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INDIVIDUALS: SNP LIST:	GROUPS: SAVED GENE LIST: GENE LIST:	INDIVIDUALS: EXCLUDE SNP LIST:	EXCLUDE GROUPS: EXCLUDE SAVED GENE LIST: EXCLUDE GENE LIST:
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VARIANT EFFECT	FUNCTIONAL CLASS	IMPACT
MUTATION TYPE:	CHR: POS:

DBSNP BUILD: EXCLUDE VARIANTS AT VARISNP	READ DEPTH: QUAL:	VARIANTS PER GENE:
SHOW ONLY VARIANTS PRESENT IN COMMON GENES BETWEEN ALL THE INDIVIDUALS SELECTED SHOW ONLY VARIANTS AT EXACTLY SAME POSITION BETWEEN ALL THE INDIVIDUALS SELECTED EXCLUDE ALL VARIANTS PRESENT IN LATEST DBSNP BUILD SHOW ONLY VARIANTS PRESENT AT HGMD

FREQUENCIES

1000 GENOMES FREQUENCY	EXCLUDE ALL VARIANTS PRESENT IN 1000GENOMES	DBSNP FREQUENCY	EXCLUDE ALL VARIANTS PRESENT IN DBSNP	ESP6500 FREQUENCY	EXCLUDE ALL VARIANTS PRESENT IN EXOME SEQUENCING PROJECT

SCORES

SIFT SCORE	EXCLUDE VARIANTS WITHOUT SIFT SCORE	POLYPHEN2 SCORE	EXCLUDE VARIANTS WITHOUT POLYPHEN SCORE
CADD	EXCLUDE VARIANTS WITHOUT CADD SCORE	MCAP	EXCLUDE VARIANTS WITHOUT M-CAP SCORE

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+ Genes 20

Genes:
ARHGAP39, ATF7IP2, C19orf33, CHD1, EHMT2, FNBP4, GJB3, GNL3, HEATR5A, KAT6B, LPIN1, MCPH1, MSH3, NINL, PDCD6, PLK5, RFPL1, RTKN2, SNAPC4, WDR60,

+ Genes associated with diseases 7

Genes at Omim

CHD1, GJB3, KAT6B, LPIN1, MCPH1, MSH3, WDR60,

CHD1	Pilarowski-Bjornsson syndrome, 617682 (3)
GJB3	Deafness, autosomal dominant 2B, 612644 (3) Deafness, autosomal dominant, with peripheral neuropathy (3) Deafness, autosomal recessive (3) Deafness, digenic, GJB2/GJB3, 220290 (3) Erythrokeratodermia variabilis et progressiva 1, 133200 (3)
KAT6B	Genitopatellar syndrome, 606170 (3) SBBYSS syndrome, 603736 (3)
LPIN1	Myoglobinuria, acute recurrent, autosomal recessive, 268200 (3)
MCPH1	Microcephaly 1, primary, autosomal recessive, 251200 (3)
MSH3	Endometrial carcinoma, somatic, 608089 (3) Familial adenomatous polyposis 4, 617100 (3)
WDR60	Short-rib thoracic dysplasia 8 with or without polydactyly, 615503 (3)

Genes at Clinical Genomics Database

GJB3, KAT6B, LPIN1, MCPH1, MSH3, WDR60,

GJB3	Deafness, autosomal recessive Deafness, autosomal dominant, with peripheral neuropathy Deafness digenic
KAT6B	Ohdo syndrome, SBBYS variant Genitopatellar syndrome
LPIN1	Myoglobinuria, acute, recurrent, autosomal recessive
MCPH1	Microcephaly, primary autosomal recessive, 1
MSH3	Endometrial carcinoma
WDR60	Short -rib thoracic dysplasia 8 with or without polydactyly

