Trio-based segregation analysis of type 1 3-methylcrotonyl-CoA carboxylase deficiency associated with rare compound heterozygous MCCC1 variants

To investigate the clinical features and molecular etiology of a pedigree presenting with unexplained global developmental delay (GDD), elucidate the transmission pattern of rare MCCC1 variants within the family, and provide a basis for genetic counseling and the precise diagnosis of similar inborn errors of metabolism. Clinical data were collected from a core pedigree featuring a 1.5-year-old proband with atypical developmental delay. Dried blood spots from the proband were analyzed using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) for biochemical screening of inherited metabolic diseases. Genomic DNA was extracted from the peripheral blood of the proband and his phenotypically normal parents. Trio-whole-genome sequencing (Trio-WGS) was employed for comprehensive genomic variant screening, followed by co-segregation analysis within the family. Candidate variants were classified according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Routine imaging and biochemical tests of the proband were unremarkable. However, LC-MS/MS revealed significantly elevated levels of C4DC+C5-OH (succinylcarnitine + 3-hydroxyisovalerylcarnitine) in the acylcarnitine profile, highly suggestive of 3-methylcrotonyl-CoA carboxylase deficiency (MCCD). Trio-WGS and pedigree validation revealed that the proband carried compound heterozygous variants in the MCCC1 gene (transcript NM_020166.5): an exonic missense variant c.863 A > G (p.Glu288Gly) inherited from the asymptomatic father, and a deep intronic deletion c.956-2124del in Intron 9 inherited from the asymptomatic mother. According to ACMG criteria, the missense variant c.863 A > G was classified as likely pathogenic, and the deep intronic deletion c.956-2124del was classified as a variant of uncertain significance (VUS). In this study, we identified a compound heterozygous configuration of MCCC1 variants: NM_020166.5(MCCC1):c.[957-2124del]; [863 A > G] in a pedigree with MCCD type 1 and neurodevelopmental abnormalities. However, given the absence of RNA data or functional assays, the functional consequence of this deep intronic variant remains to be definitively established, and its pathogenic role should be considered tentative and exploratory. Nevertheless, this study highlights the important clinical utility of combining LC-MS/MS with Trio-WGS in investigating complex recessive genetic disorders, identifying hidden non-coding variants, and guiding reproductive planning.