LRRK2 R1398H - GET-Evidence

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

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Curation:
Currentness:

LRRK2 R1398H

(LRRK2 Arg1398His)


Short summary

 

Variant evidence
Computational 1

PolyPhen2: Probably damaging 0.961
SIFT: Tolerated 0.20
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 @ chr12:40702911: 9.3% (1002/10758) in EVS
  • A @ chr12:38989177: 14.8% (19/128) in GET-Evidence
  • Frequency shown in summary reports: 9.3% (1002/10758)

Publications
 

Genomes
 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
het A @ chr12:40702911

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
hom A @ chr12:40702911

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
het A @ chr12:40702911

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
het A @ chr12:40702911

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
het A @ chr12:40702911

 

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
het A @ chr12:40702911

 

GS18504 - var-GS18504-1100-36-ASM
het A @ chr12:38989178

 

GS18517 - var-GS18517-1100-36-ASM
het A @ chr12:38989178

 

GS18956 - var-GS18956-1100-36-ASM
het A @ chr12:38989178

 

GS19025 - var-GS19025-1100-36-ASM
het A @ chr12:38989178

 

GS19238 - var-GS19238-1100-36-ASM
het A @ chr12:38989178

 

GS19239 - var-GS19239-1100-36-ASM
het A @ chr12:38989178

 

GS19670 - var-GS19670-1100-36-ASM
het A @ chr12:38989178

 

GS19703 - var-GS19703-1100-36-ASM
het A @ chr12:38989178

 

GS19704 - var-GS19704-1100-36-ASM
het A @ chr12:38989178

 

GS20502 - var-GS20502-1100-36-ASM
het A @ chr12:38989178

 

GS21767 - var-GS21767-1100-36-ASM
het A @ chr12:38989178

 

Other external references
 

    dbSNP
  • rs7133914
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    Web search results (15 hits -- see all)
  • Multiple LRRK2 variants modulate risk of Parkinson disease: a ...
    We and others found two polymorphic LRRK2 (leucine rich repeat kinase 2) variants ... In dopaminergic neuronal lines, p.R1398H had significantly lower kinase activity while p. ...
    www.ncbi.nlm.nih.gov/pubmed/20186690
  • Multiple LRRK2 variants modulate risk of Parkinson disease: a ...
    Multiple LRRK2 variants modulate risk of Parkinson disease: a Chinese ... In dopaminergic neuronal lines, p.R1398H had significantly lower kinase activity while p. ...
    www3.interscience.wiley.com/journal/123301437/abstract
  • Exon
    R1398H. G/A. rs11175694. 30. 4296. K1423K. G/A. R1441C. 31. 4321. R1441C. 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.R50H N-terminal. 4 ss48398569. 356T>C. p.L119P N-terminal. 5 rs10878245 ... p.R1398H. Roc. 30 rs11175964. 4269G>A. p.K1423K. Roc. 32 ss48398560. 4624C>T ...
    ncbi.nlm.nih.gov/bookshelf/...&blobname=lrrk2-table4.pdf
  • parkinson の検索結果 - ATGC論文チェッカー|Pubmed(パブメド)の論文検索をスムーズにするWEBツール
    Multiple LRRK2 variants modulate risk of Parkinson disease: a Chinese multicenter study. ... In dopaminergic neuronal lines, p.R1398H had significantly lower kinase activity ...
    www.atgcchecker.com/search/parkinson
  • Multiple LRRK2 variants modulate risk of Parkinson disease: a ...
    The risk of a carrier with p.R1628P is largely negated if the individual also carries p.R1398H or p.N551K. ... first evidence that multiple LRRK2 variants exert an individual ...
    www.pdonlineresearch.org/biblio/export/xml/25447
  • Parkinson Disease Knowledgebase
    LRRK2. Variant (mutation/polymorphism) information mined from UniProt : variant. Mutaion ... R1398H (Polymorphism) [ VAR_024944 ] R1398H (Polymorphism) R1441C ...
    datam.i2r.a-star.edu.sg/mdpd/detail.php?symbol=LRRK2&sec=2
  • Genetic study of an American family with DYT3 dystonia (lubag).
    In dopaminergic neuronal lines, p.R1398H had significantly lower kinase activity while p. ... The vast majority of patients with LRRK2-related PD reported in the literature ...
    lib.bioinfo.pl/pmid:18952144
  • View web only data 134KB
    p.R1398H. A 0.031. Exon30. rs11175964. c.4269G>A. p.K1423K. A 0.044 ... aHuman LRRK2 cDNA sequence (Genbank Accession number AY792511) was used as the reference ...
    jmg.bmj.com/content/suppl/2009/06/16/jmg.2008.062612.DC1/...

Other in silico analyses
 

  • NBLOSUM100 score = 1
  • GET-Evidence autoscore = 3

Edit history
 

Gene search

"GENE" or "GENE A123C":

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