PKD1 A4059V - GET-Evidence

Curation:
Currentness:

PKD1 A4059V

(PKD1 Ala4059Val)


Short summary

Probably benign.

Variant evidence
Computational

Polyphen 2 predicts possibly damaging

Functional -
Case/Control 5

Probably benign — allele frequency fairly common (4.8% or 8.9%), contradicting it as a cause of autosomal dominant polycystic kidney disease

See Stekrova J et al. 2009 (19686598).

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

 

Allele frequency

  • A @ chr16:2140554: 5.7% (610/10694) in EVS
  • A @ chr16:2080554: 4.8% (6/126) in GET-Evidence
  • Frequency shown in summary reports: 5.7% (610/10694)

Publications
 

Stekrova J, Reiterova J, Svobodova S, Kebrdlova V, Lnenicka P, Merta M, Viklicky O, Kohoutova M. New mutations in the PKD1 gene in Czech population with autosomal dominant polycystic kidney disease. BMC Med Genet. 2009 Aug 17;10:78. PubMed PMID: 19686598; PubMed Central PMCID: PMC2736583.

Mentions this variant as a polymorphism (not pathogenic) with 8.9% allele frequency in Czech patients.

Genomes
 

 

 

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
het A @ chr16:2140554

 

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
het A @ chr16:2140554

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het A @ chr16:2140554

 

GS19648 - var-GS19648-1100-36-ASM
het A @ chr16:2080555

 

GS20509 - var-GS20509-1100-36-ASM
het A @ chr16:2080555

 

NA12878

 

Other external references
 

    dbSNP
  • rs3209986
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the PKD1 gene
    Polycystic Kidney Disease 1, Autosomal Dominant
    Polycystic Kidney Disease, Autosomal Dominant
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PKD1
    PolyPhen-2
  • Score: 0.779 (possibly damaging)
    Web search results (2 hits -- see all)
  • BMC Medical Genetics
    The disease is caused by mutations of the PKD1 (affecting roughly 85% of ... Conclusion: Twenty probable mutations of the PKD1 gene in 90 Czech individuals (fifteen ...
    www.biomedcentral.com/content/pdf/1471-2350-10-78.pdf
  • New mutations in the PKD1 gene in Czech population with ...
    Mutation analysis of the PKD1 gene is complicated by the presence of ... Twenty probable mutations of the PKD1 gene in 90 Czech individuals (fifteen new ...
    biomedcentral.com/content/download/xml/1471-2350-10-78.xml

Other in silico analyses
 

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

Edit history
 

Gene search

"GENE" or "GENE A123C":

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