PIGR A580V - GET-Evidence

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PIGR A580V

(PIGR Ala580Val)


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Short summary

In a Japanese study, this variant was associated with an increased risk for immunoglobulin A nephropathy (IgAN), a rare disease. The chances of having this disease, even with this variant, is less than 0.1%.

Variant evidence
Computational 1

Gene associated with disease

See Obara W et al. 2003 (12740691).

Functional -
Case/Control 4

p=0.0003

See Obara W et al. 2003 (12740691).

Familial

This is describd as a susceptibility allele in OMIM; no family segregation data available.

See unpublished research (below).

 
Clinical importance
Severity 4
Treatability 2
Penetrance

IgA nephropathy is extremely rare. Assuming an incidence of 0.05%, this variant is associated with an additional risk of 0.023% (total of 0.073%).

See Obara W et al. 2003 (12740691).

 

Impact

Low clinical importance, Likely pathogenic

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

Inheritance pattern

other

Summary of published research, and additional commentary

 

Allele frequency

  • A @ chr1:207106478: 24.8% (2663/10758) in EVS
  • A @ chr1:205173100: 29.7% (38/128) in GET-Evidence
  • Frequency shown in summary reports: 24.8% (2663/10758)

Publications
 

Obara W, Iida A, Suzuki Y, Tanaka T, Akiyama F, Maeda S, Ohnishi Y, Yamada R, Tsunoda T, Takei T, Ito K, Honda K, Uchida K, Tsuchiya K, Yumura W, Ujiie T, Nagane Y, Nitta K, Miyano S, Narita I, Gejyo F, Nihei H, Fujioka T, Nakamura Y. Association of single-nucleotide polymorphisms in the polymeric immunoglobulin receptor gene with immunoglobulin A nephropathy (IgAN) in Japanese patients. J Hum Genet. 2003;48(6):293-9. Epub 2003 May 10. PubMed PMID: 12740691.

In a study of 389 Japanese individuals with immunoglobulin A nephropathy (IgAN) and 465 controls, this variant was found to associate with disease with an OR of 1.59. This variant is in the secretory component, but biopsies showed no correlation with immunoglobulin A levels.

Case var/var: 24, var/+: 113, /: 252
Cont var/var: 11, var/+: 109, /: 345

Genomes
 

hu3215A7 - PGP12 (hu3215A7) build 36, substitution variants, hu3215A7 build 36 substitution variants
het A @ chr1:205173101

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
het A @ chr1:207106478

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
hom A @ chr1:207106478

 

NA18507

 

NA18517

 

NA18555

 

NA19129

 

NA19240

 

snp-27

 

snp-28

 

snp-29

 

snp-30

 

snp-31

 

snp-32

 

Deleted in this revision:

snp-32

 

Other external references
 

    dbSNP
  • rs291102
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    PolyPhen-2
  • Score: 0.001 (benign)

Other in silico analyses
 

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

Edit history
 

Gene search

"GENE" or "GENE A123C":

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