Two Chinese patients with Basilicata-Akhtar syndrome caused by novel MSL3 variants: a case report and literature review

Introduction

MSL3 (OMIM#300609), known as MSL3L1, encodes male-specific lethal (MSL) complex subunit 3, located on chromosome Xp22.2, which contains 13 exons with full length 18kb (1,2). The MSL complex-associated histone acetyltransferase KAT8 regulates histone H4 lysine 16 acetylation (H4K16ac) that plays a vital role in transcriptome regulation of developmental pathways in mammals (3-5). In human, MSL1, MSL2, MSL3, and MOF (males absent on the first) form core components of the MSL complex (1,4,6). MSL3 comprises two domain, the morf-related gene (MRG) domain and the chromo domain (CD), the former is responsible for MSL complex formation, and the latter is related to chromatin targeting (7-14).

In affected individuals, developmental delay, speech delay, intellectual disability (ID), motor delay, muscular hypotonia, progressive spasticity, feeding difficulties in early infancy, constipation and overlapping facial dysmorphism are common clinical features (3,15-17). Many neurodevelopmental disorders originating from diverse etiologies exhibit overlapping clinical phenotypes (18-20). Consequently, the early diagnosis of Basilicata-Akhtar syndrome (MRXSBA) presents significant challenges. The identification of additional novel clinical phenotypes in MRXSBA would facilitate disease diagnosis. Until now there are only 42 MRXSBA individuals with variations in MSL3 gene confirmed (3,15-17). Therefore, our knowledge on the genotypic and phenotypic spectrum of MRXSBA remains very limited, especially in the Chinese population, as only one Chinese case has been reported (15). In addition, for patients with MRXSBA, no effective therapeutic approaches are currently available.

Here, we illustrate the characteristics and MSL3 variations of two unrelated Chinese patients with MRXSBA. We identified two novel variants, one of which is a truncating heterozygote and the other is a splicing semizygote. In addition, we report four novel clinical characteristics of MRXSBA hereby, including growth hormone deficiency (GHD), slow growth of permanent teeth, scoliosis, and cleft palate. One of the two patients was followed up for over 10 years. Our study establishes a critical foundation for the diagnosis of MRXSBA and provides an effective therapeutic approach for patients with MRXSBA and GHD, thereby improving growth outcomes. We present this article in accordance with the CARE reporting checklist (available at https://tp.amegroups.com/article/view/10.21037/tp-2025-227/rc).

Case presentation

Case 1

This female individual is the only child of healthy unrelated parents, was referred to the department of Endocrine and Metabolism of Shanghai Children’s Medical Center due to poor logical thinking ability and poor learning ability. She was born via cesarean section following a pregnancy marked with polyhydramnios. She went to school at the normal age, and showed a short attention span in class. Receptive language skills seemed to be better developed than expressive language for her. At 8 years old, she exhibited relatively mild dysmorphic facial features (Figure 1A). A skeletal survey showed pigeon breast and abnormalities of the fingers (Figure 1B,1C). Neuropsychological examination showed that overall intellect was slightly below average, evaluated by the Wechsler Intelligence Scale for Children-Revised (WISC-R), with Verbal IQ scores of 65–75 and Performance IQ scores of 50–60. Other behavioral abnormalities included anxiety, introverted personality, inferiority complex. Her growth parameters were as follows: weight 27.6 kg, lengths 122.4 cm (Z-score =−0.71), body mass index 18.4 kg/m² (Z-score =1.27) and occipitofrontal circumference 50 cm (21). Using whole-exome sequencing (WES) (22,23), we identified one heterozygous nonsense variant c.570C>G, p. Tyr190* in MSL3. Both alleles were wild-type in their parents, as confirmed by Sanger sequencing (Figure 1D,1E).

