rs17632542

This is a protein-altering variant in the KLK3 gene.

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GWAS Catalog Trait Associations (4)

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

prostate specific antigen amount

Hoffmann TJ et al. “Genome-wide association study of prostate-specific antigen levels in 392,522 men identifies new loci and improves prediction across ancestry groups.” Nature Genetics 57(2):334-344 (2025)
Allele T
OR 0.34
p —
N 392,522
Large GWAS
multi-ancestry
Kachuri L et al. “Genetically adjusted PSA levels for prostate cancer screening.” Nature Medicine 29(6):1412-1423 (2023)
Allele T
OR 0.37
p —
N 95,768
Large GWAS
multi-ancestry
Hoffmann TJ et al. “Genome-wide association study of prostate-specific antigen levels identifies novel loci independent of prostate cancer.” Nature Communications 8:14248 (2017)
Allele T
OR 0.44
p —
N 28,503
Large GWAS
multi-ancestry
Gudmundsson J et al. “Genetic correction of PSA values using sequence variants associated with PSA levels.” Science Translational Medicine 2(62):62ra92 (2010)
Allele T
OR 39.10
p 3.0e-46
N 7,538
Large GWAS
European

prostate carcinoma

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 T
OR 0.27
p 8.0e-59
N 573,692
Major Consortium StudyLarge GWAS
multi-ancestry
Knipe DW et al. “Genetic variation in prostate-specific antigen-detected prostate cancer and the effect of control selection on genetic association studies.” Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology 23(7):1356-1365 (2014)
Allele T
OR 0.73
p 2.0e-28
N 2,950
Large GWAS
European

prostatitis

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 T
OR 0.32
p 2.0e-11
N 411,978
Major Consortium StudyLarge GWAS
European

cancer

Ahmed M et al. “Considering hormone-sensitive cancers as a single disease in the UK biobank reveals shared aetiology.” Communications Biology 5(1):614 (2022)
Allele C
OR —
β 0.008
p 3.0e-10
N 238,404
Major Consortium StudyLarge GWAS
European
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Research that mentions this SNP (3)

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Fine mapping the KLK3 locus on chromosome 19q13.33 associated with prostate cancer susceptibility and PSA levels
AssociationN=6,860Parikh H. et al.(2011)· Human Genetics

Fine mapping study of the KLK3 locus (chromosome 19q13.33) in 3,522 prostate cancer cases and 3,338 controls identified three highly correlated SNPs (rs17632542, rs62113212, rs62113214) associated with nonaggressive prostate cancer (P = 4.72×10⁻⁵ to 5.74×10⁻⁵, OR = 0.68-0.69 per allele). The previously reported marker rs2735839 showed no significant association (P = 0.20). Baseline PSA levels were 43.7% lower in carriers of minor alleles at the three SNPs (P = 9.70×10⁻⁵), suggesting germline KLK3 variants influence PSA screening-detected prostate cancer.

Traits studied:Advanced prostate cancerNonaggressive prostate cancerProstate cancerProstate-specific antigen (PSA) levels
PubMedDOIMetascience Observatory
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Identification of a novel prostate cancer susceptibility variant in the KLK3 gene transcript
AssociationN=21,086Kote-Jarai Z. et al.(2011)· Human Genetics

Genome-wide association study identifying rs17632542 (Ile179Thr) in KLK3 gene as a strong prostate cancer susceptibility variant (combined P = 1.9 × 10⁻³⁴, OR = 0.66) across 10,405 cases and 10,681 controls. The variant was also associated with PSA levels and molecular dynamics modeling suggested it could alter protein stability or affect RNA splicing of KLK3.

Traits studied:Gleason scorePSA levelProstate cancer
PubMedDOIMetascience Observatory
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Replication of prostate cancer risk loci on 8q24, 11q13, 17q12, 19q33, and Xp11 in African Americans
ReviewStanley Hooker et al.(2010)· The Prostate

This comprehensive review examines genetic association studies on prostate cancer, discussing GWASs that have identified over 75 variants associated with PCa risk (as of February 2016), with major susceptibility regions at 8q24, 17q12, 17q24, 10q11, and 19q13. The paper also reviews candidate gene-based approaches targeting genes involved in androgen signaling, carcinogen metabolism, DNA repair, vitamin D signaling, inflammation, angiogenesis, and cellular adhesion, as well as regulatory RNA genes.

Traits studied:Prostate cancer aggressivenessProstate cancer progressionProstate cancer survivalProstate cancer susceptibilitySerum PSA level
PubMedDOIMetascience Observatory

About KLK3

Kallikreins are a subgroup of serine proteases having diverse physiological functions. Growing evidence suggests that many kallikreins are implicated in carcinogenesis and some have potential as novel cancer and other disease biomarkers. The gene is one of the fifteen kallikrein subfamily members located in a cluster on chromosome 19. It encodes a single-chain glycoprotein, a protease which is synthesized in the epithelial cells of the prostate gland, and is present in seminal plasma. It is thought to function normally in the liquefaction of seminal coagulum, presumably by hydrolysis of the high molecular mass seminal vesicle protein. The serum level of this protein, called PSA in the clinical setting, is useful in the diagnosis and monitoring of prostatic carcinoma. Alternate splicing of this gene generates several transcript variants encoding different isoforms. [provided by RefSeq, Dec 2019]

View all KLK3 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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