Grandparental genotyping enhances exome variant interpretation

Penetrance, variable expressivity and monogenic neurodevelopmental disorders

PURPOSE

Incomplete penetrance is observed for most monogenic diseases. However, for neurodevelopmental disorders, the interpretation of single and multi-nucleotide variants (SNV/MNVs) is usually based on the paradigm of complete penetrance.

METHOD

From 2020 to 2022, we proposed a collaboration study with the French molecular diagnosis for intellectual disability network. The aim was to recruit families for whom the index case, diagnosed with a neurodevelopmental disorder, was carrying a pathogenic or likely pathogenic variant for an OMIM morbid gene and inherited from an asymptomatic parent. Grandparents were analyzed when available for segregation study.

RESULTS

We identified 12 patients affected by a monogenic neurodevelopmental disorder caused by likely pathogenic or pathogenic variant (SNV/MNV) inherited from an asymptomatic parent. These genes were usually associated with de novo variants. The patients carried different variants (1 splice-site variant, 4 nonsense and 7 frameshift) in 11 genes: CAMTA1, MBD5, KMT2C, KMT2E, ZMIZ1, MN1, NDUFB11, CUL3, MED13, ARID2 and RERE. Grandparents have been tested in 6 families, and each time the variant was confirmed de novo in the healthy carrier parent.

CONCLUSION

Incomplete penetrance for SNV and MNV in neurodevelopmental disorders might be more frequent than previously thought. This point is crucial to consider for interpretation of variants, family investigation, genetic counseling, and prenatal diagnosis. Molecular mechanisms underlying this incomplete penetrance still need to be identified.

Variation among DNA banking consent forms: points for clinicians to bank on

Deoxyribonucleic acid (DNA) banking is an important laboratory service that preserves the option of future genetic testing. DNA bank consent forms are a critical tool to facilitate thorough and valid informed consent. The objectives of this study were to assess the level of consistency of current clinical DNA banking consent forms with the American Society of Human Genetics (ASHG) and the American College of Medical Genetics and Genomics (ACMG) guidance and to explore variation among the forms. The content analysis matrix included key points identified from the ASHG and ACMG documents (including benefits/risks, sample storage, access, disposition, and communication) and additional points beyond the ASHG and ACMG documents identified from the consent forms themselves during the analysis process. Forms were assessed for language addressing each point. Five consent forms were identified and analyzed for twelve key points and eight additional points. The average consistency for key points was 10.8/12 (range 8/12 to 12/12). The range for additional points was 1/8 to 5/8. There was variation across forms in the details provided related to key and additional points. Gaps in clinical DNA banking consent forms are barriers to achieving informed consent. Clinicians can consider the consent key and additional points discussed here to supplement and enrich their clinical DNA banking informed consent discussions, promote stewardship, and maximize downstream utility of banked DNA. The identification of multiple additional points beyond the ASHG and ACMG documents' key points indicates a need for this guidance to be updated.

Further characterization of Borjeson‐Forssman‐Lehmann syndrome in females due to de novo variants in PHF6

While inherited hemizygous variants in PHF6 cause X‐linked recessive Borjeson‐Forssman‐Lehmann syndrome (BFLS) in males, de novo heterozygous variants in females are associated with an overlapping but distinct phenotype, including moderate to severe intellectual disability, characteristic facial dysmorphism, dental, finger and toe anomalies, and linear skin pigmentation. By personal communication with colleagues, we assembled 11 additional females with BFLS due to variants in PHF6. We confirm the distinct phenotype to include variable intellectual disability, recognizable facial dysmorphism and other anomalies. We observed skewed X‐inactivation in blood and streaky skin pigmentation compatible with functional mosaicism. Variants occurred de novo in 10 individuals, of whom one was only mildly affected and transmitted it to her more severely affected daughter. The mutational spectrum comprises a two‐exon deletion, five truncating, one splice‐site and three missense variants, the latter all located in the PHD2 domain and predicted to severely destabilize the domain structure. This observation supports the hypothesis of more severe variants in females contributing to gender‐specific phenotypes in addition to or in combination with effects of X‐inactivation and functional mosaicism. Therefore, our findings further delineate the clinical and mutational spectrum of female BFLS and provide further insights into possible genotype–phenotype correlations between females and males.

Monogenic causes of pigmentary mosaicism

Pigmentary mosaicism of the Ito type, also known as hypomelanosis of Ito, is a neurocutaneous syndrome considered to be predominantly caused by somatic chromosomal mosaicism. However, a few monogenic causes of pigmentary mosaicism have been recently reported. Eleven unrelated individuals with pigmentary mosaicism (mostly hypopigmented skin) were recruited for this study. Skin punch biopsies of the probands and trio-based blood samples (from probands and both biological parents) were collected, and genomic DNA was extracted and analyzed by exome sequencing. In all patients, plausible monogenic causes were detected with somatic and germline variants identified in five and six patients, respectively. Among the somatic variants, four patients had MTOR variant (36%) and another had an RHOA variant. De novo germline variants in USP9X, TFE3, and KCNQ5 were detected in two, one, and one patients, respectively. A maternally inherited PHF6 variant was detected in one patient with hyperpigmented skin. Compound heterozygous GTF3C5 variants were highlighted as strong candidates in the remaining patient. Exome sequencing, using patients' blood and skin samples is highly recommended as the first choice for detecting causative genetic variants of pigmentary mosaicism.