rs2277339

This is a variant in the PRIM1 gene that changes a aspartate to an alanine.

▶

GWAS Catalog Trait Associations (24)

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

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 0.03
p 7.0e-205
N 5,314,291
Large GWAS
European, Hispanic or Latin American, East Asian, African unspecified, South Asian
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 G
OR 0.04
p 2.0e-20
N 607,511
Major Consortium StudyLarge GWAS
multi-ancestry
Schoeler T et al. “Combining cross-sectional and longitudinal genomic approaches to identify determinants of cognitive and physical decline.” Nature Communications 16(1):4524 (2025)
Allele G
OR 0.02
p 2.0e-20
N 405,540
Large GWAS
European
Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)
Allele G
OR 0.02
p 3.0e-22
N 394,642
Large GWAS
European
Chiou JS et al. “Your height affects your health: genetic determinants and health-related outcomes in Taiwan.” Bmc Medicine 20(1):250 (2022)
Allele G
OR 0.04
p 2.0e-9
N 67,452
Large GWAS
East Asian

age at menopause

Ruth KS et al. “Genetic insights into biological mechanisms governing human ovarian ageing.” Nature 596(7872):393-397 (2021)
Allele T
OR 0.35
p 2.0e-136
N 201,323
Large GWAS
multi-ancestry
Day FR et al. “Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair.” Nature Genetics 47(11):1294-1303 (2015)
Allele T
OR 0.31
p 2.0e-19
N 69,626
Large GWAS
European
Horikoshi M et al. “Elucidating the genetic architecture of reproductive ageing in the Japanese population.” Nature Communications 9(1):1977 (2018)
Allele T
OR 0.29
p 8.0e-20
N 43,861
Large GWAS
multi-ancestry
Stolk L et al. “Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways.” Nature Genetics 44(3):260-8 (2012)
Allele T
OR 0.38
p 2.0e-19
N 38,968
Large GWAS
European

appendicular lean mass

Pei YF et al. “The genetic architecture of appendicular lean mass characterized by association analysis in the UK Biobank study.” Communications Biology 3(1):608 (2020)
Allele T
OR 0.04
p 2.0e-30
N 450,243
Major Consortium StudyLarge GWAS
European

mean corpuscular hemoglobin

Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)
Allele G
OR 0.03
p 1.0e-26
N 394,642
Large GWAS
European
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 0.03
p 8.0e-25
N 478,500
Large GWAS
multi-ancestry
Vuckovic D et al. “The Polygenic and Monogenic Basis of Blood Traits and Diseases.” Cell 182(5):1214-1231.e11 (2020)
Allele G
OR 0.04
p 2.0e-24
N 408,112
Large GWAS
European
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 0.02
p 2.0e-12
N 153,950
Large GWAS
East Asian

whole body water mass

Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)
Allele G
OR 0.02
p 3.0e-23
N 394,642
Large GWAS
European

age at menarche

Horikoshi M et al. “Elucidating the genetic architecture of reproductive ageing in the Japanese population.” Nature Communications 9(1):1977 (2018)
Allele T
OR 0.29
p 8.0e-20
N 67,029
Large GWAS
multi-ancestry

base metabolic rate measurement

Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)
Allele G
OR 0.02
p 1.0e-19
N 394,642
Large GWAS
European

erythrocyte count

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 T
OR 0.01
p 8.0e-19
N 928,679
Large GWAS
multi-ancestry
Sakaue S et al. “A cross-population atlas of genetic associations for 220 human phenotypes.” Nature Genetics 53(10):1415-1424 (2021)
Allele T
OR 0.02
p 5.0e-12
N 503,987
Large GWAS
multi-ancestry

mean reticulocyte volume

Vuckovic D et al. “The Polygenic and Monogenic Basis of Blood Traits and Diseases.” Cell 182(5):1214-1231.e11 (2020)
Allele G
OR 0.03
p 7.0e-17
N 408,112
Large GWAS
European
Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)
Allele G
OR 0.03
p 1.0e-16
N 394,642
Large GWAS
European

type 2 diabetes mellitus

Suzuki K et al. “Genetic drivers of heterogeneity in type 2 diabetes pathophysiology.” Nature 627(8003):347-357 (2024)
Allele G
OR —
p 5.0e-15
N 2,535,601
Large GWAS
multi-ancestry
Vujkovic M et al. “Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis.” Nature Genetics 52(7):680-691 (2020)
Allele G
OR 0.04
p 7.0e-15
N 1,407,282
Meta-analysisLarge GWAS
multi-ancestry
Ishigaki K et al. “Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases.” Nature Genetics 52(7):669-679 (2020)
Allele G
OR 1.06
p 5.0e-8
N 210,865
Large GWAS
East Asian
▶

ClinVar annotation

Benign★★★☆
2 submitters1 publication
View on ClinVar →

About PRIM1

The replication of DNA in eukaryotic cells is carried out by a complex chromosomal replication apparatus, in which DNA polymerase alpha and primase are two key enzymatic components. Primase, which is a heterodimer of a small subunit and a large subunit, synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication. The protein encoded by this gene is the small, 49 kDa primase subunit. [provided by RefSeq, Jul 2008]

View all PRIM1 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

Community Wiki

No community notes yet for this variant. Sign in to start one.

Comments

Sign in to join the discussion.

Loading comments…