Genes at HGMD

Summary

Number of Variants: 20
Number of Genes: 20

Export to: CSV

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ARHGAP39
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	manuela_niro	8	rs138155129 dbSNP Clinvar	145773341	54.64	TCTG	T	PASS	0/1	118	CODON_DELETION	MODERATE	None	0.01777	0.01777	0.05398				None None	None None None None	ARHGAP39\|0.083072421\|54.56%
ATF7IP2
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	manuela_niro	16	rs566280429 dbSNP Clinvar	10565978	53.16	ATGT	A	PASS	0/1	101	CODON_DELETION	MODERATE	None	0.00499	0.00499	0.00841				None None	None None None None	ATF7IP2\|0.022985481\|72.74%
C19orf33
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	manuela_niro	19	rs139805446 dbSNP Clinvar	38795546	70.51	TGAA	T	PASS	0/1	128	CODON_DELETION	MODERATE	None	0.15395	0.15400	0.13221				None None	None None None None	C19orf33\|0.001107009\|94.9%
CHD1
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	manuela_niro	5	rs138635992 dbSNP Clinvar	98192164	354.12	AAGG	A	PASS	1/1	60	CODON_DELETION	MODERATE	None	0.21266	0.21270	0.29454				None None	None None None None	CHD1\|0.573996389\|12.85%
EHMT2
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	manuela_niro	6	rs565112979 dbSNP Clinvar	31855825	45.67	GAGA	G	PASS	0/1	69	CODON_DELETION	MODERATE	None	0.00519	0.00519	0.00388				None None	None None None None	EHMT2\|0.178387468\|39.23%
FNBP4
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	manuela_niro	11	rs67450550,rs397711020 dbSNP Clinvar	47788663	28.97	CG...	C	PASS	0/1	58	CODON_DELETION	MODERATE	None	0.34385	0.34380	0.28457				None None	None None None None	FNBP4\|0.128911104\|46.04%
GJB3
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	manuela_niro	1	rs727503069 dbSNP Clinvar	35251013	175.63	GC...	G	PASS	0/1	269	CODON_DELETION	MODERATE	None			0.00016				None None	None None None None	SMIM12\|0.590271494\|12.11%,GJB3\|0.12611237\|46.44%
GNL3
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	manuela_niro	3	rs111396798,rs374163260 dbSNP Clinvar	52727764	63.22	CAGG	C	PASS	0/1	207	CODON_DELETION	MODERATE	None	0.02656	0.02656	0.03318				None None	None None None None	GNL3\|0.156229255\|42.12%
HEATR5A
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	manuela_niro	14	rs142429257 dbSNP Clinvar	31856395	124.15	CAAG	C	PASS	0/1	193	CODON_DELETION	MODERATE	None	0.00679	0.00679	0.02295				None None	None None None None	HEATR5A\|0.279604078\|29.11%
KAT6B
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	manuela_niro	10	rs71929101,rs559824889 dbSNP Clinvar	76781905	31.85	GGAA	G	PASS	0/1	57	CODON_DELETION	MODERATE	None	0.00220	0.45870					None None	None None None None	KAT6B\|0.719816483\|7.97%
LPIN1
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	manuela_niro	2	rs149564563,rs886038732 dbSNP Clinvar	11922326	137.41	GTCT	G	PASS	0/1	198	CODON_DELETION	MODERATE	None	0.00998	0.00998	0.01182				None None	None None None None	LPIN1\|0.048089992\|63.3%
MCPH1
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	manuela_niro	8	.	6302587	77.19	TAAG	T	PASS	0/1	113	CODON_DELETION	MODERATE	None							None None	None None None None	MCPH1\|0.001260573\|94.1%
MSH3
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	manuela_niro	5	rs144629981,rs3045983 dbSNP Clinvar	79950741	630.25	GC...	G	PASS	1/1	114	CODON_DELETION	MODERATE	None	0.23443	0.23440	0.30955				None None	None None None None	DHFR\|0.849258328\|4.67%,MSH3\|0.44757189\|18.27%
NINL
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	manuela_niro	20	rs68078266,rs34410422 dbSNP Clinvar	25457049	63.36	GC...	G	PASS	0/1	105	CODON_DELETION	MODERATE	None	0.55731	0.55730	0.42148				None None	None None None None	NINL\|0.010538639\|80.48%
PDCD6
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	manuela_niro	5	rs147793210,rs529816592 dbSNP Clinvar	271857	36.01	CC...	C	PASS	0/1	50	CODON_DELETION	MODERATE	None	0.10244	0.10240	0.11116				None None	None None None None	PDCD6\|0.124189476\|46.79%
PLK5
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	manuela_niro	19	rs58035688,rs796379895 dbSNP Clinvar	1535193	154.89	GCCC	G	PASS	0/1	153	CODON_DELETION	MODERATE	None	0.45867	0.45870					None None	None None None None	PLK5\|0.003429971\|87.9%
RFPL1
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	manuela_niro	22	rs71324764,rs3842466 dbSNP Clinvar	29837566	156.42	TTCC	T	PASS	0/1	224	CODON_DELETION	MODERATE	None	0.26677	0.26680	0.35245				None None	None None None None	RFPL1\|0.000705614\|97.22%
RTKN2
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	manuela_niro	10	rs149331212,rs59044276 dbSNP Clinvar	63976912	20.06	TA...	T	PASS	0/1	27	CODON_DELETION	MODERATE	None	0.14058	0.14060	0.18531				None None	None None None None	RTKN2\|0.169836183\|40.34%
SNAPC4
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	manuela_niro	9	rs147271628 dbSNP Clinvar	139277994	88.94	CGCT	C	PASS	0/1	74	CODON_DELETION	MODERATE	None	0.19070	0.19070					None None	None None None None	SNAPC4\|0.002400965\|89.89%
WDR60
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	manuela_niro	7	rs145233696,rs3833679 dbSNP Clinvar	158664074	47.15	TGAA	T	PASS	0/1	45	CODON_DELETION	MODERATE	None	0.11641	0.11640	0.15404				None None	None None None None	WDR60\|0.002501665\|89.69%

+ Filter Options

FREQUENCIES

SCORES

+ Genes 20

+ Genes associated with diseases 7

Genes at Omim

Genes at Clinical Genomics Database

Genes at HGMD

Summary

ARHGAP39

ATF7IP2

C19orf33

CHD1

EHMT2

FNBP4

GJB3

GNL3

HEATR5A

KAT6B

LPIN1

MCPH1

MSH3

NINL

PDCD6

PLK5

RFPL1

RTKN2

SNAPC4

WDR60

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