Alyona L. Chukhrova

Since January 2023, the Russian Federation has implemented expanded neonatal screening for 36 hereditary disorders, which has changed the diagnostic algorithm for hyperphenylalaninemia/phenylketonuria (HPA/PKU) by introducing tandem mass spectrometry (MS/MS) on the second day of life, followed by confirmatory biochemical and molecular testing in newborns at risk. We analyzed 1247 newborns aged 5–15 days with elevated phenylalanine levels (≥120 µmol/L) and a phenylalanine to tyrosine ratio of at least 1 detected during the first stage of screening using MS/MS. At the reference center, newborns underwent repeat biochemical testing and stepwise molecular analysis of HPA-associated genes. Two pathogenic variants in HPA-associated genes were identified in 538 newborns, including 534 newborns with biallelic pathogenic variants in PAH and 4 with BH4-deficient forms (PTS, QDPR). The incidence of molecularly confirmed HPA was 1:4518 newborns (95% CI: 1:4152–1:4925). The PAH variant spectrum was dominated by p.Arg408Trp (c.1222C>T) (33.4%). Genotype-based analysis indicated that 73 newborns (13.7%) were likely responsive to cofactor therapy, whereas 222 (41.6%) were potentially responsive. These findings define the molecular epidemiology of HPA in Russia and support early genetic stratification for diagnosis and treatment.

In a number of Ehlers–Danlos syndrome types kyphoscoliotic Ehlers–Danlos syndrome (kEDS) is one of rare and most severe. It includes two autosomal recessive forms: kEDS-1 (gene PLOD1) and kEDS-2 (gene FKBP14). In addition to common in Ehlers–Danlos syndrome joint hypermobility, skin hyperextensibility, and tissue fragility, kEDS is characterized by early-onset progressing kyphoscoliosis and congenital muscular hypotonia with motor development delay; congenital myopathy is kEDS-2 facultative feature; in both forms vascular complications are probable. We present two kEDS-1 and two kEDS-2 cases in non-consanguineous Russian families. Various molecular genetic methods were used in diagnostics. The patients had all major kEDS signs. In a boy age 4.5 yrs. compound heterozygosity for a novel nonsence variant с.277delG (p.Asp93Ilefs*22) and common duplication of exons 10–16 in PLOD1 was detected; in 13 yrs. he developed symptoms of superior mesenteric artery aneurysm requiring surgery. A 4-months-old infant was homozygous for this duplication. Both kEDS-2 patients, a boy age 14 yrs. and a 7-moths-old girl, were homozygous for FKBP14 common variant c.362dupC (p.Glu122Argfs*7). The girl’s phenotype included congenital myopathy. The cases highlight importance of kEDS early recognition and of selecting DNA tests considering PLOD common extended duplication.

Pathogenic variants in the PMP22 gene can lead to hereditary peripheral demyelinating neuropathies of varying severity, including hereditary neuropathy with liability to pressure palsies (HNPP), Charcot–Marie–Tooth disease types 1A and 1E (CMT1A, CMT1E), Roussy–Lévy syndrome, and Dejerine–Sottas disease (DSS). This study describes a novel deep intronic variant c.179-2809A>G in the PMP22 gene, identified in two unrelated Avar families from Dagestan republic, Russia. This variant was identified in nine patients. In seven cases, it was detected in a heterozygous state, leading to the development of HNPP. In two cases, this variant was found in a homozygous state, resulting in a more severe CMT1A phenotype (Dejerine–Sottas disease). The performed functional analysis allowed us to characterize the deleterious effect of this variant and propose an approach for personalized antisense therapy. This work demonstrates that, in Avar people with HNPP traits, variant c.179-2809A>G should be considered as disease-causing and included in standard genetic testing.

