Submicroscopic subtelomeric deletions of chromosome 9q are associated with a recognizable mental retardation syndrome (Harada et al., 2004; Iwakoshi et al., 2004; Stewart et al., 2004; Neas et al., 2005). Common features in patients with 9q subtelomeric deletion ... Submicroscopic subtelomeric deletions of chromosome 9q are associated with a recognizable mental retardation syndrome (Harada et al., 2004; Iwakoshi et al., 2004; Stewart et al., 2004; Neas et al., 2005). Common features in patients with 9q subtelomeric deletion syndrome are severe mental retardation, hypotonia, brachy(micro)cephaly, epileptic seizures, flat face with hypertelorism, synophrys, anteverted nares, everted lower lip, carp mouth with macroglossia, and heart defects.
Kleefstra et al. (2009) reported 16 patients with 9q deletions identified by routine chromosome testing or whole genome array analysis and 6 additional patients with intragenic EHMT1 mutations and normal chromosome studies. All patients showed the core phenotype ... Kleefstra et al. (2009) reported 16 patients with 9q deletions identified by routine chromosome testing or whole genome array analysis and 6 additional patients with intragenic EHMT1 mutations and normal chromosome studies. All patients showed the core phenotype of the deletion syndrome, including mental retardation without speech development, hypotonia, and characteristic facial features. Facial features included microcephaly, brachycephaly, hypertelorism, synophrys, midface hypoplasia, protruding tongue, eversion of the lower lip, and prognathism. Birth weight was often increased compared to normal and many had childhood obesity. Motor function was delayed, but all individuals were able to walk between 2 and 3 years, except 1 patient. Eight patients had congenital heart defects, including atrial or ventricular septal defects, tetralogy of Fallot, aortic coarctation, bicuspid aortic valve, and pulmonic stenosis. Seven patients had seizures. Less common and variable features included micropenis, cryptorchidism, vesicoureteral reflux, tracheo-/bronchomalacia, and gastroesophageal reflux. Brain imaging was generally normal, but some showed dilated ventricles, abnormal myelination, or other mild changes. Five patients that reached adult age showed abrupt behavioral changes around adolescence with some later recovery. Abnormalities included apathy, aggressive periods, psychosis, autistic features, catatonia, bipolar mood disorder, and regression in daily function and cognitive abilities. There were no apparent genotype/phenotype correlations with the size of the deletion or between those with deletions and those with mutations. Kleefstra et al. (2009) concluded that haploinsufficiency for the EHMT1 gene is responsible for the main phenotypic features. Verhoeven et al. (2011) reviewed the clinical histories of 3 unrelated women, aged 43, 33, and 19 years, with Kleefstra syndrome. Two had a heterozygous intragenic loss-of-function mutation in the EHMT1 gene and the third had a heterozygous 9q34.3 microdeletion encompassing the EHMT1 gene. All had delayed psychomotor development since early childhood, and showed progressive regression in behavior. The oldest patient showed a decline in global functioning beginning at age 38 years and necessitating institutionalization. The other 2 patients showed onset of behavioral regression around puberty. On physical examination as adults, all showed the characteristic facial features of Kleefstra syndrome, as well as rigid flexion of the arms, legs, hands, and feet and slow motor functioning. Abnormal behaviors included impulsivity, poor speech, repetitive behaviors, restricted social interactions, apathy, and poor response to external stimuli. All were severely disabled. The 2 older patients showed signs of catatonia, and both had white matter abnormalities on brain imaging. All patients had a disturbed sleep-wake pattern. The findings were consistent with a neurodegenerative or regressive neurologic process.
