Cenani-Lenz syndactyly syndrome: genes and variants
Cenani-Lenz syndactyly syndrome is linked to 1 analyzed protein (LRP4). 9 DNA variants are known to cause it; 494 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Genes linked to Cenani-Lenz syndactyly 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 disease-causing and 494 uncertain variants in LRP4 are linked to Cenani-Lenz syndactyly syndrome.
Known disease-causing variants in Cenani-Lenz syndactyly syndrome
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| LRP4 E1233A | 1233 | LDL-receptor class B 14 | Disease-causing (★★) |
| LRP4 D137N | 137 | LDL-receptor class A 3 | Disease-causing (★) |
| LRP4 D300N | 300 | LDL-receptor class A 7 | Disease-causing (★) |
| LRP4 R632C | 632 | LDL-receptor class B 4 | Disease-causing (★) |
| LRP4 D99H | 99 | LDL-receptor class A 2 | Disease-causing (★) |
| LRP4 C160Y | 160 | LDL-receptor class A 4 | Disease-causing |
| LRP4 D449N | 449 | Extracellular | Disease-causing |
| LRP4 D529N | 529 | LDL-receptor class B 2 | Disease-causing |
| LRP4 T461P | 461 | Extracellular | Disease-causing |
Which prediction tools work for Cenani-Lenz syndactyly syndrome
How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).
- 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 syndactyly syndrome
- Congenital myasthenic syndrome 17, also linked to LRP4
- Sclerosteosis, also linked to LRP4
Frequently asked questions
Which genes are linked to Cenani-Lenz syndactyly syndrome?
In CATVariant, Cenani-Lenz syndactyly syndrome is linked to 1 analyzed protein: LRP4 (Low-density lipoprotein receptor-related protein 4).
How many genetic variants are linked to Cenani-Lenz syndactyly syndrome?
528 variants: 9 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 494 are of uncertain significance or have conflicting reports.
Which uncertain variants in Cenani-Lenz syndactyly syndrome look disease-causing?
None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.
Which variant effect predictor works best for Cenani-Lenz syndactyly syndrome?
Among tools not trained on clinical labels, AlphaMissense separates this disease's known disease-causing variants from harmless ones best (AUROC 0.98, based on 8 disease-causing and 13 harmless variants).
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis 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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