depolarization (GO:0051899)|microglial cell activation (GO:0001774)|monocyte differentiation (GO:0030224)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA binding (GO:0043392)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990441)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA replication (GO:0045740)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|release of cytochrome c from mitochondria (GO:0001836)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|SMAD protein import into nucleus (GO:0007184)|SMAD protein signal transduction (GO:0060395)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nuclear chromosome (GO:0000228)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	cAMP response element binding (GO:0035497)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|R-SMAD binding (GO:0070412)|Rho GTPase activator activity (GO:0005100)|RNA polymerase II activating transcription factor binding (GO:0001102)|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 (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Q82fs*22(1)		breast(2)|kidney(2)|lung(5)|skin(1)	10	all_cancers(7;8.55e-07)				Arsenic trioxide(DB01169)|Irbesartan(DB01029)|Pseudoephedrine(DB00852)|Vinblastine(DB00570)	GTTGCTGGACTGGATTATCAG	0.662			A		sarcoma																																	dbGAP		Dom	yes		1	1p32-p31	3725	jun oncogene		M	1	Deletion - Frameshift(1)	breast(1)											83.0	91.0	89.0					1																	59248498		2203	4299	6502	-	-	-	SO:0001589	frameshift_variant	0			AY217548	CCDS610.1	1p32-p31	2013-01-10	2010-08-27		ENSG00000177606	ENSG00000177606		"""basic leucine zipper proteins"""	6204	protein-coding gene	gene with protein product		165160	"""v-jun avian sarcoma virus 17 oncogene homolog"", ""v-jun sarcoma virus 17 oncogene homolog (avian)"", ""jun oncogene"""			3194415	Standard	NM_002228		Approved	c-Jun, AP-1	uc001cze.3	P05412	OTTHUMG00000008376	ENST00000371222.2:c.245delA	1.37:g.59248498delT	ENSP00000360266:p.Gln82fs		Q6FHM7|Q96G93	Frame_Shift_Del	DEL	pfam_JNK,pfam_bZIP_1,pfam_bZIP_2,superfamily_Euk_TF_DNA-bd,smart_bZIP,pfscan_bZIP,prints_Leuzip_Jun	p.Q82fs	ENST00000371222.2	37	c.245	CCDS610.1	1																																																																																			JUN	-	pfam_JNK	ENSG00000177606		0.662	JUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	JUN	HGNC	protein_coding	OTTHUMT00000023042.1	51	0.00	0	T	NM_002228		59248498	59248498	-1	no_errors	ENST00000371222	ensembl	human	known	69_37n	frame_shift_del	38	33.33	19	DEL	1.000	-
LYPD4	147719	genome.wustl.edu	37	19	42342215	42342215	+	Missense_Mutation	SNP	C	C	T			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr19:42342215C>T	ENST00000330743.3	-	4	1543	c.332G>A	c.(331-333)cGg>cAg	p.R111Q	LYPD4_ENST00000601246.1_Missense_Mutation_p.R76Q|AC020956.3_ENST00000593354.1_lincRNA|LYPD4_ENST00000343055.4_Missense_Mutation_p.R76Q	NM_173506.4	NP_775777.3	Q6UWN0	LYPD4_HUMAN	LY6/PLAUR domain containing 4	111						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.R111Q(1)		breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)	12						GAGATAAGACCGGCAGACGCG	0.537																																						dbGAP											1	Substitution - Missense(1)	breast(1)											144.0	123.0	130.0					19																	42342215		2203	4300	6503	-	-	-	SO:0001583	missense	0			AY358726	CCDS12587.1	19q13.2	2008-02-05				ENSG00000273111			28659	protein-coding gene	gene with protein product						12975309	Standard	XM_005278383		Approved	MGC42718	uc002orp.1	Q6UWN0		ENST00000330743.3:c.332G>A	19.37:g.42342215C>T	ENSP00000328737:p.Arg111Gln		Q8IYW0	Missense_Mutation	SNP	pfam_LY6_UPAR	p.R111Q	ENST00000330743.3	37	c.332	CCDS12587.1	19	.	.	.	.	.	.	.	.	.	.	c	19.73	3.881447	0.72294	.	.	ENSG00000183103	ENST00000330743;ENST00000343055	T;T	0.12361	3.35;2.69	4.03	2.99	0.34606	.	0.168538	0.28977	N	0.013538	T	0.30978	0.0782	M	0.78801	2.425	0.27504	N	0.951904	D;D	0.89917	1.0;0.999	D;P	0.67382	0.951;0.894	T	0.03750	-1.1007	10	0.42905	T	0.14	-7.2262	7.5505	0.27793	0.0:0.8837:0.0:0.1163	.	76;111	Q6UWN0-2;Q6UWN0	.;LYPD4_HUMAN	Q	111;76	ENSP00000328737:R111Q;ENSP00000339568:R76Q	ENSP00000328737:R111Q	R	-	2	0	LYPD4	47034055	0.906000	0.30813	0.830000	0.32933	0.895000	0.52256	1.655000	0.37345	1.284000	0.44531	0.457000	0.33378	CGG	LYPD4	-	NULL	ENSG00000183103		0.537	LYPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LYPD4	HGNC	protein_coding	OTTHUMT00000463039.1	116	0.00	0	C	NM_173506		42342215	42342215	-1	no_errors	ENST00000330743	ensembl	human	known	69_37n	missense	62	50.40	63	SNP	0.824	T
MLPH	79083	genome.wustl.edu	37	2	238461047	238461047	+	Silent	SNP	C	C	T			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr2:238461047C>T	ENST00000264605.3	+	15	2037	c.1743C>T	c.(1741-1743)aaC>aaT	p.N581N	MLPH_ENST00000410032.1_Silent_p.N438N|MLPH_ENST00000409373.1_Silent_p.N461N|MLPH_ENST00000338530.4_Silent_p.N553N|MLPH_ENST00000445024.2_3'UTR	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	581					melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)	p.N581N(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		GAAACCCCAACGCGAGGAAAG	0.448																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											72.0	66.0	68.0					2																	238461047		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.1743C>T	2.37:g.238461047C>T			B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	pfam_Myelin-assoc_OBP	p.R180C	ENST00000264605.3	37	c.538	CCDS2518.1	2	.	.	.	.	.	.	.	.	.	.	C	9.127	1.010528	0.19277	.	.	ENSG00000115648	ENST00000415753	.	.	.	4.91	-0.176	0.13311	.	.	.	.	.	T	0.54159	0.1841	.	.	.	0.51482	D	0.999929	.	.	.	.	.	.	T	0.46693	-0.9173	4	.	.	.	-24.8656	7.9865	0.30216	0.0:0.5567:0.0:0.4433	.	.	.	.	C	217	.	.	R	+	1	0	MLPH	238125786	0.089000	0.21612	0.928000	0.36995	0.934000	0.57294	-1.046000	0.03525	0.119000	0.18210	-0.194000	0.12790	CGC	MLPH	-	NULL	ENSG00000115648		0.448	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MLPH	HGNC	protein_coding	OTTHUMT00000257083.2	71	0.00	0	C	NM_024101		238461047	238461047	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000432475	ensembl	human	known	69_37n	missense	53	37.65	32	SNP	0.857	T
