chr12:40757328:G>A Detail (hg19) (LRRK2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr12:40,757,328-40,757,328 |
| hg38 | chr12:40,363,526-40,363,526 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_198578.3:c.7153G>A | NP_940980.3:p.Gly2385Arg |
| Ensemble | ENST00000298910.12:c.7153G>A | ENST00000298910.12:p.Gly2385Arg |
| ENST00000680790.1:c.6898G>A | ENST00000680790.1:p.Gly2300Arg |
Summary
MGeND
| Clinical significance |
Benign
Likely pathogenic
|
| Variant entry | 2 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.026 |
| ToMMo:0.029 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.021 |
Prediction
ClinVar
| Clinical Significance | Conflicting classifications of pathogenicity; risk factor |
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Benign
|
Centenarian |
germline
|
MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University | ||||
|
Likely pathogenic
|
other |
unknown
|
MGS000001
(TMGS000162) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
Conflicting interpretations of pathogenicity
|
2024-01-30 | criteria provided, conflicting interpretations | Autosomal dominant Parkinson disease 8 |
germline
unknown
|
Detail |
risk factor
|
2020-09-21 | criteria provided, single submitter | Parkinson disease |
germline
|
Detail |
Uncertain significance
|
2020-04-09 | criteria provided, single submitter | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.436 | Parkinson disease | Comprehensive research synopsis and systematic meta-analyses in Parkinson's dise... | GWASCAT | 22438815 | Detail |
| 0.440 | PARKINSON DISEASE 8 (disorder) | NA | CLINVAR | Detail | |
| 0.002 | Motor symptoms | Non-motor symptoms in Chinese Parkinson's disease patients with and without LRRK... | BeFree | 25062988 | Detail |
| 0.012 | multiple system atrophy | An association analysis of the R1628P and G2385R polymorphisms of the LRRK2 gene... | BeFree | 25511328 | Detail |
| 0.436 | Parkinson disease | The R1628P and G2385R polymorphisms of the LRRK2 gene have been identified as ex... | BeFree | 25511328 | Detail |
| 0.003 | Parkinson Disease, Familial, Type 1 | Two Lrrk2 protein substitutions (p.R1628P and p.G2385R) have since been associat... | BeFree | 20082991 | Detail |
| 0.436 | Parkinson disease | LRRK2 G2385R and R1628P mutations are associated with an increased risk of Parki... | BeFree | 25243190 | Detail |
| 0.001 | Shy-Drager Syndrome | An association analysis of the R1628P and G2385R polymorphisms of the LRRK2 gene... | BeFree | 25511328 | Detail |
| 0.216 | Parkinson disease | The objectives of this study were to identify PD subtypes using cluster analysis... | BeFree | 25732803 | Detail |
| 0.436 | Parkinson disease | The objectives of this study were to identify PD subtypes using cluster analysis... | BeFree | 25732803 | Detail |
| 0.436 | Parkinson disease | Although the changes Gly2019Ser and Gly2385Arg of LRRK2 are associated with PD i... | BeFree | 24729340 | Detail |
| 0.001 | Shy-Drager Syndrome | Analysis of the LRRK2 Gly2385Arg variant in primary dystonia and multiple system... | BeFree | 18450497 | Detail |
| 0.436 | Parkinson disease | The association between the LRRK2 G2385R variant and the risk of Parkinson's dis... | BeFree | 25027012 | Detail |
| 0.012 | multiple system atrophy | Analysis of the LRRK2 Gly2385Arg variant in primary dystonia and multiple system... | BeFree | 18450497 | Detail |
| 0.159 | Parkinsonian Disorders | The leucine-rich repeat kinase 2 (Lrrk2) G2385R substitution is associated with ... | BeFree | 17222580 | Detail |
| 0.436 | Parkinson disease | Leucine-rich repeat kinase 2 G2385R variant is a risk factor for Parkinson disea... | BeFree | 17314670 | Detail |
| <0.001 | Dystonia, Primary | Analysis of the LRRK2 Gly2385Arg variant in primary dystonia and multiple system... | BeFree | 18450497 | Detail |
| 0.009 | essential tremor | Essential tremor and the common LRRK2 G2385R variant. | BeFree | 18316234 | Detail |
