IEMbase 0565: GLYCTK-related D-glycerate kinase deficiency
Scope
| Field | Value |
|---|---|
| IEMbase ID | 565 |
| Nosology | 3.1.02.01 |
| Gene | GLYCTK |
| External IDs | OMIM:610516; ORPHA:941 |
| Generated mapping | UNMAPPED; best candidate Mevalonate_Kinase_Deficiency.yaml |
| Candidate DisMech targets | No exact GLYCTK target found |
| Review date | 2026-07-07 |
IEMbase phenotype signal
IEMbase represents GLYCTK-related D-glycerate kinase deficiency, with alternate labels D-glyceric acidaemia and GLYCTK-D. The record is autosomal recessive, mitochondrial subtype, of unknown treatability, and has no treatment rows.
Biochemical rows include decreased liver D-glycerate kinase and increased D-glycerate in CSF, plasma, and urine. Clinical rows include metabolic acidosis. Characteristic rows include early death, encephalopathy, failure to thrive, axial hypotonia, intellectual disability, microcephaly, seizures, and abnormal, delayed, or absent speech.
DisMech phenotype coverage
The generated Mevalonate_Kinase_Deficiency.yaml candidate is a lexical false
positive based on kinase-deficiency similarity. It models isoprenoid-pathway
mevalonate kinase deficiency, not GLYCTK-related D-glyceric acidemia. Targeted
search did not find an exact GLYCTK or D-glycerate kinase deficiency entry.
Concordance and completeness
Judgement: reject Mevalonate_Kinase_Deficiency.yaml; true GLYCTK/D-glyceric
acidemia local gap.
IEMbase provides a concise seed for future curation: recessive GLYCTK disease, mitochondrial subtype, low liver D-glycerate kinase, high D-glycerate across CSF/plasma/urine, metabolic acidosis, severe neurodevelopmental involvement, hypotonia, microcephaly, seizures, failure to thrive, speech delay, and early death.
Curation actions
- Reject the mevalonate kinase candidate as an exact mapping.
- Add GLYCTK-related D-glycerate kinase deficiency / D-glyceric acidemia to the metabolic curation backlog.
- Preserve IEMbase compartment-specific D-glycerate, liver enzyme, acidosis, encephalopathy, hypotonia, seizure, speech, and early-death prompts.