IEMbase 0331: RFT1-related flippase of Man5GlcNAc2-PP-Dol deficiency
Scope
| Field | Value |
|---|---|
| IEMbase ID | 331 |
| Nosology | 18.1.1.01 |
| Gene | RFT1 |
| External IDs | OMIM:612015 |
| Generated mapping | UNMAPPED |
| Candidate DisMech targets | Reject Severe_Combined_Immunodeficiency.yaml#X-linked SCID |
| Review date | 2026-07-07 |
IEMbase phenotype signal
IEMbase represents RFT1-CDG/CDG-In, lipid-linked oligosaccharide flippase deficiency. Characteristic rows include dysmorphism, epilepsy, impaired hearing, hypotonia, and impaired vision. Additional clinical rows include ataxia, cerebral atrophy on MRI, failure to thrive, feeding difficulties, hepatomegaly, inverted nipples, microcephaly, psychomotor retardation, and thrombosis.
The biochemical rows include normal creatine kinase and transaminase, increased asialotransferrin and disialotransferrin, increased fibroblast lipid-linked Man5GlcNAc2, type 1 sialotransferrin pattern, decreased tetrasialotransferrin, decreased antithrombin III, increased serum dolichol-linked Man5GlcNAc2, and decreased factor XI and protein C. No treatment rows are present.
DisMech phenotype coverage
The generated X-linked SCID candidate is a false positive. The local severe combined immunodeficiency entry is centered on IL2RG, ADA, RAG1, RAG2, IL7R, JAK3, and DCLRE1C with absent cellular immunity, recurrent infections, lymphocyte abnormalities, thymic aplasia, and HSCT/gene/PEG-ADA treatment logic. It does not cover RFT1, lipid-linked oligosaccharide flipping, or type I CDG biochemical testing.
Existing CDG entries and the CDG module provide pathway context, but there is no standalone RFT1-CDG disease entry.
Concordance and completeness
Judgement: true local disease gap; reject the SCID candidate.
IEMbase points to a multisystem glycosylation disorder with neurologic, sensory, hepatic, thrombotic, and coagulation features plus Man5GlcNAc2 lipid-linked/dolichol-linked biochemical abnormalities. That signal should not be conflated with primary severe combined immunodeficiency.
Curation actions
- Add a standalone RFT1-CDG target before treating this record as mapped.
- Do not map to severe combined immunodeficiency based on broad immune or failure-to-thrive vocabulary.
- Preserve Man5GlcNAc2, antithrombin III, factor XI, protein C, thrombosis, hearing, vision, and cerebral atrophy rows as future-curation prompts.