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IEMbase 0601: PGM3-related phosphoglucomutase 3 deficiency

Scope

Field Value
IEMbase ID 601
Nosology 18.4.06.01
Gene PGM3
External IDs OMIM:615816; OMIM:172100; ORPHA:443811
Generated mapping CANDIDATE; IKBKG_Ectodermal_Dysplasia_with_Immunodeficiency.yaml#IMD33
Candidate DisMech targets None exact
Review date 2026-07-07

IEMbase phenotype signal

IEMbase represents PGM3-related phosphoglucomutase 3 deficiency, labelled PGM3-CDG and immunodeficiency-23. The record is autosomal recessive, classified under disorders of multiple glycosylation pathways, has unknown treatability, and has no treatment rows.

Biochemical rows include increased serum N-glycans and O-glycans, normal serum sialotransferrins, normal-to-increased IgE, and decreased CD19-positive B-cell counts. Clinical rows include T-cell immunodeficiency, recurrent infections, neutropenia, atopy, intellectual disability, short stature, skeletal dysplasia, brachydactyly, facial dysmorphism, midface hypoplasia, micrognathia, downturned mouth corners, and short neck.

DisMech phenotype coverage

IKBKG_Ectodermal_Dysplasia_with_Immunodeficiency.yaml#IMD33 is a false-positive generated candidate. It models X-linked IKBKG/NEMO-related mycobacterial susceptibility and NF-kB signaling impairment, not PGM3, hexosamine/N-glycosylation biology, autosomal recessive inheritance, or the PGM3-CDG skeletal-dysmorphic immune phenotype.

Autosomal_Dominant_Hyper-IgE_Syndrome.yaml mentions PGM3 only as a gene-panel differential for STAT3-HIES. That is useful diagnostic context but not disease coverage. No exact PGM3-CDG / immunodeficiency-23 target was identified.

Concordance and completeness

Judgement: true local gap; reject IMD33 as exact coverage.

The generated candidate shares immunodeficiency wording, but the causal gene, inheritance, pathway, immune phenotype, and syndromic features are different. IEMbase 0601 should not be collapsed into IKBKG/NEMO deficiency or STAT3-HIES context.

Curation actions

  • Create or identify an exact PGM3-CDG / immunodeficiency-23 target before import.
  • Reject IKBKG_Ectodermal_Dysplasia_with_Immunodeficiency.yaml#IMD33 as an exact mapping.
  • Preserve N- and O-glycan abnormalities with normal sialotransferrins, CD19 B-cell decrease, IgE range, T-cell immunodeficiency, neutropenia, infection, atopy, skeletal dysplasia, brachydactyly, facial, growth, and neurodevelopmental prompts.