Kleefstra et al. (2006) identified 2 heterozygous de novo mutations, a nonsense mutation and a frameshift mutation, in the EHMT1 gene in patients with a typical 9q- phenotype (607001.0001-607001.0002). Of the 5 patients they reported, Kleefstra et al. ... Kleefstra et al. (2006) identified 2 heterozygous de novo mutations, a nonsense mutation and a frameshift mutation, in the EHMT1 gene in patients with a typical 9q- phenotype (607001.0001-607001.0002). Of the 5 patients they reported, Kleefstra et al. (2006) remarked that the 2 with mutations were as severely affected as the 3 with deletions, and the patients with a typical 9q deletion were as severely affected as those described in the literature. In 6 of 24 patients with a clinical phenotype consistent with 9q deletion syndrome who had normal chromosome studies, Kleefstra et al. (2009) identified 6 different intragenic mutations in the EHMT1 gene (e.g., C1042Y, 607001.0003; R260X, 607001.0004). There were 2 nonsense mutations, a deletion, 2 splice site mutations, and 1 missense mutation in a highly conserved residue. A comparison of the phenotype between these 6 patients and 16 additional patients with larger deletions of 9q showed no genotype/phenotype correlations. Kleefstra et al. (2009) concluded that haploinsufficiency for EHMT1 is the basis for the phenotypic features in this disorder. Yatsenko et al. (2009) characterized genomic rearrangements in 28 unrelated patients with 9q34.3 subtelomeric deletions. Four distinct categories were delineated: terminal deletions, interstitial deletions, derivative chromosomes, and complex rearrangements. Each kind results in haploinsufficiency of the EHMT1 gene and a characteristic phenotype. Seven (25%) patients had de novo interstitial deletions, 7 (25%) were found with derivative chromosomes or complex rearrangements, and 14 (50%) had bona fide terminal deletions. Interspersed repetitive elements (including Alu, LINE, LTR, and STR) were frequently observed at the breakpoints. Repetitive elements may play an important role by providing substrates with a specific DNA secondary structure that stabilizes broken chromosomes or assist in either DNA double-strand break repair or repair of single double-strand DNA ends generated by collapsed forks. Sequence analysis of the breakpoint junctions suggested that subtelomeric deletions may be stabilized by both homologous and nonhomologous recombination mechanisms, through a telomere-capture event, de novo telomere synthesis, or multistep breakage-fusion-bridge cycles. Genetic Heterogeneity Among 4 of 9 EHMT1 mutation-negative patients with core phenotypic features of Kleefstra syndrome but with phenotypic heterogeneity, referred to as Kleefstra syndrome spectrum (KSS), Kleefstra et al. (2012) identified de novo mutations in 4 genes, MBD5 (611472), MLL3 (606833), SMARCB1 (601607), and NR1I3 (603881), that encode epigenetic regulators. Shared phenotypic features among these patients include intellectual disability and childhood hypotonia, present in all, and behavioral problems, synophrys, and midface hypoplasia, present in a majority. Otherwise the phenotypes were quite variable. Using Drosophila, Kleefstra et al. (2012) demonstrated that MBD5, MLL3, and NR1I3, cooperate with EHMT1; SMARCB1 was known to interact directly with MLL3.
Kleefstra syndrome is characterized by intellectual disability, childhood hypotonia, and distinctive facial features. A complex pattern of other findings can also be observed [Dawson et al 2002, Cormier-Daire et al 2003, Stewart et al 2004, Kleefstra et al 2005, Yatsenko et al 2005, Kleefstra et al 2006a, Kleefstra et al 2006b, Stewart & Kleefstra 2007, Kleefstra et al 2009, Yatsenko et al 2009]....
