LRRK2 M2397T - GET-Evidence

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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.

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Curation:
Currentness:

LRRK2 M2397T

(LRRK2 Met2397Thr)


Short summary

 

Variant evidence
Computational 3

PolyPhen2: Benign, score 0.000
SIFT: Tolerated 0.33
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

  • C @ chr12:40758652: 61.4% (6606/10756) in EVS
  • C @ chr12:39044918: 49.2% (63/128) in GET-Evidence
  • Frequency shown in summary reports: 61.4% (6606/10756)

Publications
 

Genomes
 

hu011C57 - CGI sample GS01669-DNA_B05 from PGP sample 86486261
het C @ chr12:40758652

 

hu025CEA - CGI sample GS01669-DNA_D02 from PGP sample 27316983
hom C @ chr12:40758652

 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
hom C @ chr12:40758652

 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
het C @ chr12:40758652

 

hu0E64A1 - CGI sample GS01173-DNA_B02 from PGP sample 94378523
het C @ chr12:40758652

 

hu232307 - PGP14 (hu232307) build 36, substitution variants, hu232307 build 36 substitution variants
het C @ chr12:39044919

 

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
hom C @ chr12:40758652

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
het C @ chr12:40758652

 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
het C @ chr12:40758652

 

hu3215A7 - PGP12 (hu3215A7) build 36, substitution variants, hu3215A7 build 36 substitution variants
het C @ chr12:39044919

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
hom C @ chr12:40758652

 

hu34D5B9 - CGI sample GS01173-DNA_C07 from PGP sample 92161424, hu34D5B9 exome
het C @ chr12:40758652

 

hu3A8D13 - PGP13 (hu3A8D13) build 37, from CGI var (software ver 1.11.0.16), CGI sample GS000003289
hom C @ chr12:40758652

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
hom C @ chr12:40758652

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
het C @ chr12:40758652

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
het C @ chr12:40758652

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
het C @ chr12:40758652

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
hom C @ chr12:40758652

 

hu4CA5B9 - CGI sample GS01669-DNA_B03 from PGP sample 14427241
het C @ chr12:40758652

 

hu604D39 - CGI sample GS00253-DNA_B02_200_37
het C @ chr12:40758652

 

hu6E4515 - PGP15 (hu6E4515) build 37, from CGI var (software ver 1.12.0.47), CGI sample GS000005532
het C @ chr12:40758652

 

hu728FFF - PGP11 (hu728FFF) build 36, substitution variants, hu728FFF build 36 substitution variants
hom C @ chr12:39044919

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
hom C @ chr12:40758652

 

hu7A4AD1 - CGI sample GS01669-DNA_C05 from PGP sample 42408046
het C @ chr12:40758652

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
het C @ chr12:40758652

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
hom C @ chr12:40758652

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
het C @ chr12:40758652

 

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
het C @ chr12:40758652

 

huA90CE6 - PGP16 (huA90CE6) build 37, from CGI var (software ver 2.0.2.11), CGI sample GS000006909
hom C @ chr12:40758652

 

huAE4A11 - CGI sample GS01669-DNA_F02 from PGP sample 40767107
hom C @ chr12:40758652

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
hom C @ chr12:40758652

 

huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
het C @ chr12:40758652

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
het C @ chr12:40758652

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
het C @ chr12:40758652

 

huCA017E - CGI sample GS01175-DNA_B01 from PGP sample 86206034
het C @ chr12:40758652

 

huD37D14 - CGI sample GS01175-DNA_A04 from PGP sample 13272228
het C @ chr12:40758652

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
hom C @ chr12:40758652

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
hom C @ chr12:40758652

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
het C @ chr12:40758652

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
hom C @ chr12:40758652

 

GS06985 - var-GS06985-1100-36-ASM
hom C @ chr12:39044919

 

GS06994 - var-GS06994-1100-36-ASM
het C @ chr12:39044919

 

GS10851 - var-GS10851-1100-36-ASM
het C @ chr12:39044919

 

GS12004 - var-GS12004-1100-36-ASM
het C @ chr12:39044919

 

GS18501 - var-GS18501-1100-36-ASM
het C @ chr12:39044919

 

GS18502 - var-GS18502-1100-36-ASM
het C @ chr12:39044919

 

GS18504 - var-GS18504-1100-36-ASM
het C @ chr12:39044919

 

GS18508 - var-GS18508-1100-36-ASM
het C @ chr12:39044919

 

GS18517 - var-GS18517-1100-36-ASM
hom C @ chr12:39044919

 

GS18526 - var-GS18526-1100-36-ASM
het C @ chr12:39044919

 

GS18558 - var-GS18558-1100-36-ASM
het C @ chr12:39044919

 

GS18940 - var-GS18940-1100-36-ASM
het C @ chr12:39044919

 

GS18942 - var-GS18942-1100-36-ASM
het C @ chr12:39044919

 

GS18956 - var-GS18956-1100-36-ASM
hom C @ chr12:39044919

 

GS19017 - var-GS19017-1100-36-ASM
het C @ chr12:39044919

 

GS19020 - var-GS19020-1100-36-ASM
het C @ chr12:39044919

 

GS19025 - var-GS19025-1100-36-ASM
het C @ chr12:39044919

 

GS19026 - var-GS19026-1100-36-ASM
het C @ chr12:39044919

 

GS19129 - var-GS19129-1100-36-ASM
het C @ chr12:39044919

 

GS19238 - var-GS19238-1100-36-ASM
het C @ chr12:39044919

 

GS19239 - var-GS19239-1100-36-ASM
het C @ chr12:39044919

 

GS19240 - var-GS19240-1100-36-ASM
het C @ chr12:39044919

 

GS19648 - var-GS19648-1100-36-ASM
het C @ chr12:39044919

 

GS19649 - var-GS19649-1100-36-ASM
het C @ chr12:39044919

 

GS19669 - var-GS19669-1100-36-ASM
het C @ chr12:39044919

 

GS19670 - var-GS19670-1100-36-ASM
het C @ chr12:39044919

 

GS19701 - var-GS19701-1100-36-ASM
het C @ chr12:39044919

 

GS19703 - var-GS19703-1100-36-ASM
het C @ chr12:39044919

 

GS20502 - var-GS20502-1100-36-ASM
hom C @ chr12:39044919

 

GS20509 - var-GS20509-1100-36-ASM
het C @ chr12:39044919

 

GS21767 - var-GS21767-1100-36-ASM
hom C @ chr12:39044919

 

Other external references
 

    dbSNP
  • rs3761863
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    Web search results (5 hits -- see all)
  • 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&...
  • Parkinson Disease Knowledgebase
    LRRK2. Variant (mutation/polymorphism) information mined from UniProt : ... M2397T (Polymorphism) [ VAR_024965 ] M2397T (Polymorphism) suisheng ...
    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

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