IEMbase 0584: SMS-related spermine synthase deficiency
Scope
| Field | Value |
|---|---|
| IEMbase ID | 584 |
| Nosology | 2.4.11.01 |
| Gene | SMS |
| External IDs | OMIM:309583; OMIM:300105; ORPHA:477817 |
| Generated mapping | UNMAPPED; best candidate GM3_Synthase_Deficiency.yaml |
| Candidate DisMech targets | None exact |
| Review date | 2026-07-07 |
IEMbase phenotype signal
IEMbase represents SMS-related spermine synthase deficiency, with alternate labels Snyder-Robinson syndrome X-linked, SMS, and SRS. The record is classified under disorders of polyamine metabolism, lists autosomal recessive inheritance, has unknown treatability, and has no treatment rows.
The biochemical row is increased plasma N-acetylspermidine. Clinical rows include epileptic encephalopathy and intellectual disability.
DisMech phenotype coverage
GM3_Synthase_Deficiency.yaml is a false-positive generated candidate. That
entry models ST3GAL5-related GM3 synthase deficiency in glycosphingolipid
biology with severe neurodevelopmental and epilepsy phenotypes. It does not
match SMS, spermine synthase, Snyder-Robinson syndrome, polyamine metabolism,
or the N-acetylspermidine biomarker.
The local knowledge base contains only broad polyamine biology in other disease contexts and no exact Snyder-Robinson / spermine synthase deficiency target was identified.
Concordance and completeness
Judgement: true local gap; reject GM3 synthase deficiency as an exact target.
The generated candidate shares neurologic severity and epilepsy but diverges on gene, pathway, mechanism, biomarker, and disease identity. The IEMbase record should be curated as a polyamine-metabolism disorder, not a glycosphingolipid synthesis disorder.
The IEMbase inheritance and OMIM pairing should be source-reviewed during import because the disease label itself names X-linked Snyder-Robinson syndrome.
Curation actions
- Create or identify an exact SMS / Snyder-Robinson syndrome target before import.
- Reject
GM3_Synthase_Deficiency.yamlas an exact mapping. - Preserve the N-acetylspermidine, epileptic-encephalopathy, intellectual- disability, inheritance, and OMIM prompts for source review.