DiagnosisClinical Diagnosis Kleefstra syndrome is characterized by intellectual disability, childhood hypotonia, and distinctive facial features. A complex pattern of other findings can also be observed [Dawson et al 2002, Cormier-Daire et al 2003, Stewart et al 2004, Kleefstra et al 2005, Yatsenko et al 2005, Kleefstra et al 2006a, Kleefstra et al 2006b, Stewart & Kleefstra 2007, Kleefstra et al 2009, Yatsenko et al 2009].Features that should prompt consideration of this diagnosis include:Intellectual disability, usually moderate to severe and associated with severe speech delayDistinctive facial features Childhood hypotoniaMotor delayHeart defectsRenal/urologic defectsGenital defects (males)Severe infections (respiratory)Epilepsy/febrile seizuresAutistic-like features in childhood Extreme apathy or catatonic(-like) features postpubertally Structural brain abnormalitiesWhite matter abnormalitiesTestingCytogenetic testing. The 9q34.3 microdeletion cannot be identified by routine analysis of G-banded chromosomes or other conventional cytogenetic banding techniques. Molecular Genetic Testing Gene. EHMT1 is the only gene in which mutation is known to account for the majority of features in Kleefstra syndrome [Kleefstra et al 2006a, Kleefstra et al 2009].The two causes of Kleefstra syndrome: Microdeletion of 9q34.3, accounting for about 75% of Kleefstra syndrome. In 28 unrelated individuals with a 9q34.3 microdeletion, three distinct categories were identified [Yatsenko et al 2009]: 50% bona fide de novo terminal deletions25% interstitial deletions25% complex rearrangements or derivative chromosomes Intragenic EHMT1 mutation, accounting for about 25% of Kleefstra syndromeClinical testing Deletion/duplication analysis. The 9q34.3 microdeletion can be detected by any number of molecular methods that determine the copy number of sequences within the deleted region. Both whole-genome and targeted approaches can be applied (Table 1, footnote 2).Genomic approach. Because of the complex clinical presentation of Kleefstra syndrome, the majority of affected individuals are identified by a genome-wide screen for deletions/duplications. Array-based comparative genomic hybridization (aCGH) or aGH (array-based non-comparative genomic hybridization) using BAC, oligonucleotide, or SNP genotyping arrays can detect the deletion in a proband. The ability to size the deletion depends on the type of microarray used and the density of probes in the 9q34.3 region. EHMT1 targeted approach. Gene-targeted methods (e.g., fluorescence in situ hybridization [FISH], multiplex ligation-dependent probe amplification [MLPA]) can be used if the syndrome is suspected clinically or for confirming the deletion after genomic microarray analysis. Note: (1) Since 9q34.3 microdeletions could be interstitial or even intragenic, an extensive MLPA analysis comprising probes covering all EHMT1 exons is preferred. (2) FISH cannot size the deletion routinely. Most MLPA approaches can size intragenic deletions.Sequence analysis. Sequencing of the entire coding region of EHMT1 detects intragenic disease-causing mutations such as missense and frameshifts. Table 1. Summary of Molecular Genetic Testing Used in Kleefstra Syndrome View in own windowGene SymbolTest MethodMutations DetectedMutation Detection Frequency by Test Method 1Test AvailabilityEHMT1Deletion / duplication analysis 2 (genomic approach) Deletion of 9q34.3 (de novo terminal deletions, complex rearrangements or derivative chromosomes, interstitial deletion) ~75%ClinicalDeletion / duplication analysis 2 (EHMT1 targeted approach)Intragenic EHMT1 deletions and smaller contiguous gene deletions involving EHMT1Sequence analysisSequence variants 3~25% 1. The ability of the test method used to detect a mutation that is present in the indicated gene2. Testing that identifies deletions/duplications not readily detectable by sequence analysis of genomic DNA; a variety of methods including quantitative PCR, long-range PCR, multiplex ligation-dependent probe amplification (MLPA), or targeted array GH (gene/segment-specific) may be used. A full array GH analysis that detects deletions/duplications across the genome may also include this gene/segment. 3. Examples of mutations detected by sequence analysis may include small intragenic deletions/insertions and missense, nonsense, and splice site mutations.Interpretation of test resultsDeletion analysis. Depending on the initial test that identifies the 9q34.3 microdeletion, validation of the deletion by an independent method may be warranted. Note: If high-density genomic microarray platforms have been used for the identification of the microdeletion, validation of the deletion may not be necessary, as it is unlikely that more than 50-100 adjacent targets show an abnormal copy number by chance.Sequence analysis. For issues to consider in interpretation of sequence analysis results, click here.Testing Strategy To establish the diagnosis in a proband requires detection of a 9q34.3 microdeletion with involvement of at least part of EHMT1 or detection of an intragenic EHMT1 mutation. Most microdeletions are detected by genomic microarray analysis performed as part of the evaluation of developmental delay or intellectual disability.If Kleefstra syndrome is suspected based on the clinical features, a targeted technique to identify an EHMT1 microdeletion (e.g., FISH or MLPA) can be employed. If a deletion is not found by either of the above two test methods, EHMT1 sequence analysis is recommended.Note: The 9q34.3 microdeletion cannot be identified by routine chromosome analysis.Prenatal diagnosis and preimplantation genetic diagnosis (PGD) for at-risk pregnancies require prior identification of the 9q34.3 microdeletion or EHMT1 mutation in the proband and/or of balanced carrier status in a parent. Genetically Related (Allelic) Disorders No other phenotypes are known to be associated with deletion (copy number variation [CNV]) in the genes located within the 9q34.3 critical region or with mutations in EHMT1.
