CACNA1S L458H - GET-Evidence

Curation:
Currentness:

CACNA1S L458H

(CACNA1S Leu458His)


Short summary

Common polymorphism

Variant evidence
Computational 1

Polyphen 2 predicts benign

Functional -
Case/Control 5

Allele frequency supports no significant clinically significant effect

Familial -
 
Clinical importance
Severity -
Treatability -
Penetrance -
 

Impact

Low clinical importance, Likely benign

(The "low clinical importance, likely" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

unknown

Summary of published research, and additional commentary

Although Polyphen 2 predicts a damaging effect, this variant is very common (20% allele frequency in PGP+public genomes, 40% in 1000 genomes data). Other variants in this gene are implicated in causing diseases (hypokalemic periodic paralysis, malignant hyperthermia) in a dominant manner, but this variant is presumed benign due to its very common allele frequency.

Allele frequency

  • T @ chr1:201052310: 27.3% (2935/10758) in EVS
  • TGC @ chr1:199318932: 20.3% (26/128) in GET-Evidence
  • Frequency shown in summary reports: 27.3% (2935/10758)

Publications
 

Genomes
 

hu011C57 - CGI sample GS01669-DNA_B05 from PGP sample 86486261
het TGC @ chr1:201052310

 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
hom TGC @ chr1:201052310

 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
het TGC @ chr1:201052310

 

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
het TGC @ chr1:201052310

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
het TGC @ chr1:201052310

 

hu4CA5B9 - CGI sample GS01669-DNA_B03 from PGP sample 14427241
het TGC @ chr1:201052310

 

hu7A4AD1 - CGI sample GS01669-DNA_C05 from PGP sample 42408046
het TGC @ chr1:201052310

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
het TGC @ chr1:201052310

 

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
het TGC @ chr1:201052310

 

huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
hom TGC @ chr1:201052310

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
het TGC @ chr1:201052310

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
het TGC @ chr1:201052310

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
het TGC @ chr1:201052310

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
hom TGC @ chr1:201052310

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
het TGC @ chr1:201052310

 

GS06994 - var-GS06994-1100-36-ASM
het TGC @ chr1:199318933

 

GS12004 - var-GS12004-1100-36-ASM
hom TGC @ chr1:199318933

 

GS19648 - var-GS19648-1100-36-ASM
hom TGC @ chr1:199318933

 

GS19669 - var-GS19669-1100-36-ASM
het TGC @ chr1:199318933

 

GS19834 - var-GS19834-1100-36-ASM
het TGC @ chr1:199318933

 

GS20502 - var-GS20502-1100-36-ASM
het TGC @ chr1:199318933

 

Other external references
 

    dbSNP
  • rs12742169
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the CACNA1S gene
    CACNA1S-Related Malignant Hyperthermia Susceptibility
    Hypokalemic Periodic Paralysis
    Hypokalemic Periodic Paralysis Type 1
    Malignant Hyperthermia Susceptibility
    KCNE3-Related Hypokalemic Periodic Paralysis
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CACNA1S
    Web search results (8 hits -- see all)
  • AceView: Gene:CACNA1S, a comprehensive annotation of human ...
    AceView offers a comprehensive annotation of human, mouse and nematode genes reconstructed by co-alignment and clustering of all publicly available mRNAs and ESTs on ...
    ncbi.nlm.nih.gov/IEB/Research/Acembly/...&a=clones&l=CACNA1S
  • Type II- 95%
    ... SWISS-PROT ID Variant site Phosphorylation site SWISS-PROT variant ID Removed ... P80365 R186C 184 VAR_015637 PKC (0.550) AME 7593417 9661590 PKLR P30613 D390N ...
    nih.go.kr/phosphovariant/html/family_whole/TypeII-_95.txt

Other in silico analyses
 

  • NBLOSUM100 score = 6
  • GET-Evidence autoscore = 3

Edit history
 

Gene search

"GENE" or "GENE A123C":

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