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IEMbase 0389: COG6-related Component of COG complex 6 deficiency (CDG)

Scope

Field Value
IEMbase ID 389
Nosology 19.6.04.01
Gene COG6
External IDs OMIM:606977; OMIM:614576; ORPHA:464443
Generated mapping UNMAPPED; low candidate COX14-Related_COX_Deficiency.yaml
Candidate DisMech targets No exact local target
Review date 2026-07-07

IEMbase phenotype signal

IEMbase represents autosomal recessive COG6-CDG, also listed as Shaheen syndrome. The record has a type II CDG biochemical profile with increased asialotransferrin, disialotransferrin, monosialotransferrin, trisialotransferrin, and apolipoprotein C-III hypoglycosylation; decreased tetrasialotransferrin; normal-to-increased type II sialotransferrins; and increased transaminase, creatine kinase, lactate, and low vitamin K signals.

Clinical rows include ataxia, psychomotor delay, liver dysfunction, facial dysmorphism, epilepsy, hypotonia, microcephaly, growth retardation, failure to thrive, recurrent infections, hemophagocytosis, dry skin, palmoplantar hyperkeratosis, enamel hypoplasia, postaxial polydactyly, broad palpebral fissures, and retrognathia. There are no treatment rows.

DisMech phenotype coverage

There is no exact local DisMech target for COG6-CDG. The generated COX14-Related_COX_Deficiency.yaml candidate is a false positive: it models nuclear COX14-related mitochondrial complex IV assembly failure with congenital lactic acidosis, not COG-complex Golgi trafficking and type II glycosylation disease.

Local COG1-CDG and COG7-CDG files provide shared COG-complex/type II CDG context, and ALG9/MGAT2 CDG files mention COG6 in nonimmune fetal hydrops CDG series, but none is a disease-level COG6 target.

Concordance and completeness

Judgement: true COG6-CDG local gap; reject the COX14 candidate.

The IEMbase disease is a COG-complex/Golgi glycosylation disorder. The generated candidate shares only a broad mitochondrial/lactate and deficiency vocabulary, with different gene, pathway, inheritance context, and diagnostic biomarkers.

Curation actions

  • Keep this record unmapped until a COG6-CDG/Shaheen syndrome target exists.
  • Do not map to COX14-Related_COX_Deficiency.yaml.
  • Use existing COG1/COG7 files only as pathway context for type II CDG and COG-complex biology.
  • If curated, prioritize type II transferrin/ApoC-III glycosylation rows, liver dysfunction/transaminase, ataxia, psychomotor delay, infections, hemophagocytosis, skin, dental, and postaxial-polydactyly prompts.