chr12:40310461:G>A Detail (hg38) (LRRK2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr12:40,704,263-40,704,263 View the variant detail on this assembly version. |
| hg38 | chr12:40,310,461-40,310,461 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_198578.3:c.4348G>A | NP_940980.3:p.Val1450Ile |
| Ensemble | ENST00000298910.12:c.4348G>A | ENST00000298910.12:p.Val1450Ile |
| ENST00000680790.1:c.4093G>A | ENST00000680790.1:p.Val1365Ile |
Summary
MGeND
| Clinical significance |
Uncertain significance
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.001 |
| ToMMo:<0.001 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:<0.001 |
Prediction
ClinVar
| Clinical Significance |
Uncertain significance
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Uncertain significance
|
sporadic Parkinson's disease |
unknown
|
MGS000082
(TMGS000165) |
Kenjiro Kosaki Kenjiro Kosaki |
Keio University Mutation View |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Uncertain significance
|
2021-11-24 | criteria provided, single submitter | Autosomal dominant Parkinson disease 8 |
germline
unknown
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 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.4348G>A (p.Val1450Ile) AND Autosomal dominant Parkinson disease 8 | ClinVar | 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
- rs111501952 dbSNP
- Genome
- hg38
- Position
- chr12:40,310,461-40,310,461
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- LowQual
- # of samples (HGVD)
- 1196
- Mean of sample read depth (HGVD)
- 37.59
- Standard deviation of sample read depth (HGVD)
- 25.96
- Number of reference allele (HGVD)
- 2389
- Number of alternative allele (HGVD)
- 3
- Allele Frequency (HGVD)
- 0.001254180602006689
- 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))
- rs111501952
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0003
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 5
- 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)
- 8
- East Asian Heterozygous Counts (ExAC)
- 8
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 9.246417013407304E-4
- Chromosome Counts in All Race (ExAC)
- 121330
- Allele Counts in All Race (ExAC)
- 9
- Heterozygous Counts in All Race (ExAC)
- 9
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 7.417786202917663E-5
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