Simple logic might have concluded that genotype at a single locus might predict phenotype. For monogenic disorders this is frequently not the case. Allelic combinations of missense, nonsense, and compound heterozygous mutations within different genes could result in overlapping clinical phenotypes as exemplified for the Kabuki syndrome and Schinzel–Giedion syndrome.837 Now that clinical diagnostic criteria have been established838 and two genes (KMT2D and KDM6A) recognized, syndrome identification has been facilitated.839 Additional novel pathogenic variants continue to be discovered.840 It appears that hyperinsulinism, long halluces, large central incisors, and hypertrichosis are more common in Kabuki syndrome due to KDM6A mutations,841, 842 while the classic Kabuki facial features and renal/palatal anomalies are more commonly found with KMT2D mutations.839, 843 In the autosomal dominant Marfan syndrome (due to mutations in FBN1), family members with the same mutation may have severe ocular, cardiovascular, and skeletal abnormalities, while siblings or other close affected relatives with the same mutation may have mild effects in only one of these systems.844 In Gaucher disease with one of the common Ashkenazi Jewish mutations, only about one‐third of homozygotes have significant clinical disease.845 At least two‐thirds have mild or late‐onset disease or remain asymptomatic (see Chapter 21). Compound heterozygotes for this disorder involving mutations p.L444P and p.N370S have included a patient with mild disease first diagnosed at 73 years of age, while another requiring enzyme replacement therapy was diagnosed at the age of 4 years.846
In cystic fibrosis, a strong correlation exists between genotype and pancreatic function but only a weak association has been noted with the respiratory phenotype847 (see Chapter 15). Although individuals who are homozygous for the common cystic fibrosis mutation (ΔF508) can be anticipated to have classic cystic fibrosis, those with the less common mutation (p.R117H) are likely to have a milder disease.848 On occasion, an individual who is homozygous for the “severe” ΔF508 mutation might unexpectedly exhibit a mild pancreatic‐sufficient phenotype. Illustrating the complexity of genotype–phenotype associations is the instance noted by Dork et al.849 of a mildly affected ΔF508 homozygote whose one chromosome 7 carried both the common ΔF508 mutations and a cryptic p.R553Q mutation. Apparently, a second mutation in the same region may modify the effect of the common mutation, permitting some function of the chloride channel850 and thereby ameliorating the severity of the disease. Modifying genes in cystic fibrosis are being increasingly recognized851–853 (see Chapter 15).
The extensive mutational heterogeneity in hemophilia A854–856 is related not only to variable clinical severity but also to the increased likelihood of antifactor VIII antibodies (inhibitors) developing. Miller et al.857 found about a fivefold higher risk of inhibitors developing in hemophiliac males with gene deletions compared with those without deletions. In Netherton syndrome, a severe autosomal recessive ichthyosis that affects skin, hair, and immune system, upstream mutations in the SPINK5 gene correlate with more severe phenotypes.858
The many mutations and wide phenotypic range seen in neurofibromatosis type 1 is well known, and characterized by variable expressivity and age‐dependent clinical features. This variability makes phenotype prediction difficult. Among the few thousand constitutional variants in the NF1 gene, recurrent pathogenic missense variants at p.Met1149, p.Arg1276 or p.Lys1423 have been associated with a Noonan‐like phenotype.859 Moreover, these authors also found that mutations at p.Arg1276 was associated with spinal neurofibromas, and that mutations at both p.Lys1423 and p.Arg1276 were associated with a high prevalence of cardiovascular abnormalities, including pulmonic stenosis.
Chronic intestinal pseudo‐obstruction (CIPO), also known as megacystis–microcolon–intestinal–hypoperistalsis syndrome, is a severe debilitating visceral myopathy involving enteric smooth muscle.860–863 Mutations in the ACTG2 gene account for about 44–50 percent of cases. We noted in a whole‐exome sequencing study a mutational hotspot in the ACTG2 gene (Figure 1.3).863 We subsequently determined somatic ACTG2 mosaicism,864 further complicating genotype–phenotype determination.
Figure 1.3 Shown are the 16 pathogenic variants reported in the ACTG2 gene and the number of times each mutation was observed in 45 probands.863
Japanese authors have assembled mutation data for the NOTCH3 gene and recognized three mutations as major contributors to the phenotype of CADASIL.865 They also recognized gender differences in symptomatology (worse in males) that included migraines, stroke, psychiatric problems, cognitive impairments, and dementia. Although CADASIL is mostly adult onset, we have provided prenatal diagnosis for a family with an affected young father, as noted earlier.
Given the history of a previously affected offspring with a genetic disorder, the preconception visit serves as an ideal time to refocus on any putative diagnosis (or lack thereof), to check constantly updated databases where prior alterations are or are not considered pathogenic, and to perform newly available mutation analyses when applicable.
Recognition of genotype–phenotype associations remains challenging for reasons that include expressivity, penetrance, multiple causal genes, modifier alleles, compound heterozygosity, locus heterogeneity, interacting polymorphisms of small effect, and digenic inheritance. For the vast majority of monogenic disorders, even without known epigenetic influence (such as epilepsy, microcephaly, holoprosencephaly, hydrocephalus, craniosynostosis), definitive genotype–phenotype associations remain unknown.
Somatic mosaicism
We are all somatic postzygotic mosaics, either born that way or later as a consequence of spontaneously occurring mutations during our lifetimes. Using single‐cell whole‐genome sequencing of B lymphocytes, Zhang et al.866 found that the number of somatic mutations increases from <500 per cell in newborns to >3,000 per cell in centenarians. These dynamic changes involving other tissues as well, are likely to be associated with cancer and aging,867 and many disorders (Table 1.8).
Table 1.8 Selected examples of monogenic disorders with established somatic mosaicism with DNA confirmation.
| Disorder | Gene | Reference |
|---|---|---|
| Achondrogenesis type 2 | COL2A1 | 885 |
| Aicardi–Goutières syndrome | TREX1 | 886 |
| Alport syndrome | COL4A5 | 887 |
| Alzheimer disease, early‐onset | PS1 |