MT-CYB	4519	genome.wustl.edu	37	M	14805	14805	+	Missense_Mutation	SNP	A	A	G			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chrM:14805A>G	ENST00000361789.2	+	1	59	c.59A>G	c.(58-60)gAc>gGc	p.D20G	MT-TS2_ENST00000387449.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	20					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						CTCATTCATCGACCTCCCCAC	0.443																																						dbGAP											0																																										-	-	-	SO:0001583	missense	0					mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.59A>G	M.37:g.14805A>G	ENSP00000354554:p.Asp20Gly		Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	pfam_Cyt_b/b6_C,pfam_Di-haem_cyt_TM,superfamily_Di-haem_cyt_TM,superfamily_Cyt_b/b6_C,pfscan_Cyt_b/b6_N,pfscan_Cyt_b/b6_C	p.D20G	ENST00000361789.2	37	c.59		MT																																																																																			MT-CYB	-	superfamily_Di-haem_cyt_TM,pfscan_Cyt_b/b6_N	ENSG00000198727		0.443	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	MT-CYB	HGNC	protein_coding		316	0.31	1	A	YP_003024038		14805	14805	+1	no_stop_codon:bad_bp_length_for_coding_region	ENST00000361789	ensembl	human	known	69_37n	missense	238	12.82	35	SNP	NULL	G
MYH9	4627	genome.wustl.edu	37	22	36697633	36697634	+	In_Frame_Ins	INS	-	-	GAG			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr22:36697633_36697634insGAG	ENST00000216181.5	-	21	2807_2808	c.2577_2578insCTC	c.(2575-2580)gagaag>gagCTCaag	p.859_860EK>ELK		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	859					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.E859_K860insL(1)		NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						GCCAGCTGCTTCTCTCTGACCT	0.619			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated		OREG0026520	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	1	Insertion - In frame(1)	breast(1)																																								-	-	-	SO:0001652	inframe_insertion	0	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.2577_2578insCTC	22.37:g.36697633_36697634insGAG	ENSP00000216181:p.Glu859_Lys860insLeu	864	A8K6E4|O60805|Q60FE2|Q86T83	In_Frame_Ins	INS	pfam_Myosin_head_motor_dom,pfam_Myosin_tail,pfam_Myosin_N,pfam_IQ_motif_EF-hand-BS,superfamily_Regulat_G_prot_signal_superfam,superfamily_Prefoldin,superfamily_Myosin_S1_N,superfamily_STAT_TF_coiled-coil,superfamily_tRNA-bd_arm,smart_Myosin_head_motor_dom,smart_IQ_motif_EF-hand-BS,prints_Myosin_head_motor_dom,pfscan_IQ_motif_EF-hand-BS	p.859in_frame_insL	ENST00000216181.5	37	c.2578_2577	CCDS13927.1	22																																																																																			MYH9	-	NULL	ENSG00000100345		0.619	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	MYH9	HGNC	protein_coding	OTTHUMT00000259110.3	169	0.00	0	-	NM_002473		36697633	36697634	-1	no_errors	ENST00000216181	ensembl	human	known	69_37n	in_frame_ins	50	51.46	53	INS	1.000:1.000	GAG
MYH9	4627	genome.wustl.edu	37	22	36697634	36697635	+	Missense_Mutation	DNP	CT	CT	AA			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	C|T	C|T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr22:36697634_36697635CT>AA	ENST00000216181.5	-	21	2806_2807	c.2576_2577AG>TT	c.(2575-2577)gAG>gTT	p.E859V		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	859					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.E859_K860insL(1)		NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						CCAGCTGCTTCTCTCTGACCTT	0.619			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated		OREG0026520	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	1	Insertion - In frame(1)	breast(1)																																								-	-	-	SO:0001583	missense	0	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.2576_2577delinsAA	22.37:g.36697634_36697635delinsAA	ENSP00000216181:p.Glu859Val	864	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	pfam_Myosin_head_motor_dom,pfam_Myosin_tail,pfam_Myosin_N,pfam_IQ_motif_EF-hand-BS,superfamily_Regulat_G_prot_signal_superfam,superfamily_Prefoldin,superfamily_Myosin_S1_N,superfamily_STAT_TF_coiled-coil,superfamily_tRNA-bd_arm,smart_Myosin_head_motor_dom,smart_IQ_motif_EF-hand-BS,prints_Myosin_head_motor_dom,pfscan_IQ_motif_EF-hand-BS	p.E859D|p.E859V	ENST00000216181.5	37	c.2577|c.2576	CCDS13927.1	22																																																																																			MYH9	-	NULL	ENSG00000100345		0.619	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	MYH9	HGNC	protein_coding	OTTHUMT00000259110.3	174|173	0.00	0	C|T	NM_002473		36697634|36697635	36697634|36697635	-1	no_errors	ENST00000216181	ensembl	human	known	69_37n	missense	46	53.47|54.46	54|55	SNP	1.000	A
