NSD2 Gene Paper Review

Summary

The study investigates nsd2 gene haploinsufficiency and its association with developmental disorders and intellectual disability (ID). A series of individual cases with nsd2 mutations such as frameshifts and nonsense mutations implicate the gene's loss-of-function in ID and related phenotypes. While the inheritance of these mutations is not universally tested, some cases exhibit de novo mutations. For instance, patient 13-I with a frameshift variant p.Cys1183Valfs*146 and patient 14-I with a nonsense mutation p.Arg600*, both present with learning difficulties. Functional studies further corroborate the link between nsd2 dysfunction and disease, demonstrating a significant reduction in methyltransferase activity. Specifically, an in vitro methylation assay reveals that mutations like those identified in patients 10-I (S1137F) and 5-I (E1091K) disrupt the protein's ability to methylate histone H3. Overexpression studies are in agreement, showing reduced methylation levels upon expression of patient-associated nsd2 variants. In vitro enzymatic function assessments indicate that missense variant Cys869Tyr from patient 1-I, likely pathogenic, did not significantly disrupt methylation activity, suggesting additional nsd2 functions may contribute to disease pathogenesis. Collectively, the data from this cohort provide a compelling argument for nsd2 haploinsufficiency playing a critical role in developmental disorders and ID, backed by both genetic evidence from patient mutations and functional validation of impaired enzymatic activity.

Evidence of Haploinsufficiency

Patient Identifier: patient 1-I

Mutation Type: missense

Mutation Details: Cys869Tyr substitution in the PHD finger domain

Clinical Phenotype: IQ in the lower-normal range

Inheritance Tested: No

Effect on Gene Function: disrupts zinc binding within a PHD finger domain and induces improper folding and loss of function for this domain

Direct Quote: "The Cys869Tyr (patient 1-I) substitution disrupts zinc binding within a PHD finger domain (residues 831-875) and hence induces improper folding and loss of function for this domain."

Location in Paper: Results

Patient Identifier: patients 7-I and 7-II

Mutation Type: missense

Mutation Details: The Pro895Leu variant located in the core of one of NSD2’s PWWP domains

Clinical Phenotype: unknown

Inheritance Tested: No

Effect on Gene Function: The leucine substitution at Pro895 is predicted to destabilize the domain through steric clashes with the adjacent Trp885

Direct Quote: "The Pro895Leu variant (patients 7-I and 7-II) is located in the core of one of NSD2’s PWWP domains, another motif that generally functions as an epigenetic reader. The leucine substitution at Pro895 is predicted to destabilize the domain through steric clashes with the adjacent Trp885."

Location in Paper: Results

Patient Identifier: patient 12-I

Mutation Type: missense

Mutation Details: Lys1019Arg is located in a loop of the methyltransferase domain

Clinical Phenotype: Not specified in the provided text

Inheritance Tested: No

Effect on Gene Function: showed a modest reduction in methylation of nucleosomes

Direct Quote: "All remaining missense variants are located within the methyltransferase domain of NSD2. Lys1019Arg (patient 12-I) is located in a loop of the methyltransferase domain that exhibits high local mobility or is entirely missing"

Location in Paper: Results

Patient Identifier: patient 10-I

Mutation Type: missense variant

Mutation Details: Ser1137Phe (S1137F)

Clinical Phenotype: developmental disorders

Inheritance Tested: No

Effect on Gene Function: predicted to destabilize the protein domain and abrogates NSD2’s ability to methylate

Direct Quote: "Ser1137 is located in the domain’s core and substitution to phenylalanine (p.Ser1137Phe, patient 10-I) is predicted to result in steric clashes with the adjacent Leu1163 residue, leading to domain destabilization."

Location in Paper: Section describing the functional impact of variants within the NSD2 gene

Patient Identifier: patient 5-I

Mutation Type: missense variant

Mutation Details: Glu1091Lys (E1091K)

Clinical Phenotype: developmental disorders, latex allergy, limited signs of precocious puberty

Inheritance Tested: No

Effect on Gene Function: disruption of a salt bridge resulting in domain destabilization

Direct Quote: "Glu1091 forms a salt bridge to Arg1160 in the wild-type structure, which is disrupted due to the charge inversion in the Glu1091Lys variant (patient 5-I)."

