chr12:40320043:G>A Detail (hg38) (LRRK2)

Information

Genome

Assembly Position
hg19 chr12:40,713,845-40,713,845 View the variant detail on this assembly version.
hg38 chr12:40,320,043-40,320,043

HGVS

Type Transcript Protein
RefSeq NM_198578.3:c.4883G>A NP_940980.3:p.Arg1628His
Ensemble ENST00000298910.12:c.4883G>A ENST00000298910.12:p.Arg1628His
ENST00000680790.1:c.4628G>A ENST00000680790.1:p.Arg1543His
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 609007 OMIM
HGNC 18618 HGNC
Ensembl ENSG00000188906 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv45579919 TogoVar
COSMIC COSM1361432 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2019-11-25 criteria provided, multiple submitters, no conflicts not provided germline Detail
Conflicting interpretations of pathogenicity 2023-05-12 criteria provided, conflicting interpretations Autosomal dominant Parkinson disease 8 germline unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
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 Confirmation of the association between LRRK2 R1628P variant and susceptibility ... BeFree 24997548 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
0.009 essential tremor Lrrk2 R1628P variant is a risk factor for essential tremor. BeFree 25761573 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
Annotation

Annotations

DescrptionSourceLinks
NM_198578.4(LRRK2):c.4883G>A (p.Arg1628His) AND not provided ClinVar Detail
NM_198578.4(LRRK2):c.4883G>A (p.Arg1628His) AND Autosomal dominant Parkinson disease 8 ClinVar 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
Confirmation of the association between LRRK2 R1628P variant and susceptibility to Parkinson's disea... 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 R1628P variant is a risk factor for essential tremor. 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

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
rs33949390 dbSNP
Genome
hg38
Position
chr12:40,320,043-40,320,043
Variant Type
snv
Reference Allele
G
Alternative Allele
A
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))
rs33949390
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8652
East Asian Allele Counts (ExAC)
2
East Asian Heterozygous Counts (ExAC)
2
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
2.311604253351826E-4
Chromosome Counts in All Race (ExAC)
120950
Allele Counts in All Race (ExAC)
17
Heterozygous Counts in All Race (ExAC)
17
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.4055394791236047E-4
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