IEMbase 0358: LFNG-related spondylocostal dysostosis type 3
Scope
| Field | Value |
|---|---|
| IEMbase ID | 358 |
| Nosology | 18.2.02.01 |
| Gene | LFNG |
| External IDs | OMIM:609813; ORPHA:2311 |
| Generated mapping | UNMAPPED; low candidate Spondylocostal_Dysostosis.yaml |
| Candidate DisMech targets | Spondylocostal_Dysostosis.yaml#LFNG/SCDO3 |
| Review date | 2026-07-07 |
IEMbase phenotype signal
IEMbase represents LFNG-CDG, also listed as spondylocostal dysostosis type 3, an autosomal recessive O-fucose glycosylation disorder. The source disease label contains a typo, "LFNG-rerlated", but the gene and alternate name resolve to LFNG/SCDO3.
Characteristic rows include decreased body height, long slender fingers, scoliosis, normal sialotransferrins, and vertebral anomalies of the whole spine. IEMbase lists no additional clinical rows beyond these characteristic features, and the only biochemical row is sialotransferrins. No treatment rows are present.
DisMech phenotype coverage
The generated UNMAPPED status is a false negative. DisMech has a Spondylocostal Dysostosis file that explicitly includes LFNG among the autosomal recessive segmentation-clock genes causing SCDO. Local mechanism frames LFNG disease as disruption of Notch-pathway somitogenesis, producing multiple vertebral segmentation defects with rib abnormalities, short trunk, small thorax, scoliosis, and possible respiratory compromise.
Local coverage is stronger for the axial segmentation and serial somite malformation mechanism than IEMbase. IEMbase is stronger for the CDG/O-fucose labeling and the normal-sialotransferrin row.
Concordance and completeness
Judgement: false negative; resolve to the local spondylocostal dysostosis LFNG/SCDO3 context.
The resources agree on LFNG identity, autosomal recessive inheritance, spondylocostal dysostosis type 3, short stature, scoliosis, and widespread vertebral anomalies. The generated candidate points to the correct file despite being below the exact-mapping threshold.
Curation actions
- Map this record to
Spondylocostal_Dysostosis.yaml, specifically the LFNG/SCDO3 segmentation-clock context. - Preserve the source typo as a source-label issue only; do not propagate it to curated disease labels.
- Consider future enrichment with the CDG/O-fucose framing, long slender fingers, and normal sialotransferrins after source verification.