family A, only 2 of 37 candidate variants segregated with the disease in the family (Table 2 and Table S3). These two mutations were homozygous missense mutations in EXTL3 (c.1537C>T [p.Arg513Cys] [GenBank: NM_001440.3]) and CHST9 (MIM: 610191; c.1133A>G [p.Asn378Ser] [GenBank: NM_031422]) (Figure 2B)

All nine affected individuals presented with various skeletal dysplasias. In four families (A and C–E), X-rays revealed severe platyspondyly leading to disproportionate stature (Figure 1). Lumbar gibbus and kyphoscoliosis were observed in families C and D, respectively. Three individuals (from families D and E) had cervical malformations and a hypoplastic odontoid peg with cervical instability. Short stature was also present in families A and B but appeared to be the result of limb shortening. Metaphyseal abnormalities of the long bones were found in families A and E, whereas families B–D showed epiphyseal abnormalities (Figure 1). Brachydactyly was observed in affected individuals from families A, B, and D. In addition to showing skeletal abnormalities, all affected individuals in families B and C had intellectual disability (ID). This could not be assessed for individuals A:II-1, E:II-1, and E:II-2 because of their early death at 7 weeks, 6 months, and 10 months of age, respectively. Both siblings of family B were severely disabled and unable to speak and are currently wheelchair bound. Dysmorphic facial features were non-discriminatingly mild but included coarse facial features, a prominent nose, and full cheeks in almost all affected individuals (Figure S1). A single palmar crease was also observed in six of nine affected individuals. A striking phenotype present in three of the five families was T-cell-negative SCID. Affected individuals from families A and B showed a lack of T cells, whereas B cell numbers were normal (Figure 4). Family E showed idiopathic CD4+ lymphopenia and an absolute lack of naive T cells (both CD4+CD45RA+ and CD8+CD45RA+ T cells were missing). In families B and E, a typical skin rash prompted further evaluation of the blood cells. Maternal T cells were excluded, and the oligoclonal T cell reaction found in the presence of eosinophilia was compatible with an Omenn-like presentation of SCID.1,2 Worth mentioning are also the liver cysts seen in affected individuals from families A and E. Although the phenotypes were widely variable and partly contrasting (e.g., severe versus no ID, severe versus mild platyspondyly, and epiphyseal versus metaphyseal changes), all major malformations and features occurred in three organ systems only: the immune system, the skeleton, and the neurological system. All together, we classify these five families as having phenotypic variability of an EXTL3-related neuro-immuno-skeletal dysplasia phenotype. The affected individuals from families A and E died in early infancy, whereas the others are currently between 2 and 38 years of age. Individual III-1 from family D died at 30 years of age from a unknown cause. Table 1 gives an overview of the most affected organ systems in all affected individuals. Detailed case reports and clinical data for each affected individual can be found in the Supplemental Note.