rs561931

This variant is located in the PHGDH gene.

▶

GWAS Catalog Trait Associations (3)

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

serine 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 0.17

p 3.0e-60

N 14,296

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 7.0e-33

N 8,271

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 0.05

p 2.0e-15

N 4,960

Large GWAS

European

serum metabolite level

Feofanova EV et al. “A Genome-wide Association Study Discovers 46 Loci of the Human Metabolome in the Hispanic Community Health Study/Study of Latinos.” American Journal of Human Genetics 107(5):849-863 (2020)

Allele A

OR 0.21

p 3.0e-20

N 3,926

Large GWAS

Hispanic or Latin American

glycine measurement

Karjalainen MK et al. “Genome-wide characterization of circulating metabolic biomarkers.” Nature 628(8006):130-138 (2024)

Allele A

OR 0.04

p 7.0e-18

N 90,223

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 0.03

p 3.0e-13

N 114,978

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 0.03

p 5.0e-10

N 88,258

Large GWAS

European

Wittemans LBL et al. “Assessing the causal association of glycine with risk of cardio-metabolic diseases.” Nature Communications 10(1):1060 (2019)

Allele A

OR 0.03

p 8.0e-14

N 80,003

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 7.48

p 8.0e-14

N 80,003

Large GWAS

European

▶

ClinVar annotation

Benign★★★☆

4 submitters1 publication

PHGDH deficiency; Neu-Laxova syndrome 1; not provided

View on ClinVar →

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]

rs561931

GWAS Catalog Trait Associations (3)

serine measurement

serum metabolite level

glycine measurement

ClinVar annotation

About PHGDH

Community Wiki

Comments