The Discovery of a LEMD2-Associated Nuclear Envelopathy with Early Progeroid Appearance Suggests Advanced Applications for AI-Driven Facial Phenotyping.

Over a relatively short period of time, the clinical geneticist's "toolbox" has been expanded by machine-learning algorithms for image analysis, which can be applied to the task of syndrome identification on the basis of facial photographs, but these technologies harbor potential beyond the recognition of established phenotypes. Here, we comprehensively characterized two individuals with a hitherto unknown genetic disorder caused by the same de novo mutation in LEMD2 (c.1436C>T;p.Ser479Phe), the gene which encodes the nuclear envelope protein LEM domain-containing protein 2 (LEMD2). Despite different ages and ethnic backgrounds, both individuals share a progeria-like facial phenotype and a distinct combination of physical and neurologic anomalies, such as growth retardation; hypoplastic jaws crowded with multiple supernumerary, yet unerupted, teeth; and cerebellar intention tremor. Immunofluorescence analyses of patient fibroblasts revealed mutation-induced disturbance of nuclear architecture, recapitulating previously published data in LEMD2-deficient cell lines, and additional experiments suggested mislocalization of mutant LEMD2 protein within the nuclear lamina. Computational analysis of facial features with two different deep neural networks showed phenotypic proximity to other nuclear envelopathies. One of the algorithms, when trained to recognize syndromic similarity (rather than specific syndromes) in an unsupervised approach, clustered both individuals closely together, providing hypothesis-free hints for a common genetic etiology. We show that a recurrent de novo mutation in LEMD2 causes a nuclear envelopathy whose prognosis in adolescence is relatively good in comparison to that of classical Hutchinson-Gilford progeria syndrome, and we suggest that the application of artificial intelligence to the analysis of patient images can facilitate the discovery of new genetic disorders.

Focal facial dermal dysplasia, type IV, is caused by mutations in CYP26C1.

Focal facial dermal dysplasia (FFDD) Type IV is a rare syndrome characterized by facial lesions resembling aplasia cutis in a preauricular distribution along the line of fusion of the maxillary and mandibular prominences. To identify the causative gene(s), exome sequencing was performed in a family with two affected siblings. Assuming autosomal recessive inheritance, two novel sequence variants were identified in both siblings in CYP26C1-a duplication of seven base pairs, which was maternally inherited, c.844_851dupCCATGCA, predicting p.Glu284fsX128 and a missense mutation, c.1433G>A, predicting p.Arg478His, that was paternally inherited. The duplication predicted a frameshift mutation that led to a premature stop codon and premature chain termination, whereas the missense mutation was not functional based on its in vitro expression in mammalian cells. The FFDD skin lesions arise along the sites of fusion of the maxillary and mandibular prominences early in facial development, and Cyp26c1 was expressed exactly along the fusion line for these facial prominences in the first branchial arch in mice. Sequencing of four additional, unrelated Type IV FFDD patients and eight Type II or III TWIST2-negative FFDD patients revealed that three of the Type IV patients were homozygous for the duplication, whereas none of the Type II or III patients had CYP26C1 mutations. The seven base pairs duplication was present in 0.3% of healthy controls and 0.3% of patients with other birth defects. These findings suggest that the phenotypic manifestations of FFDD Type IV can be non-penetrant or underascertained. Thus, FFDD Type IV results from the loss of function mutations in CYP26C1.

Clinical spectrum of POLR3-related leukodystrophy caused by biallelic POLR1C pathogenic variants.

OBJECTIVE: To determine the clinical, radiologic, and molecular characteristics of RNA polymerase III-related leukodystrophy (POLR3-HLD) caused by biallelic POLR1C pathogenic variants. METHODS: A cross-sectional observational study involving 25 centers worldwide was conducted. Clinical and molecular information was collected on 23 unreported and previously reported patients with POLR3-HLD and biallelic pathogenic variants in POLR1C. Brain MRI studies were reviewed. RESULTS: Fourteen female and 9 male patients aged 7 days to 23 years were included in the study. Most participants presented early in life (birth to 6 years), and motor deterioration was seen during childhood. A notable proportion of patients required a wheelchair before adolescence, suggesting a more severe phenotype than previously described in POLR3-HLD. Dental, ocular, and endocrine features were not invariably present (70%, 50%, and 50%, respectively). Five patients (22%) had a combination of hypomyelinating leukodystrophy and abnormal craniofacial development, including 1 individual with clear Treacher Collins syndrome (TCS) features. Brain MRI revealed hypomyelination in all cases, often with areas of pronounced T2 hyperintensity corresponding to T1 hypointensity of the white matter. Twenty-nine different pathogenic variants (including 12 new disease-causing variants) in POLR1C were identified. CONCLUSIONS: This study provides a comprehensive description of POLR3-HLD caused by biallelic POLR1C pathogenic variants based on the largest cohort of patients to date. These results suggest distinct characteristics of POLR1C-related disorder, with a spectrum of clinical involvement characterized by hypomyelinating leukodystrophy with or without abnormal craniofacial development reminiscent of TCS.

