rs477992

This is a intron variant variant in the PHGDH gene.

▶

GWAS Catalog Trait Associations (15)

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

serine measurement

Lotta LA et al. “A cross-platform approach identifies genetic regulators of human metabolism and health.” Nature Genetics 53(1):54-64 (2021)

Allele G

OR 22.27

p 8.0e-110

N 30,955

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 G

OR 0.18

p 4.0e-31

N 8,809

Large GWAS

European

Draisma HHM et al. “Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels.” Nature Communications 6:7208 (2015)

Allele G

OR —

β 0.040

p 3.0e-21

N 7,478

Large GWAS

European

glycine measurement

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 0.03

p 2.0e-55

N 450,015

Large GWAS

multi-ancestry

Abar L et al. “Unravelling genetic architecture of circulatory amino acid levels, and their effect on risk of complex disorders.” Nar Genomics and Bioinformatics 6(2):lqae046 (2024)

Allele G

OR 0.03

p 5.0e-15

N 117,944

Large GWAS

European

peripheral neuropathy

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 0.07

p 2.0e-19

N 422,954

Major Consortium StudyLarge 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 A

OR 0.02

p 4.0e-19

N 928,679

Large GWAS

multi-ancestry

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 0.02

p 7.0e-15

N 581,827

Major Consortium StudyLarge 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 A

OR 0.02

p 6.0e-18

N 503,987

Large GWAS

multi-ancestry

hematocrit

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 G

OR 0.02

p 2.0e-16

N 562,259

Large GWAS

European

alanine measurement

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 0.02

p 3.0e-16

N 450,015

Large GWAS

multi-ancestry

ulcer of lower limb

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 0.08

p 2.0e-15

N 620,129

Major Consortium StudyLarge GWAS

multi-ancestry

chronic ulcer of skin

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 0.07

p 1.0e-14

N 611,028

Major Consortium StudyLarge GWAS

multi-ancestry

metabolite measurement

Suhre K et al. “Human metabolic individuality in biomedical and pharmaceutical research.” Nature 477(7362):54-60 (2011)

Allele A

OR —

β 0.051

p 3.0e-14

N 2,820

Large GWAS

European

hemoglobin measurement

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 G

OR 0.01

p 1.0e-13

N 563,946

Large GWAS

European

Oskarsson GR et al. “Predicted loss and gain of function mutations in ACO1 are associated with erythropoiesis.” Communications Biology 3(1):189 (2020)

Allele G

OR —

β 0.015

p 1.0e-10

N 684,122

Large GWAS

European

About PHGDH

This gene encodes the enzyme which is involved in the early steps of L-serine synthesis in animal cells. L-serine is required for D-serine and other amino acid synthesis. The enzyme requires NAD/NADH as a cofactor and forms homotetramers for activity. Mutations in this gene have been found in a family with congenital microcephaly, psychomotor retardation and other symptoms. Multiple alternatively spliced transcript variants have been found, however the full-length nature of most are not known. [provided by RefSeq, Aug 2011]

rs477992

GWAS Catalog Trait Associations (15)

serine measurement

glycine measurement

peripheral neuropathy

erythrocyte count

hematocrit

alanine measurement

ulcer of lower limb

chronic ulcer of skin

metabolite measurement

hemoglobin measurement

About PHGDH

Community Wiki

Comments