rs1047891

This is a variant in the CPS1 gene that changes a threonine to an asparagine.

▶

GWAS Catalog Trait Associations (201)

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

gamma-glutamylglycine 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 0.43
p —
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 0.42
p 1.0e-152
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 0.48
p 5.0e-216
N 8,263
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 0.45
p 1.0e-151
N 7,929
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 0.18
p 9.0e-22
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 0.17
p 1.0e-57
N 4,957
Large GWAS
European

N-acetylglycine 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 0.43
p —
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 0.35
p 2.0e-120
N 10,315
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 0.39
p 3.0e-135
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 0.38
p 1.0e-129
N 8,250
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 0.20
p 2.0e-25
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 0.23
p 3.0e-58
N 4,960
Large GWAS
European

propionylglycine 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 0.40
p 2.0e-273
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 0.37
p 3.0e-99
N 7,411
Large GWAS
multi-ancestry
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 0.36
p 9.0e-96
N 7,311
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 0.25
p 3.0e-39
N 3,771
Large GWAS
European

metabolite measurement, diet measurement

Dong X et al. “Unprocessed Red Meat and Processed Meat Consumption, Plasma Metabolome, and Risk of Ischemic Heart Disease: A Prospective Cohort Study of UK Biobank.” Journal of the American Heart Association 12(7):e027934 (2023)
Allele A
OR 0.16
p 6.0e-262
N 92,246
Major Consortium StudyLarge GWAS
European

X-16570 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 0.33
p 8.0e-195
N 14,296
Large GWAS
European

3-methylglutarylcarnitine (2) 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 0.32
p 9.0e-190
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 0.31
p 8.0e-91
N 8,220
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 0.31
p 7.0e-85
N 7,891
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 0.16
p 6.0e-16
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 0.33
p 7.0e-61
N 4,956
Large GWAS
European

glomerular filtration rate

Stanzick KJ et al. “Discovery and prioritization of variants and genes for kidney function in >1.2 million individuals.” Nature Communications 12(1):4350 (2021)
Allele A
OR 0.01
p 1.0e-158
N 1,201,930
Large GWAS
multi-ancestry
Liu H et al. “Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease.” Nature Genetics 54(7):950-962 (2022)
Allele A
OR 26.13
p 2.0e-150
N 1,508,659
Large GWAS
multi-ancestry
Wuttke M et al. “A catalog of genetic loci associated with kidney function from analyses of a million individuals.” Nature Genetics 51(6):957-972 (2019)
Allele A
OR 0.01
p 7.0e-117
N 765,348
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 0.04
p 5.0e-43
N 571,227
Major Consortium StudyLarge GWAS
multi-ancestry
Graham SE et al. “Sex-specific and pleiotropic effects underlying kidney function identified from GWAS meta-analysis.” Nature Communications 10(1):1847 (2019)
Allele A
OR 13.62
p 3.0e-42
N 350,514
Meta-analysisLarge GWAS
multi-ancestry
Morris AP et al. “Trans-ethnic kidney function association study reveals putative causal genes and effects on kidney-specific disease aetiologies.” Nature Communications 10(1):29 (2019)
Allele A
OR 0.61
p 2.0e-29
N 312,296
Large GWAS
multi-ancestry
Hughes O et al. “Genome-wide study investigating effector genes and polygenic prediction for kidney function in persons with ancestry from Africa and the Americas.” Cell Genomics 4(1):100468 (2024)
Allele A
OR 5.98
p 2.0e-9
N 145,732
Large GWAS
multi-ancestry
Hellwege JN et al. “Mapping eGFR loci to the renal transcriptome and phenome in the VA Million Veteran Program.” Nature Communications 10(1):3842 (2019)
Allele A
OR 0.64
p 3.0e-12
N 91,729
Major Consortium StudyLarge GWAS
multi-ancestry

serum homoarginine amount

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 0.28
p 6.0e-152
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 0.26
p 3.0e-60
N 9,064
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 0.23
p 5.0e-47
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 0.27
p 2.0e-67
N 8,265
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 0.18
p 7.0e-21
N 6,136
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 0.23
p 6.0e-14
N 2,466
Large GWAS
multi-ancestry

serum creatinine amount

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 0.04
p 1.0e-126
N 394,642
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 0.05
p 2.0e-50
N 602,615
Major Consortium StudyLarge GWAS
multi-ancestry
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 0.04
p 9.0e-83
N 450,015
Large GWAS
multi-ancestry
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 0.03
p 2.0e-19
N 153,950
Large GWAS
East Asian
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 0.03
p 3.0e-13
N 150,266
Large GWAS
East Asian
Karjalainen MK et al. “Genome-wide characterization of circulating metabolic biomarkers.” Nature 628(8006):130-138 (2024)
Allele A
OR 0.05
p 8.0e-31
N 136,016
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 1.0e-30
N 110,051
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 9.57
p 1.0e-21
N 84,794
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-19
N 84,405
Large GWAS
European
Graham SE et al. “Sex-specific and pleiotropic effects underlying kidney function identified from GWAS meta-analysis.” Nature Communications 10(1):1847 (2019)
Allele A
OR 0.05
p 3.0e-14
N 69,591
Meta-analysisLarge GWAS
European

3-methylglutaconate measurement

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 0.37
p 2.0e-123
N 8,197
Large GWAS
European
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 0.23
p 1.0e-88
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 0.39
p 1.0e-121
N 7,896
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 0.23
p 5.0e-31
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 0.24
p 4.0e-57
N 4,958
Large GWAS
European
▶

ClinVar annotation

Risk Factor★★★☆
13 submitters8 publications

CARBAMOYL PHOSPHATE SYNTHETASE I POLYMORPHISM; Congenital hyperammonemia, type I; Pulmonary hypertension, neonatal, susceptibility to (PHN); not specified

View on ClinVar →

About CPS1

The mitochondrial enzyme encoded by this gene catalyzes synthesis of carbamoyl phosphate from ammonia and bicarbonate. This reaction is the first committed step of the urea cycle, which is important in the removal of excess urea from cells. The encoded protein may also represent a core mitochondrial nucleoid protein. Three transcript variants encoding different isoforms have been found for this gene. The shortest isoform may not be localized to the mitochondrion. Mutations in this gene have been associated with carbamoyl phosphate synthetase deficiency, susceptibility to persistent pulmonary hypertension, and susceptibility to venoocclusive disease after bone marrow transplantation.[provided by RefSeq, May 2010]

View all CPS1 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…