Summary
This study presents the genetic analysis of several patients exhibiting symptoms of Rauch–Steindl syndrome and similar phenotypes, with a focus on mutations in the NSD2 gene and their clinical consequences. A 7-year-old girl with a de novo frameshift deletion mutation c.2721delT(p.Asn907Lysfs*5) presented with typical Rauch–Steindl syndrome features, while a proband with a missense variant exhibited delayed development, growth issues among other clinical signs. Functional studies of NSD2 haploinsufficiency via analysis of de novo frameshift variant and comparison with the clinical phenotype conclude that NSD2 deficiency leads to multisystem abnormalities associated with Rauch–Steindl syndrome. Importantly, the supporting evidence of haploinsufficiency includes inheritance information, showing de novo mutations, highlighting a novel NSD2 gene mutation, and linking predicted loss-of-function variants to specific clinical phenotypes. However, one individual showed atypical mild manifestation of WHS without detailed mutation data or inheritance testing, suggesting the NSD2 gene's contribution to the WHS phenotype might be limited. Functional analysis supports the link between NSD2 gene haploinsufficiency and disease, with mouse models and methylation activity studies backing the role of loss-of-function variants in presenting clinical signs.
Evidence of Haploinsufficiency
Patient Identifier: 7 year-old-girl
Mutation Type: deletion
Mutation Details: c.2721delT(p.Asn907Lysfs*5)
Clinical Phenotype: diagnosed with Rauch–Steindl syndrome
Inheritance Tested: Yes
Effect on Gene Function: truncating variant in NSD2
Direct Quote: "In this study, we identified a novel de novo NSD2 gene variant [c.2721delT(p.Asn907Lysfs*5)] in a Chinese girl diagnosed with Rauch–Steindl syndrome."
Location in Paper: Materials and methods
Patient Identifier: The proband
Mutation Type: de novo NSD2 variant
Mutation Details: Novel missense variant not further specified
Clinical Phenotype: Delayed development and growth, intrauterine growth restriction, severe malnutrition, mild short stature, facial dysmorphic features, mild clinodactyly, normal brain MRI, EEG, x-ray of the chest and spine, normal echocardiography, and normal abdominal ultrasound.
Inheritance Tested: Yes
Effect on Gene Function: Pathogenicity of the NSD2 variant was confirmed according to ACMG/AMP guidelines.
Direct Quote: "The candidate NSD2 variant identified by WES was confirmed by Sanger sequencing, and its pathogenicity was classified following to American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines (14)."
Location in Paper: Results
Patient Identifier: the present patient
Mutation Type: frameshift
Mutation Details: c.2721delT(p.Asn907Lysfs*5)
Clinical Phenotype: facial dysmorphism, microcephaly, intellectual disability, growth restriction, severe malnutrition, short stature, small hands and feet, muscular hypotonia, mild clinodactyly of right hand, loose skin on the hands and feet
Inheritance Tested: Yes
Effect on Gene Function: Variant may result in absence of protein production with significant decrease in mRNA level due to nonsense-mediated decay degradation.
Direct Quote: "Then, a novel de novo heterozygous frameshift variant c.2721delT(p.Asn907Lysfs*5) in the NSD2 gene (...) was identified in the proband (...). The present patient showed common phenotypes associated with Rauch–Steindl syndrome, including facial dysmorphism, microcephaly, a degree of intellectual disability, growth restriction, severe malnutrition, short stature, small hands and feet, muscular hypotonia, mild clinodactyly of right hand, and loose skin on the hands and feet, and these phenotypes are thought to be due to the loss-of-loss-of-function variant detected in NSD2."
Location in Paper: Mutation analysis; Discussion and conclusion
Patient Identifier: our patient
Mutation Type: unknown
Mutation Details: unknown
Clinical Phenotype: atypical mild manifestation of WHS
Inheritance Tested: No
Effect on Gene Function: Patient's condition suggests that NSD2 gene may not be the main cause of WHS craniofacial features and skeletal anomalies.
Direct Quote: "Compared with typical WHS patients, an atypical mild manifestation was observed in our patient."
Location in Paper: Section not specified
Clinical Features
Feature: microcephaly
Frequency: occurring in all affected patients
Direct Quote: "microcephaly, widely spaced eyes, a distinct mouth, a short philtrum, micrognathia, downturned corners of the mouth, and poorly formed ears with pits and tags. Growth restriction, postnatal growth deficiency, hypotonia with muscle underdevelopment, and developmental delay/intellectual disability of variable degrees are observed in all affected patients."
Location in Paper: Introduction
Feature: intellectual disability
Frequency: common across cases
Direct Quote: "Recent reports have confirmed that patients with novel loss-of-function or missense variants in NSD2 exhibit a variety of abnormalities including facial dysmorphism, microcephaly, intellectual disability, intrauterine and postnatal growth restriction. These findings suggest that NSD2-deficiency is responsible for multisystem abnormalities in patients with Rauch–Steindl syndrome."
Location in Paper: Discussion and conclusion
Feature: facial dysmorphism
Frequency: not specified across cases
Direct Quote: "Patients with RSS exhibit a wide range of mild phenotypic features, with core manifestations... facial dysmorphisms"
Location in Paper: Introduction
Feature: intrauterine growth restriction
Frequency: not specified across cases
Direct Quote: "Patients with RSS exhibit a wide range of mild phenotypic features, with core manifestations of microcephaly, intrauterine growth restriction, facial dysmorphisms..."
Location in Paper: Introduction
Feature: severe malnutrition
Frequency: not specified across cases
Direct Quote: "Growth restriction persisted, she had severe malnutrition"
Location in Paper: Clinical description
Functional Studies
Study Type: Molecular and genetic
Methodology: Analysis of de novo heterozygous frameshift variant in NSD2 gene with predicted effect on gene function and comparison with clinical phenotype
Conclusions: The findings suggest that NSD2-deficiency is responsible for multisystem abnormalities in patients with Rauch–Steindl syndrome.
Direct Quote: "Haploinsufficiency of NSD2 (pLi = 1.00) is thought to be an important part of the mutational mechanism of WHS. Heterozygous knockout-NSD2 mouse models show growth restriction, craniofacial malformation, and midline fusion defects. Zanoni et al. demonstrated that loss-of-function and missense variants in NSD2 lead to reduced methylation activity and are associated with a distinct developmental phenotype. These findings suggest that NSD2-deficiency is responsible for multisystem abnormalities in patients with Rauch–Steindl syndrome."
Location in Paper: Discussion and conclusion