Location in Paper: Section describing the functional impact of variants within the NSD2 gene

Patient Identifier: patient 16-I

Mutation Type: Not specified in the provided text

Mutation Details: Not specified in the provided text

Clinical Phenotype: Postmortem pathological findings, vermis hypoplasia

Inheritance Tested: No

Effect on Gene Function: Not directly specified but included in NSD2 cohort with identified pathogenic variants

Direct Quote: "Detailed clinical descriptions are provided in the supplement...for case 16-I, a male fetus whose pregnancy was terminated at the 27th week of gestation"

Location in Paper: Paragraph preceding Fig. 3

Patient Identifier: 13-I

Mutation Type: frameshift variant

Mutation Details: p.Cys1183Valfs*146

Clinical Phenotype: Learning difficulties

Inheritance Tested: No

Effect on Gene Function: A frameshift variant likely results in a truncated, non-functional protein

Direct Quote: "...13-I, and 14-I harboring...p.Cys1183Valfs*146, and p.Arg600* variants...presented with learning difficulties"

Location in Paper: Clinical data. (a)

Patient Identifier: 14-I

Mutation Type: nonsense mutation

Mutation Details: p.Arg600*

Clinical Phenotype: Learning difficulties

Inheritance Tested: No

Effect on Gene Function: A nonsense mutation is expected to produce a truncated protein, leading to loss of function

Direct Quote: "...13-I, and 14-I harboring...p.Arg600* variants respectively...presented with learning difficulties"

Location in Paper: Clinical data. (a)

Patient Identifier: Individual 3-I

Mutation Type: frameshift variant

Mutation Details: c.3223_3226dup p.Gly1076Valfs*16

Clinical Phenotype: Severe intellectual disability

Inheritance Tested: No

Effect on Gene Function: A frameshift variant likely leads to a loss of normal protein function

Direct Quote: "The latter carried truncating variants (3-I c.3223_3226dup p.Gly1076Valfs*16...), which may not be held responsible for the severe ID."

Location in Paper: Clinical data. (a)

Patient Identifier: Individual 4-I

Mutation Type: frameshift variant

Mutation Details: c.1588_1589dupAA p.Ile532Glyfs*67

Clinical Phenotype: Severe intellectual disability

Inheritance Tested: No

Effect on Gene Function: Likely loss-of-function due to the frameshift variant producing a truncated protein

Direct Quote: "The latter carried truncating variants...4-1c.1588_1589dupAA p.Ile532Glyfs*67; Bernardini et al., patient 3, exon 1–20 deletion), which may not be held responsible for the severe ID"

Location in Paper: Clinical data. (a)

Patient Identifier: 11-I

Mutation Type: frameshift

Mutation Details: p.Pro1343Glnfs*49

Clinical Phenotype: low IgA and IgG3 levels, recurrent respiratory infections

Inheritance Tested: Yes

Effect on Gene Function: Occurs too distally in the mRNA sequence to induce nonsense-mediated decay, pathogenicity supported by de novo occurrence in similarly affected individuals

Direct Quote: "Patients 11-I and 15-I carried the same protein-elongating p.Pro1343Glnfs*49 variant. Although this variant occurs too distally in the messenger RNA (mRNA) sequence to induce nonsense-mediated decay, its pathogenicity is supported by the fact that this variant, together with the previously described p.Glu1344Lysfs*49 variant,18 all occurred de novo in similarly affected individuals."

Location in Paper: Paragraph 7

Patient Identifier: 15-I

Mutation Type: frameshift

Mutation Details: p.Pro1343Glnfs*49

Clinical Phenotype: Similarly affected as other individuals with pathogenic variants

Inheritance Tested: Yes

Effect on Gene Function: Occurs too distally in the mRNA sequence to induce nonsense-mediated decay, pathogenicity supported by de novo occurrence in similarly affected individuals

Direct Quote: "Patients 11-I and 15-I carried the same protein-elongating p.Pro1343Glnfs*49 variant. Although this variant occurs too distally in the messenger RNA (mRNA) sequence to induce nonsense-mediated decay, its pathogenicity is supported by the fact that this variant, together with the previously described p.Glu1344Lysfs*49 variant,18 all occurred de novo in similarly affected individuals."

Location in Paper: Paragraph 7

Clinical Features

Feature: Developmental delay (DD) and intellectual disability (ID)

Frequency: More than 50% of patients

Direct Quote: "The core phenotype of the NSD2 cohort (>50% of patients) is characterized by DD, intrauterine growth retardation and low birth weight, feeding difficulties, failure to thrive, height and head circumference below the 5th centile (<−1.65 SDS), speech delay, and muscular hypotonia."

Location in Paper: Clinical data. (a)

Feature: Behavioral and psychological issues as well as autistic features

Frequency: 44% for behavioral and psychological issues, 33% for autistic features

Direct Quote: "Behavioral and psychological issues as well as autistic features were observed in 44% and 33%, respectively."