PIGR A580V - GET-Evidence



(PIGR Ala580Val)

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


See Obara W et al. 2003 (12740691).


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

See unpublished research (below).

Clinical importance
Severity 4
Treatability 2

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).



Low clinical importance, Likely pathogenic

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

Inheritance pattern


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)


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



hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
het A @ chr1:207106478



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


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


GS18501 - var-GS18501-1100-36-ASM
het A @ chr1:205173101


GS18502 - var-GS18502-1100-36-ASM
hom A @ chr1:205173101


GS18504 - var-GS18504-1100-36-ASM
hom A @ chr1:205173101


GS18505 - var-GS18505-1100-36-ASM
hom A @ chr1:205173101


GS18508 - var-GS18508-1100-36-ASM
het A @ chr1:205173101


GS18517 - var-GS18517-1100-36-ASM
hom A @ chr1:205173101


GS18555 - var-GS18555-1100-36-ASM
het A @ chr1:205173101


GS18942 - var-GS18942-1100-36-ASM
het A @ chr1:205173101


GS19017 - var-GS19017-1100-36-ASM
hom A @ chr1:205173101


GS19020 - var-GS19020-1100-36-ASM
hom A @ chr1:205173101


GS19025 - var-GS19025-1100-36-ASM
het A @ chr1:205173101


GS19026 - var-GS19026-1100-36-ASM
het A @ chr1:205173101


GS19129 - var-GS19129-1100-36-ASM
hom A @ chr1:205173101


GS19238 - var-GS19238-1100-36-ASM
het A @ chr1:205173101


GS19239 - var-GS19239-1100-36-ASM
hom A @ chr1:205173101


GS19240 - var-GS19240-1100-36-ASM
het A @ chr1:205173101


GS19670 - var-GS19670-1100-36-ASM
het A @ chr1:205173101


GS19700 - var-GS19700-1100-36-ASM
hom A @ chr1:205173101


GS19701 - var-GS19701-1100-36-ASM
het A @ chr1:205173101


GS19703 - var-GS19703-1100-36-ASM
het A @ chr1:205173101


GS19704 - var-GS19704-1100-36-ASM
hom A @ chr1:205173101


GS19834 - var-GS19834-1100-36-ASM
het A @ chr1:205173101


GS21767 - var-GS21767-1100-36-ASM
hom A @ chr1:205173101


Other external references

  • rs291102
  • 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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