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Frontiers of Medicine

ISSN 2095-0217

ISSN 2095-0225(Online)

CN 11-5983/R

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Front. Med.    2021, Vol. 15 Issue (6) : 877-886    https://doi.org/10.1007/s11684-021-0863-4
RESEARCH ARTICLE
Penetrance estimation of PRRT2 variants in paroxysmal kinesigenic dyskinesia and infantile convulsions
Yulan Chen1, Dianfu Chen1, Shaoyun Zhao1, Gonglu Liu2, Hongfu Li1(), Zhi-Ying Wu1()
1. Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310009, China
2. Department of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
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Abstract

Proline-rich transmembrane protein 2 (PRRT2) is the leading cause of paroxysmal kinesigenic dyskinesia (PKD), benign familial infantile epilepsy (BFIE), and infantile convulsions with choreoathetosis (ICCA). Reduced penetrance of PRRT2 has been observed in previous studies, whereas the exact penetrance has not been evaluated well. The objective of this study was to estimate the penetrance of PRRT2 and determine its influencing factors. We screened 222 PKD index patients and their available relatives, identified 39 families with pathogenic or likely pathogenic (P/LP) PRRT2 variants via Sanger sequencing, and obtained 184 PKD/BFIE/ICCA families with P/LP PRRT2 variants from the literature. Penetrance was estimated as the proportion of affected variant carriers. PRRT2 penetrance estimate was 77.6% (95% confidence interval (CI) 74.5%–80.7%) in relatives and 74.5% (95% CI 70.2%–78.8%) in obligate carriers. In addition, we first observed that penetrance was higher in truncated than in non-truncated variants (75.8% versus 50.0%, P = 0.01), higher in Asian than in Caucasian carriers (81.5% versus 68.5%, P = 0.004), and exhibited no difference in gender or parental transmission. Our results are meaningful for genetic counseling, implying that approximately three-quarters of PRRT2 variant carriers will develop PRRT2-related disorders, with patients from Asia or carrying truncated variants at a higher risk.