NEIL1	79661	genome.wustl.edu	37	15	75647320	75647320	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr15:75647320G>A	ENST00000564784.1	+	11	1747	c.1118G>A	c.(1117-1119)cGg>cAg	p.R373Q	MIR631_ENST00000384904.1_RNA|RP11-817O13.6_ENST00000563660.1_lincRNA|NEIL1_ENST00000355059.4_Missense_Mutation_p.R373Q|NEIL1_ENST00000569035.1_Missense_Mutation_p.R373Q			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)	373					base-excision repair (GO:0006284)|negative regulation of nuclease activity (GO:0032074)|nucleotide-excision repair (GO:0006289)|response to oxidative stress (GO:0006979)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)	p.R373Q(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)	13						TGCAGACCCCGGAAGGTCAAG	0.577								Base excision repair (BER), DNA glycosylases																														dbGAP											1	Substitution - Missense(1)	breast(1)											50.0	44.0	46.0					15																	75647320		2197	4294	6491	-	-	-	SO:0001583	missense	0			AK026055	CCDS10278.1	15q33.33	2008-07-18			ENSG00000140398	ENSG00000140398			18448	protein-coding gene	gene with protein product		608844				11904416	Standard	NM_024608		Approved	FLJ22402, hFPG1, NEI1, FPG1	uc002bae.4	Q96FI4	OTTHUMG00000142821	ENST00000564784.1:c.1118G>A	15.37:g.75647320G>A	ENSP00000457352:p.Arg373Gln		D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	Missense_Mutation	SNP	pfam_Endonuclease-VIII_DNA-bd,pfam_DNA_glycosylase/AP_lyase_cat,pfam_DNA_glyclase/AP_lyase_DNA-bd,superfamily_DNA_glycosylase/AP_lyase_cat,superfamily_Ribosomal_S13-like_H2TH,smart_DNA_glycosylase/AP_lyase_cat,pfscan_DNA_glycosylase/AP_lyase_cat	p.R373Q	ENST00000564784.1	37	c.1118	CCDS10278.1	15	.	.	.	.	.	.	.	.	.	.	G	3.251	-0.153275	0.06585	.	.	ENSG00000140398	ENST00000355059	T	0.10860	2.83	4.07	-2.76	0.05896	.	1.931060	0.02004	N	0.046558	T	0.06735	0.0172	N	0.21373	0.66	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.30937	-0.9961	10	0.12430	T	0.62	-1.8172	5.1906	0.15207	0.5467:0.1644:0.2889:0.0	.	373	Q96FI4	NEIL1_HUMAN	Q	373	ENSP00000347170:R373Q	ENSP00000347170:R373Q	R	+	2	0	NEIL1	73434373	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.127000	0.10547	-0.507000	0.06549	-0.258000	0.10820	CGG	NEIL1	-	NULL	ENSG00000140398		0.577	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NEIL1	HGNC	protein_coding	OTTHUMT00000419885.1	64	0.00	0	G	NM_024608		75647320	75647320	+1	no_errors	ENST00000355059	ensembl	human	known	69_37n	missense	35	50.00	35	SNP	0.000	A
NEK1	4750	genome.wustl.edu	37	4	170321765	170321765	+	Silent	SNP	G	G	A			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr4:170321765G>A	ENST00000439128.2	-	32	4177	c.3537C>T	c.(3535-3537)tgC>tgT	p.C1179C	NEK1_ENST00000507142.1_Silent_p.C1207C|NEK1_ENST00000510533.1_Silent_p.C1135C|NEK1_ENST00000512193.1_Silent_p.C1110C|NEK1_ENST00000511633.1_Silent_p.C1163C	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	1179					cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.C1207C(4)		NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		AGACACTATCGCATTCACATT	0.318																																						dbGAP											4	Substitution - coding silent(4)	lung(2)|breast(2)											54.0	48.0	50.0					4																	170321765		1823	4084	5907	-	-	-	SO:0001819	synonymous_variant	0			AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"""NIMA (never in mitosis gene a)-related kinase 1"""			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.3537C>T	4.37:g.170321765G>A			G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Silent	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.C1207	ENST00000439128.2	37	c.3621	CCDS47162.1	4																																																																																			NEK1	-	NULL	ENSG00000137601		0.318	NEK1-001	KNOWN	basic|CCDS	protein_coding	NEK1	HGNC	protein_coding	OTTHUMT00000363157.3	167	0.00	0	G			170321765	170321765	-1	no_errors	ENST00000507142	ensembl	human	known	69_37n	silent	139	41.10	97	SNP	0.991	A
PANK4	55229	genome.wustl.edu	37	1	2453186	2453186	+	Missense_Mutation	SNP	T	T	C			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr1:2453186T>C	ENST00000378466.3	-	2	190	c.178A>G	c.(178-180)Aag>Gag	p.K60E	PANK4_ENST00000491212.1_5'UTR|PANK4_ENST00000435556.3_Missense_Mutation_p.K60E	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	60					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)	p.K60E(1)		breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		GACCGCACCTTGGCGACTTTG	0.607																																						dbGAP											1	Substitution - Missense(1)	breast(1)											168.0	162.0	164.0					1																	2453186		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.178A>G	1.37:g.2453186T>C	ENSP00000367727:p.Lys60Glu		B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	pfam_Type_II_PanK,pfam_DUF89,superfamily_DUF89,pirsf_PanK_long,tigrfam_Type_II_PanK	p.K60E	ENST00000378466.3	37	c.178	CCDS42.1	1	.	.	.	.	.	.	.	.	.	.	T	17.39	3.377637	0.61735	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	D;D	0.99409	-5.85;-3.86	4.85	3.69	0.42338	.	0.377568	0.29745	N	0.011314	D	0.96219	0.8767	N	0.12887	0.27	0.43457	D	0.995651	B;B	0.10296	0.001;0.003	B;B	0.15052	0.012;0.012	D	0.92982	0.6407	10	0.05833	T	0.94	-5.2748	10.9593	0.47376	0.0:0.0:0.1571:0.8429	.	60;60	E9PHT6;Q9NVE7	.;PANK4_HUMAN	E	60	ENSP00000367727:K60E;ENSP00000421433:K60E	ENSP00000367727:K60E	K	-	1	0	PANK4	2443046	1.000000	0.71417	0.685000	0.30070	0.821000	0.46438	3.521000	0.53472	0.684000	0.31448	0.460000	0.39030	AAG	PANK4	-	pfam_Type_II_PanK,pirsf_PanK_long,tigrfam_Type_II_PanK	ENSG00000157881		0.607	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PANK4	HGNC	protein_coding	OTTHUMT00000002082.1	118	0.00	0	T			2453186	2453186	-1	no_errors	ENST00000378466	ensembl	human	known	69_37n	missense	86	39.44	56	SNP	0.987	C
