| Literature DB >> 35384273 |
Carolina Montano1, Jacquelyn F Britton2, Jacqueline R Harris2,3,4, Jennifer Kerkhof5, Benjamin T Barnes3, Jennifer A Lee6, Bekim Sadikovic5,7, Nara Sobreira2,3, Jill A Fahrner2,3.
Abstract
Kabuki syndrome is a Mendelian disorder of the epigenetic machinery characterized by typical dysmorphic features, intellectual disability, and postnatal growth deficiency. Pathogenic variants in the genes encoding the chromatin modifiers KMT2D and KDM6A are responsible for Kabuki syndrome 1 (KS1) and Kabuki syndrome 2 (KS2), respectively. In addition, 11 cases of KS1 caused by mosaic variants in KMT2D have been reported in the literature. Some of these individuals display milder craniofacial and growth phenotypes, and most do not have congenital heart defects. We report the case of an infant with severe hypoplastic left heart syndrome with mitral atresia and aortic atresia (HLHS MA-AA), pulmonary vein stenosis, and atypical facies with a somatic mosaic de novo nonsense variant in KMT2D (c.8200C>T, p.R2734*) identified on trio exome sequencing of peripheral blood and present in 11.2% of sequencing reads. KS was confirmed with EpiSign, a diagnostic genome-wide DNA methylation platform used to identify epigenetic signatures. This case suggests that use of this newly available clinical test can guide the interpretation of low-level mosaic variants identified through sequencing and suggests a new lower limit of mosaicism in whole blood required for a diagnosis of KS.Entities:
Keywords: DNA methylation; HLHS (hypoplastic left heart syndrome); KMT2D; Kabuki syndrome; episignature; mosaicism
Mesh:
Year: 2022 PMID: 35384273 PMCID: PMC9321966 DOI: 10.1002/ajmg.a.62754
Source DB: PubMed Journal: Am J Med Genet A ISSN: 1552-4825 Impact factor: 2.578
Clinical features of individuals with mosaic KMT2D variants
| Clinical features | Proband 1 | GM13‐3816 (Lepri et al., | KB450 (Lepri et al., | KB369 (Lepri et al., | 1 (Banka et al., | 2 (Banka et al., | 3 (Banka et al., | 22M (Cao et al., | 23M (Cao et al., | KMS‐025 (Murakami et al., | 1‐00596 (Manheimer et al., | 1‐00479 (Manheimer et al., |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
| c.8200C>T (p.R2734*) | c.15061C>T (p.R5021*) | c.13450C>T (p.R4484*) | c.3596_3597delTC (p.L1199Hfs*7) | c.9494delA (p.D3165Vfs*32) | c.8463_8475del (p.A2823Pfs*24) | Whole gene deletion | c.10938_10939delinsT (p.P3647Lfs*11) | c.8506C>T (p.R2836C) | c.15844C>T (p.R5282*) | c.5166del (p.S1722Rfs*9) | c.13727_13728del (p.F4576Cfs*29) |
| Alternate allele frequency in whole blood | 11.2% | 16% | 34% | 20% | <15% | Unable to quantify | 10–20% | 27.8% | 10.4% | 37% | 33% | 20% |
| Variant classification by ACMG guidelines | Path | Path | Path | Path | Path | Path | Path | Path | VUS | Path | Path | Path |
| Gender | M | F | F | F | F | F | F | NA | NA | M | NA | NA |
| Age in years (at publication) | 1 | 6.1 | 8 | 17 | 11 | 6 | 10 | NA | NA | NA | NA | NA |
| Elongated palpebral fissures | + | + | + | + | + | + | + | NA | NA | + | NA | NA |
| Sparse eyebrows | + | + | + | + | + | + | + | NA | NA | + | NA | NA |
| Palpebral ptosis | − | + | − | + | − | + | − | NA | NA | − | NA | NA |
| Broad nasal tip | + | − | + | + | + | + | − | NA | NA | + | NA | NA |
| Thin upper and full lower lip | + | + | + | + | + | + | + | NA | NA | + | NA | NA |
| Large dysmorphic ears | + | + | + | − | NA | NA | + | NA | NA | + | NA | NA |
| Fetal pads | + | − | + | + | + | + | + | NA | NA | + | NA | NA |
| Feeding difficulties | + | − | − | − | − | + | + | NA | NA | NA | NA | NA |
| Palate | High arched and V shaped | Normal | Normal | Normal | Normal | V‐shaped | Cleft lip and palate | Bilateral cleft lip and palate | NA | High arched palate | NA | NA |
| Cardiac defects | + | − | + | − | − | − | − | + | Not specified | − | + | + |
| HLHS | HLHS, aortic/mitral atresia, pulmonary vein stenosis | No | No | No | No | No | No | Not specified | Not specified | No | HLHS, Double aortic arch, aortic/mitral atresia | HLHS, aortic/mitral atresia |