Kleefstra syndrome has a clinically recognizable phenotype that includes physical, developmental, and behavioral features. Males and females are affected equally [Stewart et al 2004, Yatsenko et al 2005, Kleefstra et al 2006b, Stewart & Kleefstra 2007, Kleefstra et al 2009]. ...
Natural HistoryKleefstra syndrome has a clinically recognizable phenotype that includes physical, developmental, and behavioral features. Males and females are affected equally [Stewart et al 2004, Yatsenko et al 2005, Kleefstra et al 2006b, Stewart & Kleefstra 2007, Kleefstra et al 2009]. Birth weight is usually within the normal or above normal range whereas in childhood weight increases leading to obesity (50%) [Cormier-Daire et al 2003, Kleefstra et al 2009]. The facial appearance is characterized by a brachy(-micro)cephaly, broad forehead, synophrys, unusual shape of eyebrows (arched or straight), mildly upslanting palpebral fissures, midfacial hypoplasia, thickened ear helices, short nose with anteverted nares, fleshy everted lower lip and cupid bowed upper lip or "tented" appearance of mouth, and protruding tongue and relative prognathia (Figure 1, Figure 2). FigureFigure 1. Photographs of patients showing the characteristic facial profile comprising brachycephaly, hypertelorism, synophrys/arched eyebrows, midface hypoplasia, protruding tongue, eversion of lower lip, and prognathism of chin. Five patients (AB), (more...)FigureFigure 2. Photographs of patients showing the characteristic facial profile comprising brachycephaly, hypertelorism, synophrys/arched eyebrows, midface hypoplasia, protruding tongue, eversion of lower lip, and prognathism of chin. Three different patients (more...)With age, the facial appearance becomes coarser, with persisting midfacial hypoplasia and prognathism. An increased frequency of dental anomalies, specifically neonatal teeth and retention of primary dentition, has been observed.Individuals with Kleefstra syndrome exhibit a range of cognitive and adaptive functioning, with the majority of individuals functioning in the moderate to severe spectrum of intellectual disability, although few individuals with only mild delay and total IQ (TIQ) around 70 are known. Most affected individuals have severe expressive speech delay with hardly any speech development, whereas general language development is usually at a higher level making sign languages or use of pictograms valuable to many affected individuals.Motor development is impaired by childhood hypotonia, but almost all individuals achieve independent walking after age two to three years.In a significant number of individuals with Kleefstra syndrome, congenital defects are observed. In 50% of individuals a (conotruncal) heart defect is present. Abnormalities that have been reported are ASD/VSD, tetralogy of Fallot, aortic coarctation, bicuspid aortic valve, and pulmonic stenosis. In a number of individuals atrial flutter has been reported. Renal defects are seen in 10%-30% of cases and comprise vesico-ureteral reflux (VUR), hydronephrosis, renal cysts, and chronic renal insufficiency. Genital defects such as hypospadias, cryptorchidism, and small penis are reported in 30% of males Several affected individuals have had talipes equinovarus. Other abnormalities that have been observed are epigastric hernia, tracheo-/bronchomalacia with respiratory insufficiency, and gastroesophageal reflux. Seizures reported in 30% can include tonic-clonic seizures, absence seizures, and complex partial epilepsy.Besides issues with social behavior, the behavioral phenotype includes sleep disturbances, stereotypies, mild self-injurious behaviors, and autism spectrum disorder usually recognized in early childhood. A few reports of adolescents and adults revealed progressive extreme apathy and catatonic (-like) behavior [Verhoeven et al 2010]. Sleep disturbance is characterized by frequent nocturnal and early morning awakenings as well as excessive daytime awakening – in contrast to the sleep disturbance observed in Smith Magenis syndrome. Longitudinal data are insufficient to determine life expectancy; however, it should be noted that death in infancy or childhood can occur from complications such as heart defects and recurrent aspiration and pulmonary infections [Stewart & Kleefstra 2007].