PCDHGC3	5098	genome.wustl.edu	37	5	140857180	140857180	+	Silent	SNP	A	A	G			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr5:140857180A>G	ENST00000308177.3	+	1	1601	c.1497A>G	c.(1495-1497)caA>caG	p.Q499Q	PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGA12_ENST00000252085.3_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	499	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Q499Q(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTTGGAGCAAGGAGCTGAAA	0.512																																						dbGAP											2	Substitution - coding silent(2)	breast(2)											58.0	66.0	63.0					5																	140857180		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"""Cadherins / Protocadherins : Clustered"""	8716	other	protocadherin	"""cadherin-like 2"", ""protocadherin 2"", ""protocadherin 43"""	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.1497A>G	5.37:g.140857180A>G			O60622|Q08192|Q9Y5C4	Silent	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.Q499	ENST00000308177.3	37	c.1497	CCDS4261.1	5																																																																																			PCDHGC3	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000240184		0.512	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHGC3	HGNC	protein_coding	OTTHUMT00000251808.2	92	0.00	0	A	NM_002588		140857180	140857180	+1	no_errors	ENST00000308177	ensembl	human	known	69_37n	silent	62	38.61	39	SNP	0.000	G
PCOLCE	5118	genome.wustl.edu	37	7	100203382	100203382	+	Silent	SNP	C	C	G			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr7:100203382C>G	ENST00000223061.5	+	5	952	c.672C>G	c.(670-672)gcC>gcG	p.A224A	PCOLCE-AS1_ENST00000442166.2_RNA|PCOLCE-AS1_ENST00000446022.1_RNA|PCOLCE-AS1_ENST00000544873.1_RNA	NM_002593.3	NP_002584.2	Q15113	PCOC1_HUMAN	procollagen C-endopeptidase enhancer	224	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				multicellular organismal development (GO:0007275)|positive regulation of peptidase activity (GO:0010952)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)	p.A224A(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					TCAACGGAGCCGTGAGCGACG	0.692																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											22.0	21.0	21.0					7																	100203382		2185	4272	6457	-	-	-	SO:0001819	synonymous_variant	0			L33799	CCDS5700.1	7q22	2008-07-18			ENSG00000106333	ENSG00000106333			8738	protein-coding gene	gene with protein product	"""procollagen, type 1, COOH-terminal proteinase enhancer"", ""procollagen C-proteinase enhancer 1"""	600270				8824813, 9799793	Standard	NM_002593		Approved	PCPE, PCPE1	uc003uvo.3	Q15113	OTTHUMG00000156675	ENST00000223061.5:c.672C>G	7.37:g.100203382C>G			B2R9E1|O14550	Silent	SNP	pfam_CUB,pfam_Netrin_module_non-TIMP,superfamily_CUB,superfamily_TIMP-like_OB-fold,smart_CUB,smart_Netrin_module_non-TIMP,pfscan_CUB,pfscan_Netrin_domain	p.A224	ENST00000223061.5	37	c.672	CCDS5700.1	7																																																																																			PCOLCE	-	pfam_CUB,superfamily_CUB,smart_CUB,pfscan_CUB	ENSG00000106333		0.692	PCOLCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCOLCE	HGNC	protein_coding	OTTHUMT00000345285.1	29	0.00	0	C	NM_002593		100203382	100203382	+1	no_errors	ENST00000223061	ensembl	human	known	69_37n	silent	18	35.71	10	SNP	0.033	G
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)											99.0	89.0	92.0					3																	178952085		1912	4130	6042	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>G	3.37:g.178952085A>G	ENSP00000263967:p.His1047Arg		Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.H1047R	ENST00000263967.3	37	c.3140	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	PIK3CA	-	superfamily_Kinase-like_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	ENSG00000121879		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	131	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	75	44.85	61	SNP	1.000	G
PNPLA6	10908	genome.wustl.edu	37	19	7605077	7605077	+	Silent	SNP	C	C	T			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr19:7605077C>T	ENST00000221249.6	+	8	911	c.480C>T	c.(478-480)tgC>tgT	p.C160C	PNPLA6_ENST00000545201.2_Silent_p.C160C|PNPLA6_ENST00000414982.3_Silent_p.C208C|PNPLA6_ENST00000450331.3_Silent_p.C160C|PNPLA6_ENST00000600737.1_Silent_p.C199C	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	199					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)	p.C160C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						TGGAGCTCTGCCGCCACATGG	0.677																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											42.0	43.0	43.0					19																	7605077		2202	4299	6501	-	-	-	SO:0001819	synonymous_variant	0			AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"""Patatin-like phospholipase domain containing"""	16268	protein-coding gene	gene with protein product	"""neuropathy target esterase"""	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.480C>T	19.37:g.7605077C>T			A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Silent	SNP	pfam_cNMP-bd_dom,pfam_Patatin/PLipase_A2-rel,superfamily_Acyl_Trfase/lysoPLipase,superfamily_cNMP-bd-like,smart_cNMP-bd_dom,pfscan_cNMP-bd_dom	p.C208	ENST00000221249.6	37	c.624	CCDS32891.1	19																																																																																			PNPLA6	-	superfamily_cNMP-bd-like,smart_cNMP-bd_dom,pfscan_cNMP-bd_dom	ENSG00000032444		0.677	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	PNPLA6	HGNC	protein_coding	OTTHUMT00000459275.1	40	0.00	0	C	NM_006702		7605077	7605077	+1	no_errors	ENST00000414982	ensembl	human	known	69_37n	silent	27	27.03	10	SNP	1.000	T
