rs17319721

This is a regulatory region variant variant in the SHROOM3 gene.

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GWAS Catalog Trait Associations (5)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

serum creatinine amount, glomerular filtration rate

Pattaro C et al. “Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.” Nature Communications 7:10023 (2016)
Allele A
OR 0.01
p 1.0e-37
N 133,413
Large GWAS
multi-ancestry

chronic kidney disease, serum creatinine amount

Köttgen A et al. “New loci associated with kidney function and chronic kidney disease.” Nature Genetics 42(5):376-84 (2010)
Allele A
OR —
p 1.0e-19
N 67,093
Large GWAS
European

collagen alpha-1(XV) chain measurement

Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)
Allele A
OR 0.05
p 4.0e-18
N 47,745
Large GWAS
European

urinary system trait

Köttgen A et al. “Multiple loci associated with indices of renal function and chronic kidney disease.” Nature Genetics 41(6):712-7 (2009)
Allele A
OR 0.01
p 1.0e-12
N 19,877
Large GWAS
European
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ClinVar annotation

Benign★☆☆☆
1 submitter
View on ClinVar →
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Research that mentions this SNP (1)

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Genome-wide association study identified the human leukocyte antigen region as a novel locus for plasma beta-2 microglobulin
AssociationN=6,738Adrienne Tin et al.(2013)· Human Genetics

Genome-wide association study of plasma beta-2 microglobulin (B2M) levels in 6,738 European Americans identified two genome-wide significant loci: the HLA region on chromosome 6 (rs9264638, p=1.8×10⁻²³) and SH2B3 on chromosome 12 (rs3184504, p=3.1×10⁻⁸). Six index SNPs in the HLA region accounted for 3.2% of log(B2M) variance and their associations were largely explained by imputed classical HLA alleles (HLA-A, HLA-B, HLA-C). The HLA locus was not associated with estimated glomerular filtration rate, while the SH2B3 locus had previously been implicated as an eGFR locus, confirming B2M as a kidney function biomarker.

Traits studied:Chronic kidney diseaseGlomerular filtration rate (eGFRcr)Kidney functionPlasma beta-2 microglobulin levels
PubMedDOIMetascience Observatory

About SHROOM3

This gene encodes a PDZ-domain-containing protein that belongs to a family of Shroom-related proteins. This protein may be involved in regulating cell shape in certain tissues. A similar protein in mice is required for proper neurulation. [provided by RefSeq, Jan 2011]

View all SHROOM3 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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