LRRK2 S1647T - GET-Evidence

Note: This variant has not been sufficiently evaluated by a GET-Evidence editor.

To be considered sufficiently evaluated a variant must have both "variant evidence" and "clinical importance" scores filled in.

Please help improve GET-Evidence by evaluating evidence for this variant!

Curation:
Currentness:

LRRK2 S1647T

(LRRK2 Ser1647Thr)


Short summary

 

Variant evidence
Computational 1

PolyPhen2: Benign, score 0.000
SIFT: Affect protein function 0.04
GVGD: Class C0

Functional -
Case/Control -
Familial -
 
Clinical importance
Severity -
Treatability -
Penetrance -
 

Impact

Insufficiently evaluated not reviewed

(The "insufficiently evaluated" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

unknown

Summary of published research, and additional commentary

 

Allele frequency

  • A @ chr12:40713901: 25.8% (2767/10742) in EVS
  • A @ chr12:39000167: 12.3% (15/122) in GET-Evidence
  • Frequency shown in summary reports: 25.8% (2767/10742)

Publications
 

Zheng Y, Liu Y, Wu Q, Hong H, Zhou H, Chen J, Wang H, Xian W, Li J, Liu Z, Pei Z, Chen L. Confirmation of LRRK2 S1647T variant as a risk factor for Parkinson's disease in southern China. Eur J Neurol. 2011 Mar;18(3):538-40. doi: 10.1111/j.1468-1331.2010.03164.x. PubMed PMID: 20629711.

 

Lin CH, Wu RM, Tai CH, Chen ML, Hu FC. Lrrk2 S1647T and BDNF V66M interact with environmental factors to increase risk of Parkinson's disease. Parkinsonism Relat Disord. 2011 Feb;17(2):84-8. Epub 2010 Dec 16. PubMed PMID: 21167764.

 

Genomes
 

hu011C57 - CGI sample GS01669-DNA_B05 from PGP sample 86486261
het A @ chr12:40713901

 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het A @ chr12:40713901

 

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
hom A @ chr12:40713901

 

 

 

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
het A @ chr12:40713901

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
het A @ chr12:40713901

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
hom A @ chr12:40713901

 

 

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
het A @ chr12:40713901

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
het A @ chr12:40713901

 

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het A @ chr12:40713901

 

huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
het A @ chr12:40713901

 

huCA017E - CGI sample GS01175-DNA_B01 from PGP sample 86206034
het A @ chr12:40713901

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
hom A @ chr12:40713901

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
hom A @ chr12:40713901

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
hom A @ chr12:40713901

 

GS10851 - var-GS10851-1100-36-ASM
het A @ chr12:39000168

 

GS12004 - var-GS12004-1100-36-ASM
het A @ chr12:39000168

 

GS18504 - var-GS18504-1100-36-ASM
het A @ chr12:39000168

 

GS18526 - var-GS18526-1100-36-ASM
het A @ chr12:39000168

 

GS18558 - var-GS18558-1100-36-ASM
het A @ chr12:39000168

 

GS18956 - var-GS18956-1100-36-ASM
het A @ chr12:39000168

 

GS19129 - var-GS19129-1100-36-ASM
het A @ chr12:39000168

 

GS19240 - var-GS19240-1100-36-ASM
het A @ chr12:39000168

 

NA12878

 

Other external references
 

    dbSNP
  • rs11564148
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    Web search results (9 hits -- see all)
  • Exon
    S1647T. T/A. Y1699C. 35. 5096. Y1699C. A/G. rs11564176. 36. 5175. R1725X. C/T ... ( B) Genotypes for SNPs in LRRK2 that flank G2019S for Jewish LRRK2 positive cases. ...
    neurology.org/content/vol0/issue2006/images/data/.../E1.doc
  • Parkinson Disease Knowledgebase
    Conclusion. We have no evidence for the existence of a common variant in LRRK2 that has a ... Screening of unrelated PD patients for LRRK2 mutations is necessary to increase our ...
    datam.i2r.a-star.edu.sg/mdpd/detail.php?symbol=LRRK2&...
  • Table 4. Normal Allelic Variants Exon Accession Number ...
    p.S1647T. COR. 36 rs11564176. 5035C>T p.R1725STOP COR. 37 rs10878371. 5457T>C. p.G1819G. COR. 42 ... p.G2170G. 46 rs12581902. 6782A>T. p.N2261I. WD40. 48 ss48398567. 7155A>G. p.G2385G WD40. 49 ...
    ncbi.nlm.nih.gov/bookshelf/...&blobname=lrrk2-table4.pdf
  • Type III 97%
    ... SWISS-PROT ID Variant site Phosphorylation site SWISS-PROT variant ID ... Reference(s) for variant Reference(s) for phosphorylation site TPSD1 Q9BZJ3 P15R ...
    nih.go.kr/phosphovariant/html/family_whole/TypeIII_97.txt
  • Type III 98%
    Gene name SWISS-PROT ID Variant site Phosphorylation site SWISS-PROT variant ID ... Effect Reference(s) for variant Reference(s) for phosphorylation site ...
    nih.go.kr/phosphovariant/html/family_whole/TypeIII_98.txt
  • Parkinson Disease Knowledgebase
    LRRK2. Variant (mutation/polymorphism) information mined from UniProt : variant. Mutaion ... S1647T (Polymorphism) [ VAR_024953 ] S1647T (Polymorphism) Y1699C ...
    datam.i2r.a-star.edu.sg/mdpd/detail.php?symbol=LRRK2&sec=2
  • View web only data 134KB
    aHuman LRRK2 cDNA sequence (Genbank Accession number AY792511) was used as the reference ... characteristics of patients with LRRK2 potentially pathogenic variants, except for ...
    jmg.bmj.com/content/suppl/2009/06/16/jmg.2008.062612.DC1/...

Other in silico analyses
 

  • NBLOSUM100 score = –2
  • GET-Evidence autoscore = 3

Edit history
 

Gene search

"GENE" or "GENE A123C":

Log in