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Genotype-phenotype correlation at codon 1740 of SETD2.

Rachel Rabin1, Alireza Radmanesh2, Ian A Glass3,4

  • 1Clinical Genetic Services, Department of Pediatrics, NYU School of Medicine, New York, New York, USA.

American Journal of Medical Genetics. Part A
|July 26, 2020
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Summary

New SETD2 gene variants cause distinct developmental disorders, differing from Luscan-Lumish syndrome. Specific mutations at codon 1740 lead to severe phenotypes, suggesting novel disease mechanisms and potentially a new syndrome.

Keywords:
SETD2clinical geneticsgenotype phenotypehistone modificationneurodevelopmental

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Area of Science:

  • Genetics
  • Molecular Biology
  • Developmental Biology

Background:

  • SETD2 encodes a dual-function methyltransferase crucial for transcriptional regulation, genomic stability, and cytoskeletal functions.
  • SETD2 is involved in histone H3 lysine 36 trimethylation (H3K36me3) and alpha-tubulin lysine 40 methylation.
  • Previous studies linked heterozygous loss-of-function and missense variants to Luscan-Lumish syndrome (LLS), characterized by overgrowth and neurodevelopmental features.

Purpose of the Study:

  • To investigate the clinical phenotypes associated with de novo variants in codon 1740 of the SETD2 gene.
  • To differentiate the features of SETD2 codon 1740 variants from those observed in Luscan-Lumish syndrome.
  • To explore potential alternative pathomechanisms beyond loss-of-function for SETD2 variants.

Main Methods:

  • Clinical evaluation of 15 individuals with de novo SETD2 variants at codon 1740.
  • Genotyping to identify specific variants: c.5218C>T p.(Arg1740Trp) in Group 1 (12 individuals) and c.5219G>A p.(Arg1740Gln) in Group 2 (3 individuals).
  • Phenotypic analysis comparing individuals with different SETD2 variants and with previously described LLS cases.

Main Results:

  • Group 1 (p.(Arg1740Trp)) presented with microcephaly, profound intellectual disability, congenital anomalies, and distinct facial features.
  • Group 2 (p.(Arg1740Gln)) exhibited moderate to severe intellectual disability and normal head circumference without major congenital anomalies.
  • The severe phenotypes in codon 1740 variants suggest mechanisms beyond simple loss-of-function, possibly gain-of-function or altered epigenetic/cytoskeletal regulation.

Conclusions:

  • Variants in SETD2 codon 1740 lead to distinct phenotypes that differ significantly from Luscan-Lumish syndrome.
  • The specific variant c.5218C>T p.(Arg1740Trp) may represent a new, clinically recognizable syndrome.
  • Further research is needed to elucidate the precise molecular mechanisms underlying these divergent SETD2-related disorders.