Keywords penetrance      PRRT2      paroxysmal kinesigenic dyskinesia      infantile convulsions     
Corresponding Author(s): Hongfu Li,Zhi-Ying Wu   
Just Accepted Date: 31 August 2021   Online First Date: 25 November 2021    Issue Date: 27 December 2021
 Cite this article:   
Yulan Chen,Dianfu Chen,Shaoyun Zhao, et al. Penetrance estimation of PRRT2 variants in paroxysmal kinesigenic dyskinesia and infantile convulsions[J]. Front. Med., 2021, 15(6): 877-886.
 URL:  
https://academic.hep.com.cn/fmd/EN/10.1007/s11684-021-0863-4
https://academic.hep.com.cn/fmd/EN/Y2021/V15/I6/877
Variants Amino acid ?changes Frequency of population In silico prediction ACMG ?classification
1000 g ExAC gnomAD SIFT Polyphen-2
?(HumVar)
Mutation
?Taster
REVEL MetaLR
c.5C>T p.A2V Absent Absent Absent D D D T D US (PM2, PP3)
c.680G>A p.R227Q Absent 9.79E–06 1.36E–05 T P N T T US (PM2, BP4)
c.766delG p.V256Wfs*57 Absent Absent Absent D NA D NA NA Pathogenic ?(PVS1, PM2, ?PP3)
c.881C>T p.S294F Absent Absent Absent D D D D D US (PM2, PP3)
c.902G>C p.G301A Absent Absent Absent D D D D D US (PM2, PP3)
c.952_?953dupAT p.V319Sfs*19 Absent Absent Absent D NA D NA NA Pathogenic ?(PVS1, PM2, ?PP3)
c.962T>C p.L321P Absent Absent Absent D D D D D US (PM1, PM2, ?PP3)
c.976_?978delCTC p.L326del Absent 8.52E–06 1.23E–05 D NA D NA NA LP (PM1, PM2, ?PM4, PP3)
c.1012G>A p.V338M Absent 8.58E–06 4.17E–06 T B D T T US (PM1, PM2)
NatGene2 HSF NNSplice
c.879+ 4A>G NA Absent Absent Absent Donor site lost Donor site lost Donor site lost US (PM2, PP3)
Tab.1  Pathogenicity classification of 10 novel PRRT2 variants
Fig.1  PRRT2 variants identified in our 222 PKD index patients. (A) Diagram of PRRT2 variants superimposed to the domain structure of PRRT2 protein. PRRT2 contains 4 exons that encode a 340 amino acid protein. The “pathogenic/likely pathogenic” variants are labeled in red, and variants of “uncertain significance” are depicted in black. The number in the bracket represents the number of index patients carrying that variant. PRD, proline-rich domain; M1, transmembrane domain 1; M2, transmembrane domain 2; LOOP, domain between M1 and M2. (B) Chromatograms of 10 novel PRRT2 variants. The upper chromatogram in each frame represents the reference sequence, while the lower one represents the variant.
Fig.2  Flowchart of the study design and penetrance estimation.
Nucleotide change Protein change Number of ?families ?(n = 223) Number of ?affected/?variant ?carriersb Penetrance 1 Number of ?affected/?obligate ?carriers Penetrance 2
c.121_122delGT23 p.V41Tfs*92 1 4/5 0.8 1/2 0.5
c.133_136delCCAG25,a p.P45Rfs*44 2 0/2 0 0/2 0
c.186_187delGC22 p.P63Qfs*70 1 1/1 1 1/1 1
c.291delC4 p.N98Tfs*17 1 2/2 1 1/1 1
c.388delG12 p.A130Pfs*46 1 1/1 1 1/1 1
c.433delC6 p.R145Gfs*31 1 1/2 0.5 1/2 0.5
c.487C>T1 p.Q163X 1 5/7 0.71 3/3 1
c.514_517delTCTG19,a p.S172Rfs*3 2 3/4 0.75 2/3 0.67
c.604_607delTCAC24,a p.S202Hfs*26 2 4/5 0.8 2/2 1
c.621dupA27 p.S208Ifs*17 1 10/12 0.83 5/6 0.83
c.629dupC1 p.A211Sfs*14 1 3/3 1 2/2 1
c.629delC4 p.P210Qfs*19 1 4/7 0.57 1/3 0.33
c.649dupC1−9,11,14-20,23,25,26,28,29,a p.R217Pfs*8 173 427/536 0.80 237/307 0.77
c.649delC19−21,23,a p.R217Pfs*12 12 22/38 0.58 11/20 0.55
c.649C>T26,a p.R217X 2 2/2 1 2/2 1
c.697_698delAG20 p.S233Wfs*9 1 2/2 1 1/1 1
c.718C>T3,6,16,28,a p.R240X 6 18/19 0.95 9/10 0.9
c.741delC6 p.S248Afs*65 1 1/1 1 1/1 1
c.776dupG10,26 p.E260X 2 4/5 0.8 2/2 1
c.879+ 1G>T2,20 NA 2 3/5 0.6 1/2 0.5
c.880-2A>T5 NA 1 1/1 1 1/1 1
c.904_905insG19 p.D302Gfs*39 1 0/1 0 0/1 0
c.916G>A5 p.A306T 1 1/1 1 1/1 1
c.917C>A13 p.A306D 1 5/5 1 4/4 1
c.919C>T12 p.Q307X 1 0/1 0 0/1 0
c.950G>A2,28 p.S317N 2 11/22 0.5 3/13 0.23
c.971G>A5 p.G324E 1 2/2 1 1/1 1
c.976_978delCTCa p.L326del 1 1/1 1 1/1 1
Tab.2  Penetrance estimation of 28 PRRT2 variants identified in our and the published families
Combined Families??? P valuea
Our Published
All families, n 223 39 184
Total variant carriers (excluding index patients), n 693 61 632
?Affected, n 538 46 492
?Penetrance 1, % (95% CI) 77.6 (74.5–80.7) 75.4 (64.3–86.5) 77.8 (74.6–81.1) 0.663b
Total obligate carriers, n 396 43 353
?Affected, n 295 29 266
?Penetrance 2, % (95% CI) 74.5 (70.2–78.8) 67.4 (51.5–80.9) 75.4 (70.8–79.9) 0.261b
Tab.3  PRRT2 penetrance estimation in our and the published families
Obligate carriers, n Affected, n Penetrance, % (95% CI) P value
Variant type 0.01a
??Truncated variants 376 285 75.8 (71.4–80.1)
???Frameshift 355 267 75.2 (70.7–79.7)
???Nonsense 18 16 88.9 (65.3–98.6)
???Splice site 3 2 /
??Non-truncated variants 20 10 50.0 (27.2–72.8)
???Missense 19 9 47.4 (24.5–71.1)
???Non-frameshift deletion 1 1 /
Gender 0.271b
??Male 193 139 72.0 (65.6–78.4)
??Female 203 156 76.8 (71.0–82.7)
Parental transmission 0.334b
??Maternal 73 66 90.4 (83.5–97.3)
??Paternal 67 57 85.1 (76.3–93.8)
??Unknown 255 / /
??De novo 1 / /
Ethnic origin
??Asian 178 145 81.5 (75.7–87.2) 0.004c
??Caucasian 197 135 68.5 (62.0–75.1)
??African American 2 2 /
??Unknown 19 / /
Tab.4  PRRT2 penetrance by variant type, gender, parental transmission, and ethnic origin
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