Cenani-Lenz syndrome: genes and variants
Explore variant evidence for Cenani-Lenz syndrome across 1 analyzed protein (LRP4). Linked ClinVar records include 9 pathogenic or likely pathogenic variants, 475 variants of uncertain significance and 19 with conflicting classifications.
Coverage includes proteins already analyzed in CATVariant, not every gene involved in this condition. Database links are associations, not an assessment of clinical gene–disease validity. Computable evidence prioritizes variants for expert review and does not reclassify them. Source labels are pooled across this disease family.
Data updated 2026-10-10. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
Genes linked to Cenani-Lenz syndrome
LRP4: Low-density lipoprotein receptor-related protein 4
It coordinates Wnt-related developmental signaling and serves as the agrin coreceptor that activates MuSK at the neuromuscular junction. Biallelic or dominant pathogenic variants can cause syndactyly, Cenani-Lenz syndactyly syndrome, or congenital myasthenic syndrome depending on the mechanism.
9 ClinVar pathogenic / likely pathogenic and 494 uncertain variants in LRP4 have source records linked to Cenani-Lenz syndrome. Association strength is not clinical gene validity.
ClinVar pathogenic and likely pathogenic variants linked to Cenani-Lenz syndrome
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| LRP4 E1233A | 1233 | LDL-receptor class B 14 | Pathogenic / likely pathogenic (★★) |
| LRP4 D137N | 137 | LDL-receptor class A 3 | Pathogenic / likely pathogenic (★) |
| LRP4 D300N | 300 | LDL-receptor class A 7 | Pathogenic / likely pathogenic (★) |
| LRP4 R632C | 632 | LDL-receptor class B 4 | Pathogenic / likely pathogenic (★) |
| LRP4 D99H | 99 | LDL-receptor class A 2 | Pathogenic / likely pathogenic (★) |
| LRP4 C160Y | 160 | LDL-receptor class A 4 | Pathogenic / likely pathogenic |
| LRP4 D449N | 449 | Extracellular | Pathogenic / likely pathogenic |
| LRP4 D529N | 529 | LDL-receptor class B 2 | Pathogenic / likely pathogenic |
| LRP4 T461P | 461 | Extracellular | Pathogenic / likely pathogenic |
Which prediction tools work for Cenani-Lenz syndrome
Observed separation of ClinVar pathogenic / likely pathogenic from benign / likely benign variants (AUROC × 100). This benchmark is not a clinical recommendation.
- AlphaMissense: 98 out of 100
- CATVariant: 93 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- MetaLR: 90 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- PolyPhen-2: 81 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- SIFT: 75 out of 100
Diseases related to Cenani-Lenz syndrome
- Congenital myasthenic syndrome 17, also linked to LRP4
- Sclerosteosis, also linked to LRP4
Frequently asked questions
Which genes have records linked to Cenani-Lenz syndrome?
This view contains 1 analyzed proteins: LRP4. Links come from clinical records and association databases. They do not imply that every listed gene is a validated cause, and missing genes may not yet be analyzed.
What do the clinical classifications mean?
Linked records include 9 pathogenic or likely pathogenic variants, 475 variants of uncertain significance and 19 with conflicting classifications. Labels summarize source records; multi-condition records may not make a separate assertion for this disease. Check the original record and review status.
Does the evidence score change a VUS classification?
No. 0 VUS or conflicting variants reach the likely-pathogenic points range on the computable criteria available here. This is a research prioritization signal, not a clinical classification. Patient, family and other required evidence may be missing.
Can I download the variant evidence?
Download the CSV for all 528 variants in the selected disease scope, including clinical labels, review status, evidence criteria, predictor scores, functional measurements and population frequency where available.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from eligible public CATVariant analyses of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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