Mendel,MD - Cloud Based Genome Analysis

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VARIANT EFFECT	FUNCTIONAL CLASS	IMPACT
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SCORES

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CADD	EXCLUDE VARIANTS WITHOUT CADD SCORE	MCAP	EXCLUDE VARIANTS WITHOUT M-CAP SCORE

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Genes:
AARS2, ABCC3, ADAM15, AGXT2, ALDH16A1, AMER3, ARHGEF16, ATF6B, ATP11A, BRPF1, C6orf195, C6orf47, CCDC102A, CCDC88B, CECR5, CERS2, CMBL, CNTLN, CNTNAP3, COPS8, CYP2W1, DAB2, DAXX, DDX25, DHX34, DNAH2, EFCAB6, ELOVL5, EMC4, EPPK1, FAM178A, FAM205A, FAM206A, FARS2, FASTKD3, FILIP1, FUT5, GRAMD1A, ILK, ILVBL, KLRB1, LAMA1, LEF1, LILRB5, LIMK2, LMO2, MAGEB2, MEGF9, MLLT4, MST1, MYO10, NDUFV3, NEURL4, NISCH, NLGN2, NOL7, NPC1L1, PANK3, PDZD2, PITPNM2, PKD1, PLCG2, PLEKHG4B, PLEKHG5, PPP1R1A, PRUNE, PTBP3, PVR, RAPGEF3, RBM25, RECK, SERPINB6, SLC10A4, SLC6A19, SLC9A3, SOGA2, SPTA1, SULT1A1, TCF3, TEX2, TFRC, TRIOBP, USP30, VARS2, WDR11, WDR13, WDR18, ZFPM1, ZFYVE1, ZNF414, ZNF541, ZNF563,

+ Genes associated with diseases 19

Genes at Omim

AARS2, ELOVL5, FARS2, LAMA1, LEF1, LMO2, NPC1L1, PKD1, PLCG2, PLEKHG5, SERPINB6, SLC6A19, SLC9A3, SPTA1, TCF3, TFRC, TRIOBP, VARS2, WDR11,

AARS2	Leukoencephalopathy, progressive, with ovarian failure, 615889 (3) Combined oxidative phosphorylation deficiency 8, 614096 (3)
ELOVL5	Spinocerebellar ataxia 38, 615957 (3)
FARS2	Combined oxidative phosphorylation deficiency 14, 614946 (3) ?Spastic paraplegia 77, autosomal recessive, 617046 (3)
LAMA1	Poretti-Boltshauser syndrome, 615960 (3)
LEF1	Sebaceous tumors, somatic (3)
LMO2	Leukemia, acute T-cell (2)
NPC1L1	[Ezetimibe, nonresponse to] (3)
PKD1	Polycystic kidney disease, adult type I, 173900 (3)
PLCG2	Familial cold autoinflammatory syndrome 3, 614468 (3) Autoinflammation, antibody deficiency, and immune dysregulation syndrome, 614878 (3)
PLEKHG5	Spinal muscular atrophy, distal, autosomal recessive, 4, 611067 (3) Charcot-Marie-Tooth disease, recessive intermediate C, 615376 (3)
SERPINB6	?Deafness, autosomal recessive 91, 613453 (3)
SLC6A19	Iminoglycinuria, digenic, 242600 (3) Hyperglycinuria, 138500 (3) Hartnup disorder, 234500 (3)
SLC9A3	Diarrhea 8, secretory sodium, congenital, 616868 (3)
SPTA1	Spherocytosis, type 3, 270970 (3) Pyropoikilocytosis, 266140 (3) Elliptocytosis-2, 130600 (3)
TCF3	Agammaglobulinemia 8, autosomal dominant, 616941 (3)
TFRC	Immunodeficiency 46, 616740 (3)
TRIOBP	Deafness, autosomal recessive 28, 609823 (3)
VARS2	Combined oxidative phosphorylation deficiency 20, 615917 (3)
WDR11	Hypogonadotropic hypogonadism 14 with or without anosmia, 614858 (3)

