PGK1

Chr XXLR

phosphoglycerate kinase 1

Also known as: HEL-S-68p, MIG10, PGKA

Phosphoglycerate kinase 1 catalyzes the conversion of 1,3-diphosphoglycerate to 3-phosphoglycerate in the glycolytic pathway and acts as a polymerase alpha cofactor protein. Mutations cause phosphoglycerate kinase 1 deficiency, which presents with hemolytic anemia and neurological impairment. The condition follows X-linked recessive inheritance and the gene is highly constrained against loss-of-function variants.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismXLRLOEUF 0.471 OMIM phenotype
Clinical SummaryPGK1
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.77) — some intolerance to loss-of-function variants.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint
0.47LOEUF
pLI 0.765
Z-score 2.91
OE 0.15 (0.060.47)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.34Z-score
OE missense 0.92 (0.811.06)
144 obs / 155.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.15 (0.060.47)
00.351.4
Missense OE0.92 (0.811.06)
00.61.4
Synonymous OE1.00
01.21.6
LoF obs/exp: 2 / 13.5Missense obs/exp: 144 / 155.9Syn Z: 0.03

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

PGK1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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