rs603424

This is a intron variant variant in the PKD2L1 gene.

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GWAS Catalog Trait Associations (90)

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

platelet volume

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 0.06
p 4.0e-154
N 394,642
Large GWAS
European
Chen MH et al. “Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations.” Cell 182(5):1198-1213.e14 (2020)
Allele A
OR 0.06
p 5.0e-110
N 460,935
Large GWAS
European
Vuckovic D et al. “The Polygenic and Monogenic Basis of Blood Traits and Diseases.” Cell 182(5):1214-1231.e11 (2020)
Allele A
OR 0.05
p 1.0e-71
N 408,112
Large GWAS
European
Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele A
OR 0.06
p 8.0e-38
N 335,593
Major Consortium StudyLarge GWAS
European
Astle WJ et al. “The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.” Cell 167(5):1415-1429.e19 (2016)
Allele A
OR 0.06
p 5.0e-31
N 164,454
Large GWAS
European

myristate 14:0-to-myristoleate 14:1n5 ratio

Shin SY et al. “An atlas of genetic influences on human blood metabolites.” Nature Genetics 46(6):543-550 (2014)
Allele A
OR 0.05
p 1.0e-115
N 5,585
Large GWAS
European

metabolite measurement

Suhre K et al. “Human metabolic individuality in biomedical and pharmaceutical research.” Nature 477(7362):54-60 (2011)
Allele A
OR 0.12
p 3.0e-57
N 2,820
Large GWAS
European
Chen Y et al. “Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases.” Nature Genetics 55(1):44-53 (2023)
Allele A
OR 0.18
p 4.0e-12
N 5,151
Large GWAS
European
Schlosser P et al. “Genetic studies of paired metabolomes reveal enzymatic and transport processes at the interface of plasma and urine.” Nature Genetics 55(6):995-1008 (2023)
Allele A
OR 0.14
p 2.0e-16
N 4,870
Large GWAS
European
Tahir UA et al. “Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals.” Nature Communications 13(1):4923 (2022)
Allele A
OR 0.20
p 5.0e-11
N 2,466
Large GWAS
multi-ancestry

1-(1-enyl-palmitoyl)-2-palmitoleoyl-GPC (P-16:0/16:1) measurement

Surendran P et al. “Rare and common genetic determinants of metabolic individuality and their effects on human health.” Nature Medicine 28(11):2321-2332 (2022)
Allele A
OR 0.20
p 4.0e-50
N 14,296
Large GWAS
European
Hysi PG et al. “Metabolome Genome-Wide Association Study Identifies 74 Novel Genomic Regions Influencing Plasma Metabolites Levels.” Metabolites 12(1) (2022)
Allele A
OR 0.19
p 2.0e-25
N 8,809
Large GWAS
European
Chen Y et al. “Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases.” Nature Genetics 55(1):44-53 (2023)
Allele A
OR 0.17
p 2.0e-18
N 8,083
Large GWAS
European
Feofanova EV et al. “Whole-Genome Sequencing Analysis of Human Metabolome in Multi-Ethnic Populations.” Nature Communications 14(1):3111 (2023)
Allele A
OR 0.22
p 2.0e-22
N 6,166
Large GWAS
multi-ancestry
Yin X et al. “Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci.” Nature Communications 13(1):1644 (2022)
Allele A
OR 0.22
p 3.0e-14
N 6,136
Large GWAS
European

