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.

Single-nucleotide polymorphisms in the ELANE (Elastase, Neutrophil Expressed) gene are associated with severe congenital neutropenia, while the ELANE gene provides instructions for making a protein called neutrophil elastase. We identified disease susceptibility single-nucleotide polymorphisms (SNPs) in the ELANE gene using several computational tools. We used cutting-edge computational techniques to investigate the effects of ELANE mutations on the sequence and structure of the protein. Our study suggested that eight nsSNPs (rs28931611, rs57246956, rs137854448, rs193141883, rs201723157, rs201139487, rs137854451, and rs200384291) are the most deleterious in ELANE gene and disturb protein structure and function. The mutants F218L, R34W, G203S, R193W, and T175M have not yet been identified in patients suffering from SCN and cyclic hematopoiesis, while C71Y, P139R, C151Y, G214R, and G203C reported in our study are already associated with both of the disorders. These mutations are shown to destabilize structure and disrupt ELANE protein activation, splicing, and folding and might diminish trypsin-like serine protease efficiency. Prediction of posttranslation modifications highlighted the significance of deleterious nsSNPs because some of nsSNPs affect potential phosphorylation sites. Gene-gene interactions showed the relation of ELANE with other genes depicting its importance in numerous pathways and coexpressions. We identified the deleterious nsSNPs, constructed mutant protein structures, and evaluated the impact of mutation by employing molecular docking. This research sheds light on how ELANE failure upon mutation results in disease progression, including congenital neutropenia, and validation of these novel predicted nsSNPs is required through the wet lab.

Inborn errors of immunity can be detected by evaluating circular DNA (cDNA) fragments of T- and B-cell receptors (TREC and KREC) resulting from the receptor gene rearrangement in T and B cells. Maturation and activation of the fetal immune system is known to proceed gradually according to the gestational age, which highlights the importance of the immune status in premature infants at different gestational ages. In this article, we evaluated TREC and KREC levels in infants of various gestational ages by real-time PCR with taking into account the newborns weight and sex. The 95% confidence intervals for TREC and KREC levels (expressed in the number of cDNA copies per 105 cells) were established for different gestational groups. The importance of studying immune system development in newborns is informed by the discovered dependence of the level of naive markers on the gestational stage in the early neonatal period.

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Chromosomal pathology is one of the most common causes of congenital malformations. The CATCH-22 symptom complex is most often associated with a microdeletion of chromosome 22, upon detection of which it is customary to diagnose DiGeorge syndrome, a known primary immunodeficiency or syndrome of innate errors of immunity. According to our data on the frequency of occurrence among all chromosomal abnormalities, DiGeorge’s syndrome takes second place in the Sverdlovsk region after Down’s syndrome, but its diagnosis is not simple due to varying severity of clinical manifestations, as well as different forms of the chromosome 22 defects. Along with several typical variants of 22q11 microdeletions, there duplications of critical regions are also reported, accompanied by immunodeficiency and other symptoms of CATCH-22. The effectiveness of diagnosing chromosomal abnormalities both in pre- and postnatal period largely depends on the grouping criteria of the patients with suspected chromosomal abnormalities, and on the methods used to identify hereditary pathology. In our study, we analyzed and compared the results of studies of 23 patients with various rearrangements of the 22q11.2 region, which were observed by a geneticist and clinical immunologist. The paper presents data on the polymorphism of phenotypes associated with rearrangements of the 22q11.2 region with an analysis of pathomorphological manifestations depending on the type of structural anomaly, i.e, del22q11.2, or dup22q11.2. The results of analysis demonstrate importance of different diagnostic options for laboratory studies of microdeletion and microduplication syndromes associated with immune-dependent pathology. We also compared the results of molecular genetic diagnostics and phenotypic manifestations in deletions and duplications of the 22q11.2 region. To identify the rearrangements of 22q11.2 region, two different methods were used – Prenatal BoBs and multiplex ligase-dependent probes’ amplification (MLPA). In particular, the both methods were used in the same patient to verify diagnosis, thus enabling to show differences in their efficiency. It was concluded that 22q11.2 deletion syndrome exhibits wide heterogeneity in phenotypic traits: neurological and immunological manifestations, anomalies in musculoskeletal development and internal organs, skull deformities and facial dysmorphia. Each clinical case was unique, requiring careful analysis of clinical manifestations. It is necessary to have a wide range of laboratory options for molecular genetic verification of the diagnosis.

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