Genes at Clinical Genomics Database

AARS2, ELOVL5, FARS2, LAMA1, NPC1L1, PKD1, PLCG2, PLEKHG5, SERPINB6, SLC6A19, SPTA1, TCF3, TFRC, TRIOBP, VARS2, WDR11,

AARS2	Leukoencephalopathy, progressive, with ovarian failure
ELOVL5	Spinocerebellar ataxia 39
FARS2	Combined oxidative phosphorylation deficiency 14
LAMA1	Poretti-Boltshauser syndrome
NPC1L1	Ezetimibe, nonresponse to
PKD1	Polycystic kidney disease, adult type I
PLCG2	Autoinflammation, antibody deficiency, and immune dysregulation syndrome (APLAID) Familial cold autoinflammatory syndrome 3 (PLAID)
PLEKHG5	Spinal muscular atrophy, distal, autosomal recessive, 4 Charcot-Marie-Tooth disease C, recessive intermediate
SERPINB6	Deafness, autosomal recessive 91
SLC6A19	Hartnup disease
SPTA1	Ellipsocytosis 2 Pyropoikilocytosis , hereditary Spherocytosis, type 3
TCF3	Agammaglobulinemia 8, autosomal dominant
TFRC	Immunodeficiency 46
TRIOBP	Deafness, autosomal recessive 28
VARS2	Combined oxidative phosphorylation deficiency 20
WDR11	Kallmann syndrome Hypogonadotropic hypogonadism

Genes at HGMD

Summary

Number of Variants: 95
Number of Genes: 92

Export to: CSV

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MAGEB2
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	23 recalibrated filtered postcgp gqfiltered	X	.	30237403	939.96	C	T	PASS	1/1	18	STOP_GAINED	HIGH	NONSENSE							None None	None None None None	None
WDR13
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	23 recalibrated filtered postcgp gqfiltered	X	.	48460513	3656.75	G	A	PASS	1/1	12	STOP_GAINED	HIGH	NONSENSE							None None	None None None None	None
CNTNAP3
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	23 recalibrated filtered postcgp gqfiltered	9	.	39088492	58454.83	T	A	VQSRTrancheSNP99.90to100.00	0/1	68	STOP_GAINED	HIGH	NONSENSE						0.25	None None	None None None None	None
RECK
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	23 recalibrated filtered postcgp gqfiltered	9	.	36105267	47326.5	A	G	PASS	0/1	83	STOP_GAINED	HIGH	NONSENSE							None None	None None None None	None
FAM205A
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	23 recalibrated filtered postcgp gqfiltered	9	.	34723747	2443.63	C	A	PASS	0/1	154	STOP_GAINED	HIGH	NONSENSE						1.11	None None	None None None None	None
CNTLN
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	23 recalibrated filtered postcgp gqfiltered	9	.	17394538	62447.53	C	T	PASS	1/1	6	STOP_GAINED	HIGH	NONSENSE						0.55	None None	None None None None	None
MEGF9
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	23 recalibrated filtered postcgp gqfiltered	9	.	123367625	2175.66	C	T	PASS	0/1	61	STOP_GAINED	HIGH	NONSENSE							None None	None None None None	None
FAM206A
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	23 recalibrated filtered postcgp gqfiltered	9	.	111701910	2659.7	C	T	PASS	0/1	5	STOP_GAINED	HIGH	NONSENSE							None None	None None None None	None
PTBP3
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	23 recalibrated filtered postcgp gqfiltered	9	.	115038138	4980.24	T	A	PASS	1/1	29	STOP_GAINED	HIGH	NONSENSE							None None	None None None None	None
EPPK1
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	23 recalibrated filtered postcgp gqfiltered	8	.	144946362	5708.86	G	A	PASS	1/1	84	STOP_GAINED	HIGH	NONSENSE							None None	None None None None	None