Autosomal dominant dyskinesia caused by heterozygous pathogenic variants in the ADCY5 gene, which encodes adenylate cyclase-5, is a rare neurodegenerative disease with a typical early onset and is primarily associated with hyperkinesias, mostly complex ones. Nonfamilial cases caused by de novo gene variants predominate. Caffeine in the form of coffee has become a common treatment. Three cases have been described: a familial case in a 9-year-old boy and a 54-year-old mother; a nonfamilial case in a 4-year-old girl with a frequent ADCY5 variant, p.Arg418Gln; and a nonfamilial case in an 8-year-old boy with a known variant, p.Arg726Trp. In the familial case, the mother’s disease was much less severe than that of the son and did not require treatment; coffee was effective in the son.

In 2023, the Russian Federation expanded its national newborn screening (NBS) program from 5 to 36 conditions, 29 of which are inherited metabolic diseases (IMDs). This study presents the first nationwide results and outcomes of the expanded NBS program. Between January 2023 and December 2024, dried blood spots from 2,466,615 newborns (98.53% of the birth cohort) were analyzed for IMDs using MS/MS. Screen-positive cases were referred to the national reference center for confirmatory testing, which included biochemical (MS/MS and GC-MS) and genetic analyses (NGS). A total of 41,728 neonates (1.69%) screened positive, of whom 37,733 underwent confirmatory testing. It resulted in 834 confirmed diagnoses of IMDs (1 in 2900 live births). Phenylketonuria was the most prevalent IMD (n = 538; 1 in 4600), followed by MCADD (n = 99; 1 in 25,000). Distinct regional and ethnic variations were observed, including a high prevalence of tyrosinemia type 1 in the Chechen Republic and MCADD in North Ossetia. The integration of NGS was essential for resolving complex cases, such as identifying heterozygous carriers and dual diagnoses. These findings underscore the program’s clinical utility, highlight unique epidemiological patterns, and identify challenges such as false positives and diagnostic complexities, which will guide future refinements.

Since 2023, the Russian Federation (RF) has implemented an expanded newborn screening (NBS) program for 36 hereditary disorders, which now includes 5q spinal muscular atrophy (5q SMA). As a result of newborn screening for 5q SMA conducted in the RF during 2023–2024, 288 newborns with a homozygous deletion of exon 7 in the SMN1 gene were identified by molecular genetic methods. The overall observed incidence of 5q SMA was 1 in 8439 newborns, which does not significantly differ from the expected incidence of 1 in 7953 newborns, established by previous pilot screening projects (p > 0.05). A comparison of the genotypes of patients identified through selective and newborn screening showed statistically significant differences in the proportions of patients carrying two, three, and four or more copies of the SMN2 gene. These findings demonstrate that the NBS program is effective in detecting both individuals with more severe phenotypes, as expected, and those with milder forms of the disease.

The co-occurrence of two genetic disorders in a single patient, so called double trouble phenomenon, is a rare clinical scenario that significantly complicates the diagnostic process. This is particularly challenging when both disorders affect the nervous system, leading to overlapping phenotypes. Congenital disorders of glycosylation, including the rare congenital 1i type caused by variants in the ALG2 gene, are characterized by psychomotor delay, microcephaly, seizures, hepatomegaly, and ophthalmological abnormalities. Joubert syndrome, associated with variants in the CPLANE1 gene, presents with brain malformations, severe psychomotor delay, oculomotor apraxia, and respiratory disturbances. In this study, we describe a patient with a rare combination of congenital disorders of glycosylation 1i type and Joubert syndrome type 17, caused by previously unreported variants in the ALG2 and CPLANE1 genes. This case highlights the diagnostic challenges and the need for a comprehensive approach in managing patients with multiple genetic disorders.