Figure 1 Clinical and molecular characteristics of individual 1. (A) Facial characteristics including round face, broad nasal bridge, epicanthal folds, hypertelorism, prominent forehead, abnormal dentition, downslanting palpebral fissures, downturned corners of the mouth. (B,C) Abnormalities of the fingers including thumb asymmetry, tapered and slender fingers. (D) Family pedigree of the proband. (E) The nonsense variant (c.570C>G) in MSL3 gene identified by WES was verified by Sanger sequencing. These images are published with the consent from patients’ parents. WES, whole-exome sequencing.

Case 2

This patient has been followed for over 10 years since his initial visit. He is the first of two children of healthy unrelated parents. Between the two productions, their mother experienced one artificial termination and one biochemical pregnancy. Individual 2 was born via cesarean delivery for intrauterine distress at 39⁺⁴ weeks with birth weight of 3,240 g and birth length of 50 cm. Amniotic fluid grade III contamination was noted at birth as well as a large head circumference, and short limbs. Moreover, He had hydronephrosis, pyelodiastasis, ureteral obstruction, pyelic separation and pyelo-ureteral junction stenosis on the left side. At 4 years and 11 months of age, he was admitted to the hospital for short stature with weight 14.5 kg, height 94.7 cm (Z-score =−3.20), body mass index 16.17 kg/m² (Z-score =0.70) and was diagnosed with GHD (21). WISC-R test showed mild ID (language 50–60, movement 50–60). At 14 years, dysmorphic facial features (Figure 2A) were markedly evident. Skeletal examination (Figure 2B,2C) showed chest deformities, mild scoliosis (5°–10°), hallux valgus, and ankle clonus. He also had muscle weakness, especially distal finger muscle weakness, left neck tenderness and salivation. Brain magnetic resonance imaging (MRI) (Figure 2D,2E) was performed revealing dilated ventricles, deep frontal sulcus and extremely hypoplastic pituitary. And he showed mild cleft palate, badly permanent tooth growth and poor occlusion, and hyperopia (400 degrees). One hemizygous splice site variant c.1466+2T>C in MSL3 was detected by WES (22,23). The Sanger sequencing results indicated that their parents are both normal (Figure 2F,2G).

Figure 2 Clinical features and genetic sequencing findings of individual 2. (A) Facial characteristics including round face, protruding ears, thick auricle, beaked nose with broad nasal bridge and downturned corners of the mouth. (B) Chest deformities including pigeon breast and funnel chest. (C) Scoliosis showed by spine imaging. (D) Enlarged lateral ventricle and deepened frontal sulcus showed by cranial magnetic resonance imaging. (E) Hypoplastic pituitary demonstrated by brain magnetic resonance imaging. (F) Family pedigree of individual 2. (G) Sanger sequencing revealed the patient harbored a hemizygous splice variant (c.1466+2T>C) in MSL3 gene. These images are published with the consent from patients’ parents.

Pathogenicity analysis of the identified variants

The novel variants c.570C>G, p. Tyr190* and c.1466+2T>C identified in this study were classified as “pathogenic” and “likely pathogenic”, respectively, according to the American College of Medical Genetics and Genomics (ACMG) 2015 guidelines (24). In addition, the two variants all affected the MRG domain of MSL3.

Phenotypic differences between the Chinese cohort and individuals of other ethnicities

We conducted a systematic literature review and compared phenotypic profiles between individuals of other ethnicities and three Chinese individuals (including one previously reported individual and two newly identified in this study) (3,15-17). As shown in Table 1, frequencies of most clinical phenotypes exhibited significant congruence between two cohorts. Hypotonia demonstrated statistically significant in the two cohorts, with substantially higher prevalence in non-Chinese populations. In addition, the frequency of macrocephaly showed notable elevation in individuals of other ethnicities, while no statistically significant difference was observed.