PTCH1	5727	genome.wustl.edu	37	9	98215818	98215818	+	Missense_Mutation	SNP	C	C	T	rs566619057		TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr9:98215818C>T	ENST00000331920.6	-	20	3690	c.3391G>A	c.(3391-3393)Gtg>Atg	p.V1131M	PTCH1_ENST00000430669.2_Missense_Mutation_p.V1065M|PTCH1_ENST00000375274.2_Missense_Mutation_p.V1130M|PTCH1_ENST00000418258.1_Missense_Mutation_p.V980M|PTCH1_ENST00000437951.1_Missense_Mutation_p.V1065M|PTCH1_ENST00000429896.2_Missense_Mutation_p.V980M|PTCH1_ENST00000421141.1_Missense_Mutation_p.V980M	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	1131					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.V1131M(4)|p.V1130M(3)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				AGAGTGGACACGGCGCCATCC	0.562													C|||	1	0.000199681	0.0	0.0	5008	,	,		19974	0.001		0.0	False		,,,				2504	0.0					dbGAP											7	Substitution - Missense(7)	breast(4)|prostate(3)											93.0	77.0	82.0					9																	98215818		2203	4300	6503	-	-	-	SO:0001583	missense	0			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.3391G>A	9.37:g.98215818C>T	ENSP00000332353:p.Val1131Met		A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	pfam_Patched,pfscan_SSD,tigrfam_TM_rcpt_patched	p.V1131M	ENST00000331920.6	37	c.3391	CCDS6714.1	9	.	.	.	.	.	.	.	.	.	.	C	17.43	3.388576	0.61956	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000375275;ENST00000430669;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.95980	-3.87;-3.87;-3.87;-3.87;-3.87;-3.87;-3.87	5.44	5.44	0.79542	.	0.055575	0.64402	D	0.000001	D	0.96349	0.8809	L	0.40543	1.245	0.54753	D	0.999983	P;D;D	0.76494	0.928;0.999;0.968	P;D;P	0.68765	0.551;0.96;0.68	D	0.95486	0.8565	10	0.39692	T	0.17	-24.0556	19.4628	0.94924	0.0:1.0:0.0:0.0	.	1065;1130;1131	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	M	1131;1065;980;980;567;1065;980;1130	ENSP00000332353:V1131M;ENSP00000389744:V1065M;ENSP00000399981:V980M;ENSP00000396135:V980M;ENSP00000410287:V1065M;ENSP00000414823:V980M;ENSP00000364423:V1130M	ENSP00000332353:V1131M	V	-	1	0	PTCH1	97255639	1.000000	0.71417	0.961000	0.40146	0.396000	0.30629	4.700000	0.61803	2.837000	0.97791	0.655000	0.94253	GTG	PTCH1	-	pfam_Patched,tigrfam_TM_rcpt_patched	ENSG00000185920		0.562	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTCH1	HGNC	protein_coding	OTTHUMT00000053229.2	31	0.00	0	C	NM_000264		98215818	98215818	-1	no_errors	ENST00000331920	ensembl	human	known	69_37n	missense	24	36.84	14	SNP	0.997	T
RP1	6101	genome.wustl.edu	37	8	55533670	55533670	+	Silent	SNP	C	C	T			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr8:55533670C>T	ENST00000220676.1	+	2	292	c.144C>T	c.(142-144)ttC>ttT	p.F48F		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	48	Doublecortin 1. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)	p.F48F(2)		NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			ACCCCCAATTCGGCGGGGTCA	0.552																																					Colon(91;1014 1389 7634 14542 40420)	dbGAP											2	Substitution - coding silent(2)	large_intestine(1)|breast(1)											102.0	91.0	95.0					8																	55533670		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.144C>T	8.37:g.55533670C>T				Silent	SNP	pfam_Doublecortin_dom,superfamily_Doublecortin_dom,smart_Doublecortin_dom,pfscan_Doublecortin_dom	p.F48	ENST00000220676.1	37	c.144	CCDS6160.1	8																																																																																			RP1	-	superfamily_Doublecortin_dom,smart_Doublecortin_dom,pfscan_Doublecortin_dom	ENSG00000104237		0.552	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RP1	HGNC	protein_coding	OTTHUMT00000378532.2	140	0.00	0	C	NM_006269		55533670	55533670	+1	no_errors	ENST00000220676	ensembl	human	known	69_37n	silent	114	36.67	66	SNP	0.008	T
SCN4A	6329	genome.wustl.edu	37	17	62018350	62018350	+	Silent	SNP	G	G	A			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr17:62018350G>A	ENST00000435607.1	-	24	5368	c.5292C>T	c.(5290-5292)gaC>gaT	p.D1764D	SCN4A_ENST00000578147.1_Silent_p.D1764D	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1764					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.D1764D(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCTCAGGGGCGTCATCCCCGC	0.627																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											66.0	71.0	70.0					17																	62018350		2148	4240	6388	-	-	-	SO:0001819	synonymous_variant	0			U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.5292C>T	17.37:g.62018350G>A			Q15478|Q16447|Q7Z6B1	Silent	SNP	pfam_Ion_trans_dom,pfam_Na_trans_assoc,pfam_PKD1_2_channel,prints_Na_channel_a4su,prints_Na_channel_asu,prints_PKD_2,pfscan_IQ_motif_EF-hand-BS	p.D1764	ENST00000435607.1	37	c.5292	CCDS45761.1	17																																																																																			SCN4A	-	NULL	ENSG00000007314		0.627	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SCN4A	HGNC	protein_coding		85	0.00	0	G	NM_000334		62018350	62018350	-1	no_errors	ENST00000435607	ensembl	human	known	69_37n	silent	56	44.00	44	SNP	0.000	A
