Exome-based investigation of the genetic basis of human pigmentary glaucoma

van der Heide, Carly; Goar, Wes; Meyer, Kacie J.; Alward, Wallace L. M.; Boese, Erin A.; Sears, Nathan C.; Roos, Ben R.; Kwon, Young H.; DeLuca, Adam P.; Siggs, Owen M.; Gonzaga-Jauregui, Claudia; Sheffield, Val C.; Wang, Kai; Stone, Edwin M.; Mullins, Robert F.; Anderson, Michael G.; Fan, Bao Jian; Ritch, Robert; Craig, Jamie E.; Wiggs, Janey L.; Scheetz, Todd E.; Fingert, John H.

doi:10.1186/s12864-021-07782-0

BMC Genomics

Table 4 MRAP mutations detected in PDS cases

From: Exome-based investigation of the genetic basis of human pigmentary glaucoma

						Cohort 1				Cohort 2										Cohort 1 and 2				gnomAD v2.1.1
						IA PDS		IA Normals		NY EEI PDS		MEE PDS		MEE Controls		Australian PDS		Australian Controls		Total Cases		Total Controls		Non-Finnish European	African and African American	South Asian
Mutations detected						n = 198		n = 359		n = 88		n = 150		N = 1500		n = 177		n = 145		n = 613		N = 2004		n > 55,000	n > 24,000	N > 15,000
SNP ID	MRAP Mutation		SIFT	PolyPhen	Blosum62	Instances	Genotype frequency	Instances	Genotype frequency	Instances	Genotype frequency	Instances	Genotype frequency	Instances	Genotype frequency	Instances	Genotype frequency	Instances	Genotype frequency	Instances	Genotype frequency	Instances	Genotype frequency	Genotype frequency	Genotype frequency	Genotype frequency
rs80358231	NM_178817.4:c.3G > A	p.Met1?	Deleterious	Possibly damaging	NA	1	0.51%	0	0%	0	0%	0	0%	0	0%	0	0%	0	0%	1	0.16%	0	0%	0.019%	0.016%	0%
rs138040820	NM_178817.4:c.18C > A	p.Asn6Lys	Deleterious	Probably damaging	0	2	1.0%	0	0%	0	0%	0	0%	2	0.13%	0	0%	0	0%	2	0.33%	2	0.10%	0.10%	0.040%	0%
rs781703497	NM_178817.4:c.190G > A	p.Ala64Thr	Deleterious	Benign	0	0	0%	0	0%	0	0%	1	0.67%	0	0%	0	0%	0	0%	1	0.16%	0	0%	0.0031%	0.0080%	0.059%
rs200277269	NM_178817.4:c.247G > A	pGly83Ser	Tolerated	Benign	−1	0	0%	0	0%	0	0%	0	0%	1	0.067%	0	0%	0	0%	0	0%	1	0.050%	0.0078%	0.21%	0.0065%
NA	NM_206898.1:c.301G > A	p.Ala101Thr	Tolerated	Benign	0	1	0.51%	0	0%	0	0%	0	0%	0	0%	0	0%	0	0%	1	0.16%	0	0%	0%	0%	0%
rs139379303	NM_178817.4:c.322G > A	p.Ala108Thr	Tolerated	Benign	0	0	0%	0	0%	0	0%	0	0%	3	0.20%	0	0%	0	0%	0	0%	3	0.15%	0.011%	0%	0%
rs200921993	NM_178817.4:c.359A > C	p.Asp120Ala	Tolerated	Benign	−2	0	0%	0	0%	0	0%	0	0%	12	0.80%	0	0%	0	0%	0	0%	12	0.60%	0.78%	1.1%	0.019%
rs200448756	NM_178817.4:c.446A > G	p.Asn149Ser	Tolerated	Benign	1	0	0%	0	0%	0	0%	0	0%	0	0%	0	0%	1	0.69%	0	0%	1	0.050%	0.0079%	0.0081%	0%
rs142897309	NM_178817.4:c.508 T > A	p.Leu170Met	Deleterious	Possibly damaging	2	0	0%	0	0%	0	0%	0	0%	2	0.13%	0	0%	0	0%	0	0%	2	0.10%	0.011%	0.57%	0%
Total						4	2.0%	0	0%	0	3.4%	1	0.67%	20	1.3%	0	0%	1	0.69%	5	0.82%	21	1.0%
Fisher’s Exact Test						p = 0.016				NA		p = 0.71				p = 0.45				NA
Cochran-Mantel-Haenszel										p = 0.49										p = 0.71
Mutations detected but excluded due to prevalence in control populations (> 2.5%)
rs75858661	NM_178817.4:c.148G > A	p.Val50Met	Deleterious	Probably damaging	1	0	0%	0	0%	3	3.4%	1	0.67%	3	0.20%	1	0.57%	0	0%	5	0.82%	3	0.15%	0.029%	8.0%	0.020%
rs79126334	NM_178817.4:c.234C > G	p.Cys78Trp	Deleterious	Probably damaging	−2	0	0%	0	0%	0	0%	2	1.3%	6	0.40%	0	0%	0	0%	2	0.33%	6	0.30%	0.017%	11%	0.0065%
rs115917390	NM_206898.1:c.257G > T	p.Arg86Leu	Tolerated	Benign	−2	0	0%	0	0%	0	0%	1	0.67%	4	0.27%	0	0%	0	0%	1	0.16%	4	0.20%	0.017%	5.6%	0.0065%
rs140113354	NM_206898.1:c.302C > T	p.Ala101Val	Tolerated	Benign	0	3	1.5%	0	0%	0	0%	0	0%	14	0.93%	0	0%	0	0%	3	0.49%	14	0.70%	0.51%	0.04%	3.7%
rs114530014	NM_178817.4:c.389C > T	p.Thr130Ile	Deleterious	Benign	−1	0	0%	0	0%	0	0%	0	0%	10	0.67%	1	0.57%	0	0%	1	0.16%	10	0.50%	0.022%	9.8%	0%

These variants in the bottom section were detected at a frequency > 2.5% in control populations of Non-Finnish European, African, or South Asian ancestry (gnomAD database) and were excluded from further analysis. Abbreviations in the table are: Iowa (IA), Massachusetts Eye and Ear (MEE), New York Eye and Ear Infirmary (NYEEI)

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