| Literature DB >> 35860667 |
Yuwen Zhao1,2, Kailin Zhang1,2, Hongxu Pan1, Yige Wang1, Xiaoxia Zhou1, Yaqin Xiang1, Qian Xu1, Qiying Sun3, Jieqiong Tan4, Xinxiang Yan1, Jinchen Li2,3,4, Jifeng Guo1,2,4,5, Beisha Tang1,2,4,5, Zhenhua Liu1,2,4,5.
Abstract
Objectives: Parkinson's disease (PD) is a neurodegenerative disorder with the manifestation of motor symptoms and non-motor symptoms. Previous studies have indicated the role of several transmembrane (TMEM) protein family genes in PD pathogenesis. Materials andEntities:
Keywords: Parkinson’s disease; TMEM protein family genes; burden analysis; common variants; genetic analysis; rare variants
Year: 2022 PMID: 35860667 PMCID: PMC9289399 DOI: 10.3389/fnagi.2022.889057
Source DB: PubMed Journal: Front Aging Neurosci ISSN: 1663-4365 Impact factor: 5.702
Analysis of rare variant burden within targeted genes in Parkinson’s disease.
| Gene | MAF < 1% | MAF < 0.1% | |||||||
| Missense | Dmis | LoF | LoF + Dmis | Missense | Dmis | LoF | LoF + Dmis | ||
|
| WES cohort | 9 (0.147) | 6 (0.874) | – | 6 (0.874) | 6 (0.648) | 4 (0.475) | – | 4 (0.475) |
| WGS cohort | 10 (0.755) | 6 (0.355) | – | 6 (0.355) | 7 (0.829) | 4 (0.456) | – | 4 (0.456) | |
|
| WES cohort |
| 12 (0.069) | 1 (0.635) | 13 (0.071) |
|
| 1 (0.635) |
|
| WGS cohort | 12 (0.582) | 11 (0.420) | 1 (0.125) | 12 (0.191) | 11 (0.383) | 10 (0.216) | 1 (0.125) | 11 (0.071) | |
|
| WES cohort | 27 (0.259) | 17 (0.444) | – | 17 (0.444) | 24 (0.691) | 17 (0.444) | – | 17 (0.444) |
| WGS cohort | 27 (0.071) | 12 (0.526) | 1 (0.413) | 13 (0.551) |
| 12 (0.526) | 1 (0.413) | 13 (0.551) | |
|
| WES cohort | 11 (0.511) | 10 (0.510) | – | 10 (0.510) | 11 (0.511) | 10 (0.510) | – | 10 (0.510) |
| WGS cohort | 8 (0.689) | 8 (0.689) | – | 8 (0.689) | 7 (0.603) | 7 (0.603) | – | 7 (0.603) | |
|
| WES cohort | 51 (0.151) | 29 (0.592) | 7 (0.618) | 36 (0.601) | 42 (0.284) | 25 (0.729) | 6 (0.492) | 31 (0.820) |
| WGS cohort | 49 (0.396) | 25 (0.646) | 4 (0.182) | 29 (0.441) | 40 (0.299) | 21 (0.630) | 3 (0.095) | 24 (0.343) | |
|
| WES cohort | 6 (0.403) | 5 (0.442) | – | 5 (0.442) | 6 (0.403) | 5 (0.442) | – | 5 (0.442) |
| WGS cohort | 5 (0.764) | 4 (0.830) | 1 (0.582) | 5 (0.885) | 5 (0.764) | 4 (0.830) | 1 (0.582) | 5 (0.885) | |
Data were show as Number of Variants (SKAT-O P-value). MAF, minor allele frequency; Dmis, damaging missense variant (predicted by CADD ≥ 12.37); LoF, loss of function variant. Bold text indicates a statistically significant association with a p-value less than 0.05.
FIGURE 1Schematic diagram of six PD-related transmembrane (TMEM) protein family genes. Schematic diagram showing the transmembrane regions of six PD-related TMEM protein family genes and the rare damaging missense and loss-of-function variants of TMEM230 (A), TMEM59 (B), TMEM108 (C), TMEM163 (D), TMEM175 (E), and TMEM229B (F) in both cohorts.
Parkinson’s disease (PD) patient specific variants of TMEM230.
| Gene | Position (hg19) | Ref | Alt | NM number | AAChange | Consequence | gnomAD_ | gnomAD_ | ExAC_EAS | CADD | WES cohort | WGS cohort | ||
| Case ( | Control ( | Case ( | Control ( | |||||||||||
|
| 20:5081468 | G | A | NM_001009923 | c.521C > T:p.S174F | Missense | – | – | – | 31 | 0 | 0 | 1 | 0 |
|
| 20:5081495 | T | C | NM_001009923 | c.494A > G:p.Y165C | Missense | 0.0002 | – | 0.0001 | 21.1 | 0 | 0 | 2 | 0 |
|
| 20:5093650 | C | G | NM_001009923 | c.25G > C:p.V9L | Missense | – | – | – | 22.7 | 0 | 0 | 1 | 0 |