Intervention

Individual 2 initiated recombinant human growth hormone (rhGH) treatment at 4 years and 11 months of age with a dosage of 0.15 IU/kg/day. Satisfactory height trajectory was maintained in follow-up appointments with rhGH administered in the doses (Figure 3). During the treatment period, the child’s scoliosis did not worsen and no other growth hormone (GH) treatment-related adverse effects occurred. In addition, he received rehabilitation training two hours a day to improve the gross motor development and the ability has been greatly improved.

Figure 3 Growth curve of individual 2 showed obvious short stature before intervention and good improvement in height after receiving rhGH treatment (20). rhGH, recombinant human growth hormone.

All procedures performed in this study were in accordance with the ethical standards of the Ethics Committee of Shanghai Children’s Medical Center (No. SCMCIRB-K2020060-1) and with the Helsinki Declaration and its subsequent amendments. Written informed consent was obtained from all the patients’ guardians for publication of this case report and accompanying images. A copy of the written consent is available for review by the editorial office of this journal.

Discussion

In this study, we recruited two unrelated Chinese patients with MRXSBA. To our knowledge, this is the first report of patients with MRXSBA in China among genders (3,15-17). In 2020, Brunet et al. reported a Chinese male individual with MRXSBA who presented with cleft lip and oligohydramnios, which may be the unique characteristics of the syndrome in Chinese populations, as they have not been documented in other ethnic groups (3,15-17). However, the genetic testing results of this Chinese male patient reported before revealed additional findings beyond a MSL3 variant. Microarray results detected two interstitial chromosomal microduplications involving Xp22.33 or Yp11.22 regions (specific origin undetermined), both encompassing the entire SHOX gene. Parental testing was not performed; therefore, the pathogenicity of these microduplications remained unconfirmed (15). The clinical phenotypes observed in this male could be attributed to the combined effects of three genetic variants. We examined all individuals previously published and the two individuals in our study. We observed that features like macrocephaly and hypotonia were more frequent in individuals of other ethnicities. However, due to the limited sample size of our Chinese cohort, certain phenotypic manifestations may have been undetected. Alternatively, the relatively short follow-up period might have prevented the full manifestation of these features in the observed population. Further evidence from larger Chinese cohorts is required to substantiate this finding in the future. Partnering with other institutions is one highly effective approach. Additionally, we revealed four novel clinical characteristics in individual 2, including GHD, slow growth of permanent teeth, scoliosis, and cleft palate. Due to lack of more cases supported, it remains to be confirmed whether the above emerging clinical phenotypes are indeed part of the phenotypic spectrum of MRXSBA. In addition, the clinical severity of the two cases in our study exhibited no obvious​ differences, which was difficult to reconcile with the classical X-chromosomal inheritance pattern, similar to the findings previously published by Brunet et al. (15). Basilicata et al. reported a heterozygous female carrier of a pathogenic MSL3 variant was just mildly affected (3). Here, we consider that the variant she harbored is so special that the affected X chromosome is more likely to be inactivated, combined with​environmentally modulated epigenetic alterations, collectively result in the distinctive phenotypic manifestation. Overall​, these phenomena are far from explanation and further studies should attempt elucidating the precise molecular basis.

To date, 42 individuals carrying MSL3 variants have been reported since the first case was described in 2018 (3,15-17). Forty MSL3 causative variants (multigene deletions excluded) have been identified, including nonsense, missense, splicing variants, frameshift variants and multi-exon deletions and small deletion (Figure 4). Of these, nonsense (13/40, 33%) and frameshift (15/40, 38%) were the most prevalent variant types, and loss-of-function variants accounted for the largest proportion (36/40, 90%) (3,15-17). The nonsense variant and the splice variant identified in our study further indicated the MSL3 gene was intolerant to loss-of-function variants. Besides, all currently reported pathogenic variants clustered within the last eight exons of the MSL3 gene, which encode the MRG domain (3,15-17). In our study, the c.570C>G, p. Tyr190* variant was identified in exon 6, and the c.1466+2T>C variant was detected in intron 12 of the gene. These findings provide more evidence supporting the opinion that the C-terminal MRG domain was responsible for MSL complex function and the N-terminal CD domain was redundant.