SLC2A9	56606	genome.wustl.edu	37	4	9836553	9836553	+	Silent	SNP	G	G	A			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr4:9836553G>A	ENST00000264784.3	-	11	1424	c.1371C>T	c.(1369-1371)gtC>gtT	p.V457V	SLC2A9_ENST00000506583.1_Silent_p.V428V|SLC2A9_ENST00000309065.3_Silent_p.V428V	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	457					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)|sugar:proton symporter activity (GO:0005351)	p.V457V(1)|p.V428V(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35					Losartan(DB00678)|Probenecid(DB01032)	AGAGCCAGTTGACGGTGCCTG	0.542																																						dbGAP											2	Substitution - coding silent(2)	breast(2)											70.0	62.0	65.0					4																	9836553		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF210317	CCDS3406.1, CCDS3407.1	4p16.1	2013-05-22			ENSG00000109667	ENSG00000109667		"""Solute carriers"""	13446	protein-coding gene	gene with protein product	"""urate voltage-driven efflux transporter 1"""	606142				10860667, 17710649	Standard	NM_020041		Approved	Glut9, GLUTX, URATv1	uc003gmc.3	Q9NRM0	OTTHUMG00000044263	ENST00000264784.3:c.1371C>T	4.37:g.9836553G>A			Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Silent	SNP	pfam_Sub_transporter,pfam_MFS,superfamily_MFS_dom_general_subst_transpt,pfscan_MFS_dom,prints_Sugar/inositol_transpt,tigrfam_Sugar/inositol_transpt	p.V457	ENST00000264784.3	37	c.1371	CCDS3407.1	4																																																																																			SLC2A9	-	pfam_Sub_transporter,superfamily_MFS_dom_general_subst_transpt,pfscan_MFS_dom,tigrfam_Sugar/inositol_transpt	ENSG00000109667		0.542	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SLC2A9	HGNC	protein_coding	OTTHUMT00000207055.1	38	0.00	0	G			9836553	9836553	-1	no_errors	ENST00000264784	ensembl	human	known	69_37n	silent	28	46.15	24	SNP	1.000	A
TBL1XR1	79718	genome.wustl.edu	37	3	176765098	176765098	+	Missense_Mutation	SNP	C	C	A			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr3:176765098C>A	ENST00000430069.1	-	9	1113	c.854G>T	c.(853-855)gGa>gTa	p.G285V	TBL1XR1-AS1_ENST00000454723.2_RNA|TBL1XR1_ENST00000457928.2_Missense_Mutation_p.G285V			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	285					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.G285V(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			CTTGTCTACTCCAGCACTTAG	0.348																																						dbGAP											1	Substitution - Missense(1)	breast(1)											29.0	29.0	29.0					3																	176765098		1813	4045	5858	-	-	-	SO:0001583	missense	0			AK022956	CCDS46961.1	3q26.33	2013-01-10	2008-01-17		ENSG00000177565	ENSG00000177565		"""WD repeat domain containing"""	29529	protein-coding gene	gene with protein product		608628	"""transducin (beta)-like 1X-linked receptor 1"""			11063877, 11931768	Standard	NM_024665		Approved	IRA1, FLJ12894, TBLR1, C21, DC42	uc003fix.4	Q9BZK7	OTTHUMG00000157140	ENST00000430069.1:c.854G>T	3.37:g.176765098C>A	ENSP00000405574:p.Gly285Val		D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Missense_Mutation	SNP	pfam_WD40_repeat,pfam_LisH_dimerisation_subgr,superfamily_WD40_repeat_dom,smart_LisH_dimerisation,smart_WD40_repeat,prints_G-protein_beta_WD-40_rep,pfscan_LisH_dimerisation,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.G285V	ENST00000430069.1	37	c.854	CCDS46961.1	3	.	.	.	.	.	.	.	.	.	.	C	26.7	4.766676	0.90020	.	.	ENSG00000177565	ENST00000430069;ENST00000457928;ENST00000536758	T;T	0.64260	-0.09;-0.09	5.78	5.78	0.91487	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.82190	0.4983	M	0.85542	2.76	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.84128	0.0410	10	0.72032	D	0.01	-6.4391	18.9909	0.92791	0.0:1.0:0.0:0.0	.	285	Q9BZK7	TBL1R_HUMAN	V	285;285;147	ENSP00000405574:G285V;ENSP00000413251:G285V	ENSP00000405574:G285V	G	-	2	0	TBL1XR1	178247792	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.733000	0.93635	0.655000	0.94253	GGA	TBL1XR1	-	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	ENSG00000177565		0.348	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TBL1XR1	HGNC	protein_coding	OTTHUMT00000347587.3	77	0.00	0	C	NM_024665		176765098	176765098	-1	no_errors	ENST00000430069	ensembl	human	known	69_37n	missense	52	45.83	44	SNP	1.000	A
THBS1	7057	genome.wustl.edu	37	15	39883768	39883768	+	Missense_Mutation	SNP	A	A	G			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr15:39883768A>G	ENST00000260356.5	+	16	2641	c.2476A>G	c.(2476-2478)Atg>Gtg	p.M826V	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	826					activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)	p.M826V(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		AGACACTGATATGGATGGGGT	0.488																																						dbGAP											1	Substitution - Missense(1)	breast(1)											225.0	193.0	204.0					15																	39883768		2200	4297	6497	-	-	-	SO:0001583	missense	0				CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.2476A>G	15.37:g.39883768A>G	ENSP00000260356:p.Met826Val		A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	pfam_Thrombospondin_C,pfam_Thrombospondin_1_rpt,pfam_VWF_C,pfam_Thrombospondin_3-like_rpt,pfam_EGF-like_Ca-bd,superfamily_ConA-like_lec_gl,superfamily_Thrombospondin_1_rpt,smart_Laminin_G,smart_VWF_C,smart_Thrombospondin_1_rpt,smart_EGF-like_Ca-bd,smart_EGF-like,pfscan_EG-like_dom,pfscan_Thrombospondin_1_rpt,pfscan_VWF_C	p.M826V	ENST00000260356.5	37	c.2476	CCDS32194.1	15	.	.	.	.	.	.	.	.	.	.	A	10.96	1.497960	0.26861	.	.	ENSG00000137801	ENST00000260356	D	0.97575	-4.44	5.7	5.7	0.88788	.	0.000000	0.43747	D	0.000531	D	0.94000	0.8078	L	0.40543	1.245	0.29814	N	0.831376	B;B	0.20368	0.044;0.006	B;B	0.25987	0.065;0.016	D	0.88086	0.2810	10	0.21540	T	0.41	-28.0761	10.868	0.46866	0.8252:0.0:0.0:0.1748	.	741;826	B4E3J7;P07996	.;TSP1_HUMAN	V	826	ENSP00000260356:M826V	ENSP00000260356:M826V	M	+	1	0	THBS1	37671060	0.968000	0.33430	0.939000	0.37840	0.977000	0.68977	2.291000	0.43540	2.166000	0.68216	0.533000	0.62120	ATG	THBS1	-	pfam_Thrombospondin_3-like_rpt	ENSG00000137801		0.488	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	THBS1	HGNC	protein_coding	OTTHUMT00000257831.2	195	0.00	0	A	NM_003246		39883768	39883768	+1	no_errors	ENST00000260356	ensembl	human	known	69_37n	missense	139	41.18	98	SNP	0.937	G
