chr12:40283897:C>T Detail (hg38) (LRRK2)

Information

Genome

Assembly Position
hg19 chr12:40,677,699-40,677,699 View the variant detail on this assembly version.
hg38 chr12:40,283,897-40,283,897

HGVS

Type Transcript Protein
RefSeq NM_198578.3:c.2264C>T NP_940980.3:p.Pro755Leu
Ensemble ENST00000298910.12:c.2264C>T ENST00000298910.12:p.Pro755Leu
ENST00000343742.6:c.2264C>T ENST00000343742.6:p.Pro755Leu
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.002
ToMMo:0.005
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.009

Prediction

ClinVar

Clinical Significance Benign Likely benign
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 tgv45578481 TogoVar
COSMIC
MONDO
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
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2023-10-11 criteria provided, multiple submitters, no conflicts Autosomal dominant Parkinson disease 8 germline unknown Detail
Benign 2021-05-05 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.440 PARKINSON DISEASE 8 (disorder) NA CLINVAR Detail
0.009 essential tremor To evaluate the frequency of the LRRK2 P755L variant in North American Caucasian... BeFree 17482357 Detail
0.436 Parkinson disease To evaluate the frequency of the LRRK2 P755L variant in North American Caucasian... BeFree 17482357 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_198578.4(LRRK2):c.2264C>T (p.Pro755Leu) AND Autosomal dominant Parkinson disease 8 ClinVar Detail
NM_198578.4(LRRK2):c.2264C>T (p.Pro755Leu) AND not provided ClinVar Detail
NA DisGeNET Detail
To evaluate the frequency of the LRRK2 P755L variant in North American Caucasian patients with PD, w... DisGeNET Detail
To evaluate the frequency of the LRRK2 P755L variant in North American Caucasian patients with PD, w... 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
rs34410987 dbSNP
Genome
hg38
Position
chr12:40,283,897-40,283,897
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1204
Mean of sample read depth (HGVD)
127.06
Standard deviation of sample read depth (HGVD)
60.86
Number of reference allele (HGVD)
2404
Number of alternative allele (HGVD)
4
Allele Frequency (HGVD)
0.0016611295681063123
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))
rs34410987
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0049
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
82
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8642
East Asian Allele Counts (ExAC)
79
East Asian Heterozygous Counts (ExAC)
79
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.009141402453135848
Chromosome Counts in All Race (ExAC)
121258
Allele Counts in All Race (ExAC)
84
Heterozygous Counts in All Race (ExAC)
84
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
6.927377987431757E-4
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