| Urogenital anomalies | − | − | − | − | − | Right ectopic kidney | − | NA | NA | Cryptorchidism and multicystic dysplastic kidney | NA | NA |
| IQ impairment/development and learning | + | Borderline | Borderline | Moderate | Mild delay | Moderate delay | Severe, no speech | NA | Global developmental delay | Mild intellectual disability and developmental delay | NA | NA |
| Compromised adaptive functioning | Mild | On average | Mild | NA | NA | NA | NA | NA | ||||
| Hypotonia in infancy | + | + | NA | − | + | + | NA | + | NA | NA | NA | |
| Motor delay | + | NA | Mild | Yes | Mild | NA | NA | NA | NA | NA | ||
| Vision | Exopthalmos | − | − | − | Hypermetropia and right convergent squint | Hypermetropia and right convergent squint | Pale optic discs | NA | Congenital nystagmus | NA | NA | NA |
| Hearing | − | − | − | − | No problems | Decreased hearing at low frequencies. Sensitive to loud noises | No problems | NA | NA | NA | NA | NA |
| Joint dislocations | − | − | Right hip dysplasia | − | Congenital left hip dislocation needing open reduction | None | None | NA | NA | NA | NA | NA |
| Endocrine anomalies | − | − | − | Precocius puberty | Precocious puberty at 8 | Postnatal hypoglycemia requiring dextrose infusion – resolved | None | NA | NA | NA | NA | NA |
| Head circumference | 85th | 10th | − | <50th | 90th percentile | 0.4th percentile | 25–50th percentile | NA | Microcephaly | NA | NA | NA |
| Height | 80th | 75–90th | − | <25th | 50–75th | 50–75th | 50–75th | NA | Short stature | NA | NA | NA |
| Weight | 70–80th | 97th | − | >50th | 99th | 91–98th | Not known | NA | NA | NA | NA | NA |
| Immunity related problems | Recurrent infections | − | − | − | Recurrent otitis media | Recurrent otitis media | NA | NA | Otitis media | NA | NA | |
| Other | Inoperable heart disease | Pigmentary anomalies, body asymmetry | Diaphragmatic hernia | Generalized anxiety disorder, multiple phobias, autistic‐like behavior | Joint hyperextensibility with small lateral incisors | Constipation, broad thumbs and toes, anteriorly placed anus, irregularly spaced teeth | Hemangiomatous lesion on right thigh and epilepsy | Holoprosencephaly | Soft skin, abnormal facial shape | Lipoma | NA | NA |
FIGURE 1Clinical features of the patient described in this report at 13 months of age (4 months after initial evaluation). (a) Facial features include arched eyebrows with lateral sparseness, long palpebral fissures with eversion of lateral third of the lower eyelids, long eyelashes, broad nasal tip, short columella, and epicanthal folds. Unique features included exophthalmos due to shallow orbits, depressed nasal bridge, and a bulbous nose. (b, c) Lateral views illustrating prominent ears. Persistence of (d) fingertip and (e) toe pads
FIGURE 2EpiSign DNA methylation analysis of peripheral blood from a patient with a somatic mosaic nonsense variant in KMT2D, the causative gene for Kabuki syndrome 1 (KS1). (a) Hierarchical clustering and (b) multidimensional scaling plots indicate that the patient (red) has a DNA methylation signature similar to subjects with a confirmed KS episignature (blue) and distinct from controls (green). Each row of the heatmap represents one CpG probe on the DNA methylation array, and each column represents one individual's sample. The heatmap color scale from blue to red represents the DNA methylation level (beta value) from 0 (no methylation) to 1 (fully methylated). (c) MVP score, a multiclass supervised classification system capable of discerning between multiple episignatures by generating a probability score for each episignature. The elevated patient score for KS compared to other syndromes suggests an episignature similar to the KS reference signature; however, the decreased probability compared to what is typically observed for constitutional KS (score >0.5) likely results from the low‐level mosaicism of the variant