LAMA2-associated muscular dystrophy is a rare genetic disorder caused by pathogenic or likely pathogenic variants in the LAMA2 gene. The aim of this study is to characterize the spectrum of pathogenic/likely pathogenic variants in the LAMA2 gene among Russian patients, identify frequent pathogenic variants specific to this population, and estimate the prevalence of this disorder in Russia. Data were collected and analyzed from patients with confirmed diagnoses of LAMA2-associated muscular dystrophy using various molecular genetic methods in research centers from 2008 to 2024. Data were obtained from 90 unrelated patients with LAMA2-associated muscular dystrophy, out of which 83 presented with the more severe form, MDC1A1, while seven had milder form of LAMA2-associated muscular dystrophy. The most common pathogenic variants identified were nonsense mutations (40% of cases), followed by frameshift variants (29.3%), splicing variants (21.4%), gross deletions (5.3%), and missense variants (4%). It is worth noting that missense variants were found exclusively in patients with the milder form of LAMA2-associated muscular dystrophy. The most prevalent identified pathogenic variant was c.7536del (15%), characteristic of Slavic populations with an established founder effect. Additionally, a common pathogenic variant, c.8245-2A>G, was found predominantly in Kazan Tatars. The estimated prevalence of LAMA2-associated muscular dystrophy in Russia is approximately 1 in 117,700.

Pathogenic variants in the USH2A gene are the primary cause of both non-syndromic autosomal recessive inherited retinitis pigmentosa (RP) and the syndromic form, characterized by retinal degeneration and sensorineural hearing loss. This study presents a comparative assessment of the genetic variant spectrum in the USH2A gene among Russian patients in two clinical groups. A retrospective analysis was conducted on massive parallel panel sequencing data from 2415 blood samples of unrelated patients suspected of having hereditary retinal diseases. The copy number of USH2A exons was determined using the quantitative MLPA method with the MRC-Holland SALSA MLPA kit. Biallelic pathogenic and likely pathogenic variants in the USH2A gene were identified in 69 patients (8.7%). In the group of patients with isolated hereditary RP (55 patients), the most frequent pathogenic variants were p.(Glu4445_Ser4449delinsAspLeu) (20.9%), p.(Trp3955*) (15.5%), and p.(Cys934Trp) (5.5%). In patients with the syndromic form (14 patients), the most frequent variants were p.(Trp3955*) (35.7%) and c.8682-9A>G (17.9%). It was found that patients with isolated vision impairment rarely had two “null” variants (17.8%), whereas this was common among patients with both hearing and vision impairment (71.4%) (p ≤ 0.05), explaining the severity of the disease and the earlier onset of clinical symptoms in the syndromic form of RP. Ten previously undescribed loss-of-function variants were identified. The estimated prevalence of USH2A-associated retinal dystrophy in Russia was 1.9 per 100,000 individuals. The obtained data on the differences in the spectra of genetic variants in the USH2A gene in the two studied groups highlight the importance of establishing genotype–phenotype correlations and predicting disease severity, aiming at potential early cochlear implantation and selection of target therapy.

During the expanded neonatal screening program conducted in 2023, we analyzed samples obtained from 1,227,130 out of 1,256,187 newborns in the Russian Federation in order to detect 5q spinal muscular atrophy (5q SMA). Within the 253-sample risk group formed based on the results of the first screening stage, 5 samples showed a discrepancy between the examination results obtained via various screening methods and quantitative MLPA (used as reference). The discrepancy between the results was caused by the presence of either a c.835-18C>T intronic variant or a c.842G>C p.(Arg281Thr) missense variant in the SMN1 gene, both of which are located in the region complementary to the sequences of annealing probes for ligation and real-time PCR. Three newborns had the c.835-18C>T variant in a compound heterozygous state with a deletion of exons 7–8 of the SMN1 gene, one newborn with two copies of the SMN1 gene had the same variant in a heterozygous state, and one newborn had both variants—c.835-18C>T and c.842G>C p.(Arg281Thr)—in a compound heterozygous state. Additional examination was carried out for these variants, involving segregation analysis in families, carriage analysis in population cohorts, and RNA analysis. Based on the obtained results, according to the ACMG criteria, the c.835-18C>T intronic variant should be classified as likely benign, and the c.842G>C p.(Arg281Thr) missense substitution as a variant of uncertain clinical significance. All five probands are under dynamic monitoring. No 5q SMA symptoms were detected in these newborns neonatally or during a 1-year follow-up period.