Dominant variants in the splicing factor PUF60 cause a recognizable syndrome with intellectual disability, heart defects and short stature

Abstract

Verheij syndrome, also called 8q24.3 microdeletion syndrome, is a rare condition characterized by ante- and postnatal growth retardation, microcephaly, vertebral anomalies, joint laxity/dislocation, developmental delay (DD), cardiac and renal defects and dysmorphic features. Recently, PUF60 (Poly-U Binding Splicing Factor 60 kDa), which encodes a component of the spliceosome, has been discussed as the best candidate gene for the Verheij syndrome phenotype, regarding the cardiac and short stature phenotype. To date, only one patient has been reported with a de novo variant in PUF60 that probably affects function (c.505C>T leading to p.(His169Tyr)) associated with DD, microcephaly, craniofacial and cardiac defects. Additional patients were required to confirm the pathogenesis of this association and further delineate the clinical spectrum. Here we report five patients with de novo heterozygous variants in PUF60 identified using whole exome sequencing. Variants included a splice-site variant (c.24+1G>C), a frameshift variant (p.(Ile136Thrfs*31)), two nonsense variants (p.(Arg448*) and p.(Lys301*)) and a missense change (p.(Val483Ala)). All six patients with a PUF60 variant (the five patients of the present study and the unique reported patient) have the same core facial gestalt as 8q24.3 microdeletions patients, associated with DD. Other findings include feeding difficulties (3/6), cardiac defects (5/6), short stature (5/6), joint laxity and/or dislocation (5/6), vertebral anomalies (3/6), bilateral microphthalmia and irido-retinal coloboma (1/6), bilateral optic nerve hypoplasia (2/6), renal anomalies (2/6) and branchial arch defects (2/6). These results confirm that PUF60 is a major driver for the developmental, craniofacial, skeletal and cardiac phenotypes associated with the 8q24.3 microdeletion.

Figure 1

Facial characteristics of the individuals with PUF60 variants. (a–c) Frontal and lateral views of patient 1 at birth (a) at 3 years and 3 months (b) and at 1 year (c) demonstrating facial dysmorphism including a square face, full cheeks, prominent forehead with bitemporal narrowing, low-set eyebrows, asymmetric and posterior rotated ears, bilateral colobomatous microphtalmia with horizontal nystagmus and convergent strabismus, bilateral epicanthal folds, wide nasal bridge with broad nasal tip and anteverted nares, thin upper lip with a long philtrum, micrognathism and broad short neck. (d) Lateral view of the neck of patient 1 showing a branchial cleft cyst (arrow). (e) Full-body view of patient 1 showing the contrast between the normal head circumference and the low body height and weight with relatively short arms, and a pectus excavatum. (f, g) Frontal and lateral views of patient 3 at birth (f) and at 3 years and 10 months (g) showing an elongated face, bilateral epicanthal folds, short up-slanted palpebral fissures, long eyelashes, anteverted nares, long prominent philtrum, thin upper lip and a short neck. (h–k) Frontal and lateral views of patient 4 at the age of 8 months (h), 2 years (i) and 17 years (k). (j) Lateral view of the neck of patient 4 showing a branchial cleft cyst (arrow). (l, m) Frontal and lateral view of patient 5 at the age of 11 years (l) showing deep set eyes, broad nasal bridge with protruding ears. (m) Flat feet with short halluces and sandal-gap deformity.

Figure 2

Fundus and brain MRI results. (a) Fundus view showing the retinal coloboma (full-line arrow) of left eye involving the optic disk (dotted-line arrow) – type IV of the Gopal classification. (b–d) Brain and optic nerve MRI (2 months) showing bilateral microphthalmia (b) associated with irido coloboma (black arrow) and retinal coloboma (white arrow), and the bilaterally thin (hypoplastic) optic nerve hypoplasia predominantly in the intra-orbital portion (c, d) (white arrows).

Figure 3

Genetic location of the PUF60 variants identified to date. (a) Schematic human chromosome 8. The vertical red line indicates the position of the PUF60 gene at 8q24.3. (b) Variants identified in PUF60 by WES in the five patients of the present study and in the patient reported by dauber et al, and conserved amino acid sequences among mammals. (c) A focus on the PUF60 locus with a schematic representation of exons (vertical black bars). (d) Distribution of amino-acid changes in PUF60. RRM, RNA recognition motif. A full color version of this figure is available at the European Journal of Human Genetics journal online.