Focal preauricular dermal dysplasia: distinctive congenital lesions with a bilateral and symmetric distribution.

We present three unrelated children with distinctive congenital facial skin lesions. All three children had two to three well-circumscribed, round or oval vesicular lesions, 1/2-1 cm in diameter on each cheek at birth. The lesions were located along an arc from the top of the ear to the corner of the mouth. Patient 1 was born with a unilateral cleft lip and palate, and a cutaneous hemangioma in the right palm. She is developing normally. Patient 2 has neurological sequelae after suffering an unexplained large left-sided intracerebral hemorrhage perinatally. Patient 3 has a small chin, somewhat cupped ears and a nevus on the left foot. He is developing normally. This condition has been described in the dermatological literature as focal facial dermal hypoplasia with preauricular localization. No cases with associated anomalies have been published previously. Most cases have been sporadic but familial occurrence compatible with autosomal dominant and autosomal recessive inheritance has been documented. If an embryonic fusion defect of the mandibular and maxillary prominences underlies the anomaly, the cleft lip and palate seen in one of our patients may be non-coincidental. No mutations in the TWIST2 gene were found in DNA extracted from peripheral leukocytes in the two children who were investigated.

Characterization of a Norwegian cherubism cohort; molecular genetic findings, oral manifestations and quality of life.

Bilateral multilocular radiolucencies of the mandible are the main feature of cherubism (OMIM #118400), a rare autosomal dominant disorder primarily affecting the jaw. Typically, symmetrical swelling of the lower face is evident from around three years of age and increases until puberty. The underlying radiolucent lesions consist of vascular fibrotic stroma with scattered multinuclear giant cells. By age 30 years the facial contours are often unremarkable. Missing and displaced teeth as well as premature tooth loss are characteristic. Diagnosis rests upon a combination of clinical, radiographic, histological and molecular findings. SH3BP2 is currently the only gene known to be associated with cherubism. This cross-sectional study describes oral manifestations, quality of life and results of mutation analysis of SH3BP2 in 11 females and 13 males ages five to 84 years with cherubism. One individual with molecularly confirmed Noonan syndrome was excluded from the cohort. Standard statistical tools were used to analyze quality of life data. Mutation analysis was positive in all 22 familial and negative in both sporadic cases. Disease manifestations in mutation carriers varied from none to severe. Although intra-familial variability was marked, we found no evidence of non-penetrance, and females were on average more severely affected than males. Dental sequelae were pronounced; adults lacked a mean of 13 teeth (range 2-28), 13 of 17 individuals aged 16 years and older had removable or fixed dentures and five had dental implants; implant survival rate was 79%. In spite of pronounced disease manifestations and dental sequelae, adult quality of life was good.

Severe hypohidrotic ectodermal dysplasia in a girl caused by a de novo 9;X insertion that includes XIST and disrupts the EDA gene.

X-linked hypohidrotic ectodermal dysplasia (XLHED) is caused by mutations in the EDA gene. A girl with severe hypohidrotic ectodermal dysplasia and normal mental development had completely skewed X chromosome inactivation with only the paternal X active in peripheral blood cells. Routine chromosome analysis and sequencing of the EDA gene were normal. However, whole chromosome painting revealed a 9;X insertion. FISH analyses with BAC probes towards the EDA gene and the more distal region containing the XIST locus showed that an X chromosome fragment of at least 4 Mb containing XIST was inserted into 9p13 in conjunction with a de novo pericentric inversion of chromosome 9. The proximal breakpoint was within the EDA gene and the distal breakpoint was distal to the XIST locus. Both parents had normal chromosomes, and the mother had random X inactivation in peripheral blood cells. Because XIST was lacking on the X chromosome with the disrupted EDA gene, the normal X chromosome was inactivated resulting in severe XLHED.