PRIMPOL Mutation: Functional Study Does Not Always Reveal the Truth

We have critically read the article entitled “Human PrimPol mutation associated with high myopia has a DNA replication defect” by Keen et al.¹ The authors revealed that a point mutation (p.Y89D) in PRIMPOL identified in patients with high myopia² showed a major disruption of the catalytic and replication activities and, thus, established an association between replication stress and human disease (particularly high myopia) for the p.Y89D mutation in PRIMPOL.¹ This variant was predicted to be benign or possibly damaging by SIFT (available in the public domain at http://sift.jcvi.org/www/SIFT_enst_submit.html) and PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/), respectively. PRIMPOL encodes a primase-polymerase protein that is expressed in the eye tissue as well as in 22 other human tissues (available in the public domain at http://www.ncbi.nlm.nih.gov/unigene/). 

However, whole exome sequencing of 1220 samples from unrelated probands with different forms of genetic eye diseases revealed the heterozygous variant (c.265T>G, p.Y89D) in PRIMPOL in two of 407 patients with high myopia and 13 of 813 patients with other ocular diseases (see Table); this was confirmed by Sanger sequencing (see Figure). Further screening of additional samples identified the p.Y89D variant in seven of 384 normal controls (see Table). The seven normal controls had unaided visual acuity of 0.8 or better and refraction between −0.50 and +1.00 diopters (D; spherical equivalent, see Table). This variant also was present in the 1000 Genomes database with a minor allele frequency of 0.0018 (9/5008) (available in the public domain at http://browser.1000genomes.org/index.html), but it was not present in the Exome Variant Server (available in the public domain at http://evs.gs.washington.edu/EVS/). The frequencies of this variant were not significantly different (P > 0.05, Pearson χ² test) among individuals with high myopia, other forms of genetic eye diseases, and normal controls. These data suggest that the p.Y89D variant in PRIMPOL occurs randomly in the general population. Therefore, the findings of Keen et al.¹ are expected to be reevaluated. Nevertheless, the p.Y89D variant in PRIMPOL is highly unlikely to have roles in high myopia whether it caused major disruption of catalytic and replication activities or not. 

Figure

 

Sequence chromatography. Sequence change detected in the individuals with the variant was shown at the top, whereas normal sequence was shown at the bottom.

Table

 

Clinical Data of Individuals With the p.Y89D Variant in PRIMPOL

ID	Sex	Age at Exam, y	Diagnosis	Visual Acuity Right; Left	Spherical Equivalent Right; Left	Axial Length, mm Right; Left
HM738	F	14	HM	1.0; 1.0	−14.25 D; −21.75 D	28.06; 30.53
HM760	F	10	HM	0.4; 0.5	−13.50 D; −13.00 D	27.24; 26.99
RP105	M	12	RP	CF/30 cm; CF/30 cm	−11.50 D; −11.00 D	NA; NA
RP291	F	19	RP	0.6; 0.01	+1.75 D; +1.12 D	21.46; 21.64
RP297	M	53	RP	0.08; 0.06	NA; NA	NA; NA
RP383	M	7	RP	0.03; 0.03	NA; NA	NA; NA
QT272	M	7	CORD	CF/30 cm; 0.05	+1.00 D; +1.75 D	NA; NA
QT307	M	2	CORD	OP/30 cm; OP/30cm	NA; NA	NA; NA
QT352	F	4	CORD	NA; NA	+4.50 D; +4.75 D	NA; NA
QT626	F	3	LCA	NA; NA	NA; NA	NA; NA
QT1232	F	10	STGD	0.12; 0.12	NA; NA	23.21; 23.41
QT1302	F	1	LCA	NA; NA	NA; NA	NA; NA
G60	M	37	POAG	0.2; 0.6	NA; NA	NA; NA
G616	F	73	PACG	0.7; NLP	NA; NA	21.30; NA
RB109	F	35	RB	NLP; 1.5	NA; NA	NA; NA
MNC71	F	22	NC	1.2; 1.2	PL; +1.00 D	NA; NA
MNC790	F	19	NC	1.5; 1.5	PL; PL	24.11; 24.06
MNC855	M	20	NC	1.5; 1.5	PL; PL	23.50; 23.40
MNC942	F	22	NC	1.5; 1.5	+0.25; +1.00 D	23.10; 22.72
MNC957	M	20	NC	1.5; 1.5	PL; +0.25 D	24.08; 23.84
MNC962	M	22	NC	1.5; 1.5	−0.25 D; −0.25 D	24.38; 24.70
MNC965	F	19	NC	1.2; 1.2	−0.25 D; +0.25 D	23.32; 23.16

 F, female; M, male; HM, high myopia; RP, retinitis pigmentosa; CORD, cone-rod dystrophy; LCA, Leber congenital amaurosis; STGD, Stargardt disease; POAG, primary open-angle glaucoma; PACG; primary angle closure glaucoma; RB, retinoblastoma; NC, normal controls; CF, counting fingers; OP, objects pursuit; NLP, no light perception; PL, plano; NA, not available.

Acknowledgments

The authors thank the patients and the family members for their participation. 

Supported by Grant U1201221 from the National Natural Science Foundation of China, S2013030012978 from Natural Science foundation of Guangdong, 2011A080300002 from Guangdong Department of Science & Technology Translational Medicine Center, and by fundamental research funds of the State Key Laboratory of Ophthalmology (QZ).