Predicting the Most Deleterious Missense Nonsynonymous Single-Nucleotide Polymorphisms of Hennekam Syndrome-Causing CCBE1 Gene, In Silico Analysis

Hennekam lymphangiectasia-lymphedema syndrome has been linked to single-nucleotide polymorphisms in the CCBE1 (collagen and calcium-binding EGF domains 1) gene. Several bioinformatics methods were used to find the most dangerous nsSNPs that could affect CCBE1 structure and function. Using state-of-the-art in silico tools, this study examined the most pathogenic nonsynonymous single-nucleotide polymorphisms (nsSNPs) that disrupt the CCBE1 protein and extracellular matrix remodeling and migration. Our results indicate that seven nsSNPs, rs115982879, rs149792489, rs374941368, rs121908254, rs149531418, rs121908251, and rs372499913, are deleterious in the CCBE1 gene, four (G330E, C102S, C174R, and G107D) of which are the highly deleterious, two of them (G330E and G107D) have never been seen reported in the context of Hennekam syndrome. Twelve missense SNPs, rs199902030, rs267605221, rs37517418, rs80008675, rs116596858, rs116675104, rs121908252, rs147974432, rs147681552, rs192224843, rs139059968, and rs148498685, are found to revert into stop codons. Structural homology-based methods and sequence homology-based tools revealed that 8.8% of the nsSNPs are pathogenic. SIFT, PolyPhen2, M-CAP, CADD, FATHMM-MKL, DANN, PANTHER, Mutation Taster, LRT, and SNAP2 had a significant score for identifying deleterious nsSNPs. The importance of rs374941368 and rs200149541 in the prediction of post-translation changes was highlighted because it impacts a possible phosphorylation site. Gene-gene interactions revealed CCBE1’s association with other genes, showing its role in a number of pathways and coexpressions. The top 16 deleterious nsSNPs found in this research should be investigated further in the future while researching diseases caused CCBE1 gene specifically HS. The FT web server predicted amino acid residues involved in the ligand-binding site of the CCBE1 protein, and two of the substitutions (R167W and T153N) were found to be involved. These highly deleterious nsSNPs can be used as marker pathogenic variants in the mutational diagnosis of the HS syndrome, and this research also offers potential insights that will aid in the development of precision medicines. CCBE1 proteins from Hennekam syndrome patients should be tested in animal models for this purpose.

Mutation in the CREBBP Gene in the Girl with Toe Walking Syndrome: Clinical Case

Background. Pathogenic variants of the CREBBP gene have been revealed in patients with Rubinstein–Taybi and Menke–Hennekam syndromes, however, the toe walking symptom was not mentioned in these pathologies.Clinical Case Description. The pathogenic nucleotide variant c.5600G>A in heterozygous state in the CREBBP gene was revealed in our 9-year-old female patient with refractory toe walking and developmental speech delay. There were no abnormalities typical for Rubinstein–Taybi syndrome, but there were several signs of Menke–Hennekam syndrome.Conclusion. The genetic anomaly associated with toe walking is described. This observation allows us to critically relate to the hypothesis about the idiopathic genesis of this form of gait disorder at the absence of obvious neurological or orthopedic causes of its development.

Hennekam syndrome: an uncommon cause of chylous ascites and intestinal lymphangiectasia in the tropics

Paediatric chylous ascites in tropics is commonly caused by infections and trauma. We describe the clinical characteristics of an uncommon inherited cause of chylous ascites, Hennekam syndrome, treated by nutritional modification.

Genetic testing for Hennekam syndrome

Hennekam Syndrome (HS) is a combination of congenital lymphatic malformation, lymphangiectasia and other disorders. It is a very rare disorder with autosomal recessive inheritance. We developed the test protocol “Hennekam Syndrome” on the basis of the latest research findings and diagnostic protocols on lymphatic malformation in HS. The genetic test is useful for confirming diagnosis, as well as for differential diagnosis, couple risk assessment and access to clinical trials.