TMEM145	284339	genome.wustl.edu	37	19	42820840	42820840	+	Missense_Mutation	SNP	C	C	A			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr19:42820840C>A	ENST00000301204.3	+	10	795	c.754C>A	c.(754-756)Ctc>Atc	p.L252I	TMEM145_ENST00000598766.1_Missense_Mutation_p.L276I	NM_173633.2	NP_775904.2	Q8NBT3	TM145_HUMAN	transmembrane protein 145	252					G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)		p.L252I(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	27		Prostate(69;0.00682)				CTCCAGCTTCCTCATCTTCCT	0.667																																						dbGAP											1	Substitution - Missense(1)	breast(1)											86.0	79.0	81.0					19																	42820840		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK075286	CCDS12603.1	19q13.2	2008-02-05				ENSG00000167619			26912	protein-coding gene	gene with protein product							Standard	NM_173633		Approved	FLJ90805	uc002otk.1	Q8NBT3		ENST00000301204.3:c.754C>A	19.37:g.42820840C>A	ENSP00000301204:p.Leu252Ile			Missense_Mutation	SNP	pfam_Rhodopsin-like_GPCR_TM_domain	p.L252I	ENST00000301204.3	37	c.754	CCDS12603.1	19	.	.	.	.	.	.	.	.	.	.	C	11.58	1.679881	0.29783	.	.	ENSG00000167619	ENST00000301204	T	0.39787	1.06	3.76	3.76	0.43208	Rhodopsin-like GPCR transmembrane domain (1);	0.000000	0.56097	D	0.000027	T	0.43765	0.1262	N	0.17723	0.515	0.48452	D	0.999652	D	0.65815	0.995	D	0.66602	0.945	T	0.19095	-1.0316	10	0.18276	T	0.48	-25.8863	13.4686	0.61270	0.0:1.0:0.0:0.0	.	252	Q8NBT3	TM145_HUMAN	I	252	ENSP00000301204:L252I	ENSP00000301204:L252I	L	+	1	0	TMEM145	47512680	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.414000	0.52693	1.838000	0.53458	0.455000	0.32223	CTC	TMEM145	-	pfam_Rhodopsin-like_GPCR_TM_domain	ENSG00000167619		0.667	TMEM145-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMEM145	HGNC	protein_coding	OTTHUMT00000463737.1	93	0.00	0	C	NM_173633		42820840	42820840	+1	no_errors	ENST00000301204	ensembl	human	known	69_37n	missense	63	39.42	41	SNP	1.000	A
USP54	159195	genome.wustl.edu	37	10	75276172	75276172	+	Missense_Mutation	SNP	C	C	G			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr10:75276172C>G	ENST00000339859.4	-	19	4112	c.4012G>C	c.(4012-4014)Ggg>Cgg	p.G1338R	USP54_ENST00000422491.2_Missense_Mutation_p.G520R|RP11-137L10.6_ENST00000600206.1_RNA|USP54_ENST00000394811.2_Missense_Mutation_p.G426R|RP11-137L10.6_ENST00000593790.1_RNA|USP54_ENST00000497106.1_5'UTR|RP11-137L10.6_ENST00000595069.1_RNA|USP54_ENST00000428547.1_Missense_Mutation_p.G1188R|USP54_ENST00000408019.1_Missense_Mutation_p.G1338R|RP11-137L10.6_ENST00000597958.1_RNA|RP11-137L10.6_ENST00000600607.1_RNA			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	1338					ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)	p.G426R(1)|p.G1338R(1)		breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					TCCTGCTGCCCCCATCCAGAA	0.547																																					Colon(195;880 2046 8854 25025 38456)	dbGAP											2	Substitution - Missense(2)	breast(2)											79.0	82.0	81.0					10																	75276172		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348		"""Ubiquitin-specific peptidases"""	23513	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 29"", ""ubiquitin specific protease 54"""	C10orf29		14715245	Standard	NM_152586		Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.4012G>C	10.37:g.75276172C>G	ENSP00000345216:p.Gly1338Arg		A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Missense_Mutation	SNP	pfam_Peptidase_C19,pfscan_Peptidase_C19	p.G1338R	ENST00000339859.4	37	c.4012	CCDS7329.2	10	.	.	.	.	.	.	.	.	.	.	C	6.292	0.421916	0.11928	.	.	ENSG00000166348	ENST00000339859;ENST00000408019;ENST00000428547;ENST00000394811;ENST00000422491	T;T;T;T;T	0.26223	1.94;1.94;1.92;1.75;1.79	5.87	3.03	0.35002	.	.	.	.	.	T	0.17152	0.0412	L	0.27053	0.805	0.80722	D	1	B;B	0.25390	0.028;0.125	B;B	0.24541	0.054;0.028	T	0.04811	-1.0925	9	0.42905	T	0.14	-0.8638	8.9683	0.35890	0.0:0.7155:0.0:0.2845	.	520;1338	E7EW90;Q70EL1	.;UBP54_HUMAN	R	1338;1338;1188;426;520	ENSP00000345216:G1338R;ENSP00000386080:G1338R;ENSP00000408714:G1188R;ENSP00000378290:G426R;ENSP00000407368:G520R	ENSP00000345216:G1338R	G	-	1	0	USP54	74946178	1.000000	0.71417	0.996000	0.52242	0.276000	0.26787	1.299000	0.33424	0.382000	0.24878	-0.143000	0.13931	GGG	USP54	-	NULL	ENSG00000166348		0.547	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	USP54	HGNC	protein_coding	OTTHUMT00000316563.2	147	0.00	0	C	NM_152586		75276172	75276172	-1	no_errors	ENST00000339859	ensembl	human	known	69_37n	missense	88	40.14	59	SNP	0.998	G
