ENPP1 – Generalized Arterial Calcification of Infancy

Generalized arterial calcification of infancy (GACI) is a severe autosomal recessive disorder characterized by early‐onset arterial medial calcification, intimal proliferation, vascular stenosis, and heart failure, often resulting in death within the first six months of life. Biallelic inactivating variants in ENPP1 (HGNC:3356) have been identified in the majority of GACI cases, establishing ENPP1 as the principal genetic etiology. Molecular screening across multiple cohorts identified ENPP1 pathogenic variants in approximately 75% of affected individuals, with over 55 unrelated probands reported (PMID:20016754). Segregation analysis in consanguineous and nonconsanguineous families confirms autosomal recessive inheritance, with compound heterozygous and homozygous variants co‐segregating with disease in affected siblings and offspring (PMID:15940697). Functional concordance is robust: ENPP1 loss‐of‐function leads to deficient extracellular pyrophosphate (PPi), permitting pathologic hydroxyapatite deposition. Extensive experimental models, including Enpp1 knockout mice and patient fibroblast assays, recapitulate the human phenotype, supporting a Definitive ClinGen gene–disease classification.

1. Clinical Validity

• ClinGen classification: Definitive. Rationale: Over 55 unrelated probands with biallelic ENPP1 variants (PMID:20016754), multi‐family and sibling co‐segregation, and concordant in vivo and in vitro functional studies.

2. Genetic Evidence

• Inheritance: Autosomal recessive.
• Segregation: 5 affected relatives in sib and extended families (PMID:15940697).
• Case series: >55 probands with ENPP1 variants in 41 of 55 patients; 40 distinct homozygous or compound heterozygous mutations across 23 unrelated families (PMID:15605415; PMID:20016754).
• Variant spectrum: missense (e.g., p.Pro305Thr founder allele in British extraction), nonsense, splice‐site (e.g., c.715+1G>C), frameshift, and large deletions. Recurrent variants include c.1025G>T (p.Gly342Val) and c.783C>G (p.Tyr261Ter). Carrier frequency estimates suggest underdiagnosis, with prevalence ~1:64,000 pregnancies (PMID:36461014).

3. Functional / Experimental Evidence

• Mechanism: Loss of ENPP1 enzymatic activity → reduced extracellular PPi → unopposed hydroxyapatite deposition in arterial media.
• Assays: Patient fibroblasts show decreased PPi generation, increased calcification; Enpp1asj/asj mice exhibit early arterial calcification and hypertension, rescued by recombinant ENPP1‐Fc (INZ‐701) restoring PPi levels and preventing calcification (PMID:33900645).
• Structural studies: ENPP1 crystal structures elucidate nucleotide binding and support variant‐specific loss of function (PMID:23027977).

4. Conflicting Evidence

• A minority of GACI cases lack ENPP1 variants and harbor ABCC6 mutations, indicating locus heterogeneity and overlapping PXE features (PMID:22209248). One case with no coding ENPP1 mutation suggests deep intronic or regulatory alleles may contribute (PMID:19452427).

5. Integration & Conclusion

ENPP1 deficiency causes GACI through a well‐defined biochemical pathway of PPi dysregulation. Genetic and functional data are mutually reinforcing: clinical cases with biallelic ENPP1 variants manifest hallmark vascular calcifications; experimental models replicate pathology and respond to enzyme replacement. While other genes (ABCC6) can mimic the phenotype, ENPP1 remains the predominant GACI gene. Additional evidence from population studies and novel variant curation further solidifies this association.

Key take‐home: Early molecular diagnosis of ENPP1‐related GACI enables timely intervention, informs genetic counseling, and paves the way for emerging enzyme replacement therapies.

References

• The mutational spectrum of ENPP1 as arising after the analysis of 23 unrelated patients with generalized arterial calcification of infancy (GACI). Human mutation | 2005 PMID:15605415
• Hypophosphatemia, hyperphosphaturia, and bisphosphonate treatment are associated with survival beyond infancy in generalized arterial calcification of infancy. Circulation. Cardiovascular genetics | 2008 PMID:20016754
• Generalized arterial calcification of infancy: different clinical courses in two affected siblings. American journal of medical genetics. Part A | 2005 PMID:15940697
• Generalized arterial calcification of infancy and pseudoxanthoma elasticum can be caused by mutations in either ENPP1 or ABCC6. American journal of human genetics | 2012 PMID:22209248
• Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling. PNAS | 2012 PMID:23027977
• INZ-701 Prevents Ectopic Tissue Calcification and Restores Bone Architecture and Growth in ENPP1-Deficient Mice. Journal of bone and mineral research | 2021 PMID:33900645
• Estimating the genetic prevalence of ENPP1 deficiency. (Mastermind review) | 2023 PMID:36461014

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