Figure 4 Protein structure of MSL3 with the CD and the MRG domain. Locations of previously reported variants (multigene deletions excluded) and the two variants identified in this study that marked in red. CD, chromo domain; MRG, morf-related gene.

Currently, there is still no specific treatment for patients with MRXSBA. In our study, the gross motor development of individual 2 got great improvement through rehabilitation training. In addition, individual 2 is the first reported case with MRXSBA and GHD and the first reported case with GH treatment. The correlation between GHD and MRXSBA is not clear, and the occurrence of GHD in this patient may be related to his pituitary pheochromocytoma. In this patient, the Z value of height improved from −3.20 before treatment to −0.93 at the last follow-up with GH treatment. However, GH treatment may provoke adverse effects. GH treatment may be associated with an increased risk of tumors, especially for patients combined with tumor susceptible diseases (25). According to all reports of MRXSBA, there were two cases with haemangioma and one case with intradural lipoma, and none of the cases have developed malignant tumors, and the oldest patient reported was a 30-year-old female (3,15). There is no evidence that MRXSBA is associated with tumor risk. Even so, we still recommend a complete tumor-related evaluation and regular follow-up for patients treated with GH. We followed up this patient comprehensively, his tumor markers and imaging tests did not suggest any tumor-related manifestations. And meanwhile, the patient was found to have mild scoliosis before GH treatment, which did not worsen during the follow-up period; and he did not experience any other adverse effects. In addition, the patient’s height had stabilized at the time of the last follow-up, and the patient had entered the transition to adulthood. GH was suspended from the patient’s last follow-up. Certainly, GH stimulation tests, such as GHRH in combination with arginine test, will be performed again (26). After evaluation, if the patient still has GHD, GH therapy will need to be continued. Throughout the transition process, rhGH therapy enables patients to achieve appropriate levels of somatic development, induces an increase in lean mass and normalizes metabolism (26). During the transition period, serum concentrations of IGF1 should be monitored every 4–6 weeks until the optimal maintenance dose of rhGH is reached. Repeat follow-up of IGF1 every 6 to 12 months (27).

Conclusions

In conclusion, we identified two novel loss-of-function variants in MSL3 in two Chinese individuals. Our study supports the notion that the MRG domain is intolerant to loss-of-function variants and responsible for MSL3 function. Comparative analysis between the Chinese cohort and patients of other ethnicities indicated obvious differences​in the prevalence of most clinical phenotypes, ​except for hypotonia and macrocephaly. The novel phenotypes, including GHD, slow growth of permanent teeth, scoliosis, and cleft palate have extended the MRXSBA phenotype spectrum. In addition, our study indicates that GH treatment could be an option to improve the height in individuals with MRXSBA and GHD.

Acknowledgments

We really appreciate the patients and their families for participation in this study.

Footnote

Reporting Checklist: The authors have completed the CARE reporting checklist. Available at https://tp.amegroups.com/article/view/10.21037/tp-2025-227/rc

Peer Review File: Available at https://tp.amegroups.com/article/view/10.21037/tp-2025-227/prf

Funding: This study was supported by the National Key R&D Program of China (No. 2023YFC2706305); Joint Research Project of the Pudong New Area Health Commission (No. PW2021D-13); and the National Clinical Key Specialty Construction Project (No. 10000015Z155080000004).

Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://tp.amegroups.com/article/view/10.21037/tp-2025-227/coif). The authors have no conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. All procedures performed in this study were in accordance with the ethical standards of the Ethics Committee of Shanghai Children’s Medical Center (No. SCMCIRB-K2020060-1) and with the Helsinki Declaration and its subsequent amendments.Written informed consent was obtained from all the patients’ guardians for publication of this case report and accompanying images. A copy of the written consent is available for review by the editorial office of this journal.

Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.

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