rs1133400

This is a protein-altering variant in the INPP5A gene.

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GWAS Catalog Trait Associations (18)

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

heel bone mineral density

Morris JA et al. “An atlas of genetic influences on osteoporosis in humans and mice.” Nature Genetics 51(2):258-266 (2019)
Allele A
OR 0.03
p 1.0e-43
N 426,824
Large GWAS
European
Kemp JP et al. “Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis.” Nature Genetics 49(10):1468-1475 (2017)
Allele A
OR 0.03
p 2.0e-17
N 142,487
Large GWAS
European

urate measurement

Major TJ et al. “A genome-wide association analysis reveals new pathogenic pathways in gout.” Nature Genetics 56(11):2392-2406 (2024)
Allele A
OR 0.02
p 3.0e-12
N 630,117
Large GWAS
European
Cho C et al. “Large-scale cross-ancestry genome-wide meta-analysis of serum urate.” Nature Communications 15(1):3441 (2024)
Allele A
OR 0.02
p 3.0e-10
N 1,029,323
Meta-analysisLarge GWAS
multi-ancestry

hematocrit

Sakaue S et al. “A cross-population atlas of genetic associations for 220 human phenotypes.” Nature Genetics 53(10):1415-1424 (2021)
Allele G
OR 0.01
p 2.0e-11
N 503,490
Large GWAS
multi-ancestry
Jee YH et al. “Genome-wide association studies in a large Korean cohort identify quantitative trait loci for 36 traits and illuminate their genetic architectures.” Nature Communications 16(1):4935 (2025)
Allele G
OR 0.01
p 3.0e-10
N 928,679
Large GWAS
multi-ancestry

diastolic blood pressure

Jee YH et al. “Genome-wide association studies in a large Korean cohort identify quantitative trait loci for 36 traits and illuminate their genetic architectures.” Nature Communications 16(1):4935 (2025)
Allele A
OR 0.01
p 4.0e-11
N 928,679
Large GWAS
multi-ancestry
Koskeridis F et al. “Multi-trait association analysis reveals shared genetic loci between Alzheimer's disease and cardiovascular traits.” Nature Communications 15(1):9827 (2024)
Allele A
OR 0.01
p 2.0e-9
N 1,212,859
Large GWAS
European
Keaton JM et al. “Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits.” Nature Genetics 56(5):778-791 (2024)
Allele A
OR 0.11
p 1.0e-9
N 1,028,980
Large GWAS
multi-ancestry
Surendran P et al. “Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals.” Nature Genetics 52(12):1314-1332 (2020)
Allele A
OR 0.11
p 2.0e-8
N 810,865
Meta-analysisLarge GWAS
European

free cholesterol to total lipids in large LDL percentage

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele G
OR 0.01
p 5.0e-11
N 450,015
Large GWAS
multi-ancestry

mean arterial pressure

Sakaue S et al. “A cross-population atlas of genetic associations for 220 human phenotypes.” Nature Genetics 53(10):1415-1424 (2021)
Allele G
OR 0.01
p 8.0e-11
N 506,365
Large GWAS
multi-ancestry

triglycerides to total lipids in IDL percentage

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele G
OR 0.01
p 8.0e-11
N 450,015
Large GWAS
multi-ancestry

triglycerides to total lipids in small LDL percentage

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele G
OR 0.01
p 8.0e-11
N 450,015
Large GWAS
multi-ancestry

hypertension

Surendran P et al. “Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals.” Nature Genetics 52(12):1314-1332 (2020)
Allele A
OR 6.48
p 9.0e-11
N 1,164,961
Meta-analysisLarge GWAS
European

body height

Yengo L et al. “A saturated map of common genetic variants associated with human height.” Nature 610(7933):704-712 (2022)
Allele G
OR 0.01
p 1.0e-10
N 5,314,291
Large GWAS
European, Hispanic or Latin American, East Asian, African unspecified, South Asian
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Research that mentions this SNP (1)

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A distinct and replicable variant of the squamous cell carcinoma gene inositol polyphosphate‐5‐phosphatase modifies the susceptibility of arsenic‐associated skin lesions in Bangladesh
AssociationN=4,222Wei Jie Seow et al.(2015)· Cancer

A case-control study of 540 cases and 400 controls in Bangladesh examined 25 candidate SNPs in inflammation, one-carbon metabolism, and skin cancer genes for associations with arsenic-induced skin lesions. Six SNPs showed significant gene-environment interactions with water arsenic exposure (PEMT rs2278952 P=0.004, rs897453 P=0.05; DHFR rs1650697 P=0.02; IL10 rs3024496 P=0.04; INPP5A rs1133400 P=0.03; XPC rs2228000 P=0.01), and the INPP5A rs1133400 interaction was successfully replicated in an independent population of 488 cases and 2,794 controls (P=0.03).

Traits studied:Arsenic-induced skin lesionsBasal cell carcinoma (BCC)Bowen's diseaseHyperkeratosisKeratosisMelanosisSquamous cell carcinoma (SCC)
PubMedDOIMetascience Observatory

About INPP5A

The protein encoded by this gene is a membrane-associated type I inositol 1,4,5-trisphosphate (InsP3) 5-phosphatase. InsP3 5-phosphatases hydrolyze Ins(1,4,5)P3, which mobilizes intracellular calcium and acts as a second messenger mediating cell responses to various stimulation. [provided by RefSeq, Jul 2008]

View all INPP5A variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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