rs1050239

This is a variant in the SMPD1 gene that changes a glycine to an arginine.

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GWAS Catalog Trait Associations (3)

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

protein measurement

Pietzner M et al. “Mapping the proteo-genomic convergence of human diseases.” Science (new York, N.y.) 374(6569):eabj1541 (2021)
Allele A
OR 0.39
p 2.0e-141
N 10,708
Large GWAS
European
Western D et al. “Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and implicates causal proteins for Alzheimer's disease.” Nature Genetics 56(12):2672-2684 (2024)
Allele A
OR 0.22
p 1.0e-14
N 3,506
Large GWAS
European

blood protein amount

Gudjonsson A et al. “A genome-wide association study of serum proteins reveals shared loci with common diseases.” Nature Communications 13(1):480 (2022)
Allele A
OR 0.35
p 8.0e-71
N 5,368
Large GWAS
European
Emilsson V et al. “Co-regulatory networks of human serum proteins link genetics to disease.” Science (new York, N.y.) 361(6404):769-773 (2018)
Allele A
OR 0.31
p 2.0e-31
N 3,200
Large GWAS
European
Hillary RF et al. “Genome and epigenome wide studies of neurological protein biomarkers in the Lothian Birth Cohort 1936.” Nature Communications 10(1):3160 (2019)
Allele A
OR 0.61
p 4.0e-13
N 750
Small GWAS
European

level of sphingomyelin phosphodiesterase in blood serum

Png G et al. “Mapping the serum proteome to neurological diseases using whole genome sequencing.” Nature Communications 12(1):7042 (2021)
Allele A
OR 0.33
p 4.0e-20
N 2,892
Large GWAS
European
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ClinVar annotation

Benign★★★☆
13 submitters3 publications

Niemann-Pick disease, type A; Niemann-Pick disease, type B; not specified

View on ClinVar →
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Research that mentions this SNP (1)

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Identification of miRSNPs associated with the risk of multiple myeloma
AssociationN=4,726Angelica Macauda et al.(2017)· International Journal of Cancer

A genome-wide association study investigating miRNA-binding site SNPs (miRSNPs) in multiple myeloma susceptibility. Among 2,894 MM cases and 1,832 controls from the IMMEnSE consortium, two SNPs showed initial association (rs286595 in MRPL22, rs1419881 in TCF19). Meta-analysis with published GWAS data revealed significant associations for rs13409 (POU5F1, OR=0.92), rs1049623 (DDR1, OR=0.92), rs1049633 (DDR1, OR=0.87), and rs1419881 (TCF19, OR=0.91), all showing decreased MM risk.

Traits studied:Multiple myeloma
PubMedDOIMetascience Observatory

About SMPD1

The protein encoded by this gene is a lysosomal acid sphingomyelinase that converts sphingomyelin to ceramide. The encoded protein also has phospholipase C activity. Defects in this gene are a cause of Niemann-Pick disease type A (NPA) and Niemann-Pick disease type B (NPB). Multiple transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2010]

View all SMPD1 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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