High diagnostic yield in skeletal ciliopathies using massively parallel genome sequencing, structural variant screening and RNA analyses

J Hum Genet. 2021 Oct;66(10):995-1008. doi: 10.1038/s10038-021-00925-x. Epub 2021 Apr 20.


Skeletal ciliopathies are a heterogenous group of disorders with overlapping clinical and radiographic features including bone dysplasia and internal abnormalities. To date, pathogenic variants in at least 30 genes, coding for different structural cilia proteins, are reported to cause skeletal ciliopathies. Here, we summarize genetic and phenotypic features of 34 affected individuals from 29 families with skeletal ciliopathies. Molecular diagnostic testing was performed using massively parallel sequencing (MPS) in combination with copy number variant (CNV) analyses and in silico filtering for variants in known skeletal ciliopathy genes. We identified biallelic disease-causing variants in seven genes: DYNC2H1, KIAA0753, WDR19, C2CD3, TTC21B, EVC, and EVC2. Four variants located in non-canonical splice sites of DYNC2H1, EVC, and KIAA0753 led to aberrant splicing that was shown by sequencing of cDNA. Furthermore, CNV analyses showed an intragenic deletion of DYNC2H1 in one individual and a 6.7 Mb de novo deletion on chromosome 1q24q25 in another. In five unsolved cases, MPS was performed in family setting. In one proband we identified a de novo variant in PRKACA and in another we found a homozygous intragenic deletion of IFT74, removing the first coding exon and leading to expression of a shorter message predicted to result in loss of 40 amino acids at the N-terminus. These findings establish IFT74 as a new skeletal ciliopathy gene. In conclusion, combined single nucleotide variant, CNV and cDNA analyses lead to a high yield of genetic diagnoses (90%) in a cohort of patients with skeletal ciliopathies.

MeSH terms

  • Adult
  • Aged
  • Bone Diseases, Developmental / epidemiology
  • Bone Diseases, Developmental / genetics*
  • Bone Diseases, Developmental / pathology
  • Ciliopathies / epidemiology
  • Ciliopathies / genetics*
  • Ciliopathies / pathology
  • Cytoplasmic Dyneins / genetics
  • Cytoskeletal Proteins / genetics
  • Female
  • Genetic Predisposition to Disease*
  • Genome, Human / genetics
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Intercellular Signaling Peptides and Proteins / genetics
  • Intracellular Signaling Peptides and Proteins / genetics
  • Male
  • Membrane Proteins / genetics
  • Microtubule-Associated Proteins / genetics
  • Middle Aged
  • Muscle, Skeletal / metabolism
  • Muscle, Skeletal / pathology
  • Protein Isoforms / genetics*
  • Whole Genome Sequencing


  • C2cd3 protein, human
  • Cytoskeletal Proteins
  • DYNC2H1 protein, human
  • EVC protein, human
  • EVC2 protein, human
  • Intercellular Signaling Peptides and Proteins
  • Intracellular Signaling Peptides and Proteins
  • KIAA0753 protein, human
  • Membrane Proteins
  • Microtubule-Associated Proteins
  • Protein Isoforms
  • TTC21B protein, human
  • WDR19 protein, human
  • Cytoplasmic Dyneins