1-palmitoleoyl-GPC (16:1) measurement

Surendran P et al. “Rare and common genetic determinants of metabolic individuality and their effects on human health.” Nature Medicine 28(11):2321-2332 (2022)
Allele A
OR 0.18
p 8.0e-43
N 14,296
Large GWAS
European
Feofanova EV et al. “Whole-Genome Sequencing Analysis of Human Metabolome in Multi-Ethnic Populations.” Nature Communications 14(1):3111 (2023)
Allele A
OR 0.14
p 1.0e-18
N 11,272
Large GWAS
multi-ancestry
Hysi PG et al. “Metabolome Genome-Wide Association Study Identifies 74 Novel Genomic Regions Influencing Plasma Metabolites Levels.” Metabolites 12(1) (2022)
Allele A
OR 0.20
p 1.0e-24
N 8,809
Large GWAS
European
Chen Y et al. “Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases.” Nature Genetics 55(1):44-53 (2023)
Allele A
OR 0.18
p 2.0e-19
N 8,227
Large GWAS
European
Yin X et al. “Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci.” Nature Communications 13(1):1644 (2022)
Allele A
OR 0.22
p 4.0e-14
N 6,136
Large GWAS
European
Schlosser P et al. “Genetic studies of paired metabolomes reveal enzymatic and transport processes at the interface of plasma and urine.” Nature Genetics 55(6):995-1008 (2023)
Allele A
OR 0.09
p 9.0e-12
N 4,959
Large GWAS
European

lysophosphatidylcholine measurement

Harshfield EL et al. “Genome-wide analysis of blood lipid metabolites in over 5000 South Asians reveals biological insights at cardiometabolic disease loci.” Bmc Medicine 19(1):232 (2021)
Allele A
OR 0.20
p 1.0e-42
N 13,814
Large GWAS
European
Lotta LA et al. “A cross-platform approach identifies genetic regulators of human metabolism and health.” Nature Genetics 53(1):54-64 (2021)
Allele A
OR 12.53
p 5.0e-36
N 16,836
Large GWAS
European

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 G
OR 0.03
p 4.0e-41
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 G
OR 0.03
p 3.0e-12
N 142,487
Large GWAS
European

level of folate receptor beta in blood

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 0.09
p 3.0e-40
N 47,745
Large GWAS
European

LDL particle size

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele A
OR 0.03
p 4.0e-38
N 450,015
Large GWAS
multi-ancestry
Richardson TG et al. “Characterising metabolomic signatures of lipid-modifying therapies through drug target mendelian randomisation.” Plos Biology 20(2):e3001547 (2022)
Allele A
OR 0.04
p 3.0e-13
N 115,082
Large GWAS
European
Davyson E et al. “Metabolomic Investigation of Major Depressive Disorder Identifies a Potentially Causal Association With Polyunsaturated Fatty Acids.” Biological Psychiatry 94(8):630-639 (2023)
Allele A
OR 0.04
p 3.0e-11
N 88,329
Large GWAS
European

palmitoleate 16:1n7 measurement

Feofanova EV et al. “Whole-Genome Sequencing Analysis of Human Metabolome in Multi-Ethnic Populations.” Nature Communications 14(1):3111 (2023)
Allele A
OR 0.22
p 9.0e-37
N 9,349
Large GWAS
multi-ancestry
Surendran P et al. “Rare and common genetic determinants of metabolic individuality and their effects on human health.” Nature Medicine 28(11):2321-2332 (2022)
Allele A
OR 0.13
p 8.0e-22
N 14,296
Large GWAS
European
Hysi PG et al. “Metabolome Genome-Wide Association Study Identifies 74 Novel Genomic Regions Influencing Plasma Metabolites Levels.” Metabolites 12(1) (2022)
Allele A
OR 0.15
p 5.0e-16
N 8,809
Large GWAS
European
Chen Y et al. “Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases.” Nature Genetics 55(1):44-53 (2023)
Allele A
OR 0.13
p 1.0e-11
N 8,290
Large GWAS
European
Shin SY et al. “An atlas of genetic influences on human blood metabolites.” Nature Genetics 46(6):543-550 (2014)
Allele A
OR —
β 0.037
p 1.0e-14
N 7,776
Large GWAS
European
Yin X et al. “Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci.” Nature Communications 13(1):1644 (2022)
Allele A
OR 0.21
p 1.0e-13
N 6,136
Large GWAS
European

About PKD2L1

This gene encodes a member of the polycystin protein family. The encoded protein contains multiple transmembrane domains, and cytoplasmic N- and C-termini. The protein may be an integral membrane protein involved in cell-cell/matrix interactions. This protein functions as a calcium-regulated nonselective cation channel. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

View all PKD2L1 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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