rs505404

This is a intron variant variant in the PSMD13 gene.

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GWAS Catalog Trait Associations (2)

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

platelet count

Gieger C et al. “New gene functions in megakaryopoiesis and platelet formation.” Nature 480(7376):201-8 (2011)

Allele G

OR 4.66

p 7.0e-25

N 48,666

Large GWAS

European

bone tissue density

Medina-Gomez C et al. “Life-Course Genome-wide Association Study Meta-analysis of Total Body BMD and Assessment of Age-Specific Effects.” American Journal of Human Genetics 102(1):88-102 (2018)

Allele T

OR —

β 0.052

p 9.0e-13

N 66,945

Meta-analysisLarge GWAS

multi-ancestry

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Research that mentions this SNP (1)

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A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects

AssociationN=13,582Khader Shameer et al.(2014)· Human Genetics

A genome-wide association study (GWAS) of platelet count (PLT) and mean platelet volume (MPV) in 13,582 and 6,291 participants respectively from the eMERGE network identified 5 chromosomal regions associated with PLT and 8 with MPV at genome-wide significance (P<5E-8). Key findings include variants in ARHGEF3 (rs1354034, P=6E-24 for PLT; P=9E-34 for MPV), SH2B3 (rs3184504, P=5E-12), and multiple other loci. The study replicated 20 SNPs for PLT and 22 for MPV from prior meta-analyses and demonstrated pleiotropic effects with myocardial infarction, autoimmune, and hematologic disorders through phenome-wide association study (PheWAS).

Traits studied:Autoimmune disordersBlood pressureEosinophil countHematologic disordersMean platelet volume (MPV)Myocardial infarctionPlatelet count (PLT)Type 1 diabetes

PubMed DOI Metascience Observatory

About PSMD13

The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a non-ATPase subunit of the 19S regulator. Two transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]