LRRK2 S1647T - GET-Evidence

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

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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 -


Insufficiently evaluated not reviewed

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

Inheritance pattern


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)


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.



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




Other external references

  • rs11564148
    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. ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • Parkinson Disease Knowledgebase
    LRRK2. Variant (mutation/polymorphism) information mined from UniProt : variant. Mutaion ... S1647T (Polymorphism) [ VAR_024953 ] S1647T (Polymorphism) Y1699C ...
  • 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 ...

Other in silico analyses

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

Edit history

Gene search

"GENE" or "GENE A123C":

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