Skip to content

IEMbase 0595: SLC39A8-related congenital disorder of glycosylation

Scope

Field Value
IEMbase ID 595
Nosology 22.3.11.01
Gene SLC39A8
External IDs OMIM:616721; ORPHA:468699
Generated mapping CANDIDATE; ALG12_Congenital_Disorder_of_Glycosylation.yaml
Candidate DisMech targets None exact
Review date 2026-07-07

IEMbase phenotype signal

IEMbase represents SLC39A8-related congenital disorder of glycosylation, also labelled CDG2N-CDG, CDG-IIn, and solute carrier family 39 zinc transporter deficiency. The record is autosomal recessive, classified under disorders of manganese metabolism, flagged as treatable, and lists galactose, manganese, and uridine.

Biochemical rows include serum sialotransferrin type 2 pattern, very decreased blood manganese, decreased serum zinc, normal urinary zinc, and normal-to-increased urinary manganese. Clinical rows include hyperreflexia, osteopenia, recurrent infections, seizures, short stature, cerebellar and cerebral atrophy on MRI, hypotonia, intellectual disability, scoliosis, and strabismus.

DisMech phenotype coverage

ALG12_Congenital_Disorder_of_Glycosylation.yaml is a false-positive CDG-class candidate. ALG12-CDG models an ER mannosyltransferase defect in N-glycan precursor assembly and a type I CDG pattern. It does not represent SLC39A8, manganese/zinc transport, CDG-IIn/type II glycosylation, or manganese supplementation response.

The local Manganism.yaml entry is also not an exact target because it models toxic manganese excess rather than inherited manganese transporter deficiency with low blood manganese. No exact SLC39A8-CDG target was identified.

Concordance and completeness

Judgement: true local gap; reject ALG12-CDG as exact coverage.

IEMbase's distinguishing features are SLC39A8 transporter biology, manganese metabolism, type II transferrin glycosylation, low blood manganese, zinc abnormalities, and nutritional treatment. Those should not be collapsed into generic CDG or manganese-toxicity context.

Curation actions

  • Create or identify an exact SLC39A8-CDG / CDG-IIn target before import.
  • Reject ALG12_Congenital_Disorder_of_Glycosylation.yaml as an exact mapping.
  • Preserve manganese, zinc, type 2 sialotransferrin, galactose/manganese/uridine treatment, MRI atrophy, seizure, osteopenia, infection, hypotonia, intellectual-disability, scoliosis, strabismus, and hyperreflexia prompts.