| 0.159 | Parkinsonian Disorders | In addition, we found that the proband and his mother carried the G2385R variant... | BeFree | 23124679 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_198578.4(LRRK2):c.7153G>A (p.Gly2385Arg) AND Autosomal dominant Parkinson disease 8 | ClinVar | Detail |
| NM_198578.4(LRRK2):c.7153G>A (p.Gly2385Arg) AND Parkinson disease | ClinVar | Detail |
| NM_198578.4(LRRK2):c.7153G>A (p.Gly2385Arg) AND not provided | ClinVar | Detail |
| Comprehensive research synopsis and systematic meta-analyses in Parkinson's disease genetics: The PD... | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| Non-motor symptoms in Chinese Parkinson's disease patients with and without LRRK2 G2385R and R1628P ... | DisGeNET | Detail |
| An association analysis of the R1628P and G2385R polymorphisms of the LRRK2 gene in multiple system ... | DisGeNET | Detail |
| The R1628P and G2385R polymorphisms of the LRRK2 gene have been identified as exclusively associated... | DisGeNET | Detail |
| Two Lrrk2 protein substitutions (p.R1628P and p.G2385R) have since been associated with susceptibili... | DisGeNET | Detail |
| LRRK2 G2385R and R1628P mutations are associated with an increased risk of Parkinson's disease in th... | DisGeNET | Detail |
| An association analysis of the R1628P and G2385R polymorphisms of the LRRK2 gene in multiple system ... | DisGeNET | Detail |
| The objectives of this study were to identify PD subtypes using cluster analysis (CA) and to determi... | DisGeNET | Detail |
| The objectives of this study were to identify PD subtypes using cluster analysis (CA) and to determi... | DisGeNET | Detail |
| Although the changes Gly2019Ser and Gly2385Arg of LRRK2 are associated with PD in different populati... | DisGeNET | Detail |
| Analysis of the LRRK2 Gly2385Arg variant in primary dystonia and multiple system atrophy in Taiwan. | DisGeNET | Detail |
| The association between the LRRK2 G2385R variant and the risk of Parkinson's disease: a meta-analysi... | DisGeNET | Detail |
| Analysis of the LRRK2 Gly2385Arg variant in primary dystonia and multiple system atrophy in Taiwan. | DisGeNET | Detail |
| The leucine-rich repeat kinase 2 (Lrrk2) G2385R substitution is associated with familial parkinsonis... | DisGeNET | Detail |
| Leucine-rich repeat kinase 2 G2385R variant is a risk factor for Parkinson disease in Asian populati... | DisGeNET | Detail |
| Analysis of the LRRK2 Gly2385Arg variant in primary dystonia and multiple system atrophy in Taiwan. | DisGeNET | Detail |
| Essential tremor and the common LRRK2 G2385R variant. | DisGeNET | Detail |
| In addition, we found that the proband and his mother carried the G2385R variant of the LRRK2, a str... | DisGeNET | Detail |
Overlapped Transcript Coordinates
| Gene | Transcript ID | Exon Number | Chromosome | Start | Stop | Type | Amino Mutation | Transcript Position | Links |
|---|
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs34778348 dbSNP
- Genome
- hg19
- Position
- chr12:40,757,328-40,757,328
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 95.87
- Standard deviation of sample read depth (HGVD)
- 39.32
- Number of reference allele (HGVD)
- 2356
- Number of alternative allele (HGVD)
- 64
- Allele Frequency (HGVD)
- 0.026446280991735537
- Gene Symbol (HGVD)
- LRRK2
- ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- PASS
- Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- rs34778348
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0291
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 488
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8618
- East Asian Allele Counts (ExAC)
- 178
- East Asian Heterozygous Counts (ExAC)
- 172
- East Asian Homozygous Counts (ExAC)
- 3
- East Asian Allele Frequency (ExAC)
- 0.020654444186586216
- Chromosome Counts in All Race (ExAC)
- 120612
- Allele Counts in All Race (ExAC)
- 191
- Heterozygous Counts in All Race (ExAC)
- 183
- Homozygous Counts in All Race (ExAC)
- 4
- Allele Frequency in All Race (ExAC)
- 0.0015835903558518224
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