WWTR1	25937	genome.wustl.edu	37	3	149243909	149243909	+	Silent	SNP	C	C	A			TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr3:149243909C>A	ENST00000465804.1	-	7	1165	c.909G>T	c.(907-909)ggG>ggT	p.G303G	WWTR1_ENST00000360632.3_Silent_p.G303G|WWTR1_ENST00000467467.1_Silent_p.G303G|RNU6-1098P_ENST00000516772.1_RNA	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	303					cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.G303G(1)		breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			AATGATATGGCCCTCTGCAAA	0.458			T	CAMTA1	epitheliod hemangioendothelioma																																	dbGAP		Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	1	Substitution - coding silent(1)	breast(1)											93.0	85.0	88.0					3																	149243909		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408			24042	protein-coding gene	gene with protein product		607392				11118213, 15096513	Standard	NM_015472		Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.909G>T	3.37:g.149243909C>A			D3DNH7|Q8N3P2|Q9Y3W6	Silent	SNP	pfam_WW_Rsp5_WWP,superfamily_WW_Rsp5_WWP,smart_WW_Rsp5_WWP,pfscan_WW_Rsp5_WWP	p.G303	ENST00000465804.1	37	c.909	CCDS3144.1	3																																																																																			WWTR1	-	NULL	ENSG00000018408		0.458	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WWTR1	HGNC	protein_coding	OTTHUMT00000356498.1	103	0.00	0	C	NM_015472		149243909	149243909	-1	no_errors	ENST00000360632	ensembl	human	known	69_37n	silent	88	25.42	30	SNP	0.994	A
XKR6	286046	genome.wustl.edu	37	8	10755750	10755750	+	Silent	SNP	G	G	A	rs549267712		TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr8:10755750G>A	ENST00000416569.2	-	3	1664	c.1638C>T	c.(1636-1638)gcC>gcT	p.A546A	XKR6_ENST00000304437.2_Silent_p.A267A	NM_173683.3	NP_775954.2	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related family, member 6	546						integral component of membrane (GO:0016021)		p.A546A(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(8)|ovary(2)|prostate(1)|skin(3)	31				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		GTTCCGTTACGGCTCTGGTGG	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		16697	0.0		0.0	False		,,,				2504	0.001					dbGAP											1	Substitution - coding silent(1)	breast(1)											53.0	41.0	45.0					8																	10755750		2203	4298	6501	-	-	-	SO:0001819	synonymous_variant	0			BC024146	CCDS5978.2	8p23.1	2009-05-27	2006-01-12	2005-07-28	ENSG00000171044	ENSG00000171044			27806	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 7"", ""chromosome 8 open reading frame 21"", ""X Kell blood group precursor-related family, member 6"", ""chromosome 8 open reading frame 5"""	C8orf7, C8orf21, C8orf5			Standard	NM_173683		Approved		uc003wtk.1	Q5GH73	OTTHUMG00000129351	ENST00000416569.2:c.1638C>T	8.37:g.10755750G>A			Q8TBA0	Missense_Mutation	SNP	pfam_Transport_prot_XK	p.P323L	ENST00000416569.2	37	c.968	CCDS5978.2	8	.	.	.	.	.	.	.	.	.	.	G	4.089	0.014456	0.07959	.	.	ENSG00000171044	ENST00000382461	.	.	.	4.78	3.85	0.44370	.	.	.	.	.	T	0.57989	0.2091	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54337	-0.8309	4	.	.	.	-8.0936	8.0168	0.30385	0.0985:0.1699:0.7316:0.0	.	.	.	.	L	323	.	.	P	-	2	0	XKR6	10793160	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	3.470000	0.53100	1.137000	0.42214	-0.367000	0.07326	CCG	XKR6	-	NULL	ENSG00000171044		0.637	XKR6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	XKR6	HGNC	protein_coding	OTTHUMT00000383958.1	23	0.00	0	G	NM_173683		10755750	10755750	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000382461	ensembl	human	putative	69_37n	missense	15	28.57	6	SNP	1.000	A
ZNF592	9640	genome.wustl.edu	37	15	85341673	85341673	+	Missense_Mutation	SNP	G	G	T	rs201965611		TCGA-B6-A0RN-01A-12D-A099-09	TCGA-B6-A0RN-10A-01D-A099-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	bbbcb493-2937-4a7b-8454-0abbbb379927	5465e36a-97f7-4408-81c1-9f8e836c1279	g.chr15:85341673G>T	ENST00000560079.2	+	7	2992	c.2704G>T	c.(2704-2706)Gtg>Ttg	p.V902L	ZNF592_ENST00000299927.3_Missense_Mutation_p.V902L	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	902					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V902L(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			ACTCTTGTTCGTGCAGAAGCC	0.577																																						dbGAP											1	Substitution - Missense(1)	breast(1)											65.0	55.0	58.0					15																	85341673		2203	4299	6502	-	-	-	SO:0001583	missense	0			D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"""Zinc fingers, C2H2-type"""	28986	protein-coding gene	gene with protein product		613624	"""spinocerebellar ataxia, autosomal recessive 5"""	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.2704G>T	15.37:g.85341673G>T	ENSP00000452877:p.Val902Leu		Q2M1T2|Q504Y9	Missense_Mutation	SNP	smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.V902L	ENST00000560079.2	37	c.2704	CCDS32317.1	15	.	.	.	.	.	.	.	.	.	.	G	6.526	0.465249	0.12402	.	.	ENSG00000166716	ENST00000299927	T	0.27557	1.66	5.65	3.6	0.41247	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.626322	0.17293	N	0.179550	T	0.16257	0.0391	N	0.21545	0.675	0.23361	N	0.997837	B	0.02656	0.0	B	0.04013	0.001	T	0.25502	-1.0130	10	0.10636	T	0.68	-3.0E-4	6.2943	0.21077	0.2842:0.5322:0.1836:0.0	.	902	Q92610	ZN592_HUMAN	L	902	ENSP00000299927:V902L	ENSP00000299927:V902L	V	+	1	0	ZNF592	83142677	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.784000	0.38674	1.368000	0.46115	0.650000	0.86243	GTG	ZNF592	-	smart_Znf_C2H2-like,pfscan_Znf_C2H2	ENSG00000166716		0.577	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF592	HGNC	protein_coding	OTTHUMT00000418779.2	66	0.00	0	G	NM_014630		85341673	85341673	+1	no_errors	ENST00000299927	ensembl	human	known	69_37n	missense	41	42.25	30	SNP	1.000	T