Data collected so far indicate that individuals with an intragenic EHMT1 mutation (e.g., missense, nonsense) and those with a 9q34.3 microdeletion have similar clinical findings; however, the pulmonary infections and aspiration difficulties appear to be more severe in individuals with larger 9q34 deletions (≥3 Mb) than in those with smaller deletions or EHMT1 defects only. ...
Genotype-Phenotype Correlations Data collected so far indicate that individuals with an intragenic EHMT1 mutation (e.g., missense, nonsense) and those with a 9q34.3 microdeletion have similar clinical findings; however, the pulmonary infections and aspiration difficulties appear to be more severe in individuals with larger 9q34 deletions (≥3 Mb) than in those with smaller deletions or EHMT1 defects only.
Disorders in the differential diagnosis of Kleefstra syndrome:...
Differential DiagnosisDisorders in the differential diagnosis of Kleefstra syndrome:Down syndromeSmith-Magenis syndrome (SMS)Pitt-Hopkins syndrome Rett syndrome (see MECP2-related disorders)2q37 deletion syndrome
To establish the extent of disease and needs of an individual diagnosed with the Kleefstra syndrome, the following evaluations are recommended following the initial diagnosis:...
ManagementEvaluations Following Initial Diagnosis To establish the extent of disease and needs of an individual diagnosed with the Kleefstra syndrome, the following evaluations are recommended following the initial diagnosis:Complete review of systems Physical and neurologic examinationRenal ultrasound examination to evaluate for possible renal/urologic anomaliesEchocardiogram and ECG to evaluate for possible structural cardiac anomalies and atrial rhythm defects; follow-up depending on the severity of any cardiac anomaly identifiedSpeech/language evaluation including audiologic examinationAssessment for signs and symptoms of gastroesophageal reflux (GER)Physical and/or occupational therapy assessmentSleep history EEG if seizures are suspectedNeuroimaging (MRI) especially in the presence of findings such as seizures and/or movement disorder, extreme apathy/catatonia and/or regression in psychomotor development Treatment of ManifestationsThe following are indicated:Ongoing routine pediatric care by a pediatrician or neurologist, psychiatrist and/or (for adults) specialist in the care of adults with intellectual disability Depending on the age of the affected individual, referral to an early childhood intervention program, ongoing special education programs, and/or vocational training Speech/language therapy, physical and occupational therapy, and sensory integration therapySpecialized neurologic and psychiatric care for individuals with extreme behavior problems and/or movement disorder. Behavioral therapies include special education techniques that may help minimize behavioral outbursts in the school setting by emphasizing individualized instruction, structure, and a set daily routine. Therapeutic management of the sleep disorder. No well-controlled treatment trials have been reportedSpecialized neurologic care for individuals with epilepsy; management of seizures in accordance with standard practiceStandard treatment for cardiac, renal, urologic, and other medical issuesAuditory amplification if hearing loss is identifiedSurveillanceCardiac and renal/urologic abnormalities should be monitored as needed.Evaluation of Relatives at RiskSee Genetic Counseling for issues related to testing of at-risk relatives for genetic counseling purposes.Therapies Under InvestigationSearch ClinicalTrials.gov for access to information on clinical studies for a wide range of diseases and conditions. Note: There may not be clinical trials for this disorder.
Information in the Molecular Genetics and OMIM tables may differ from that elsewhere in the GeneReview: tables may contain more recent information. —ED....
Molecular GeneticsInformation in the Molecular Genetics and OMIM tables may differ from that elsewhere in the GeneReview: tables may contain more recent information. —ED.Table A. Kleefstra Syndrome: Genes and DatabasesView in own windowGene SymbolChromosomal LocusProtein NameLocus SpecificHGMDEHMT19q34.3Histone-lysine N-methyltransferase, H3 lysine-9 specific 5EHMT1 homepage - Mendelian genesEHMT1Data are compiled from the following standard references: gene symbol from HGNC; chromosomal locus, locus name, critical region, complementation group from OMIM; protein name from UniProt. For a description of databases (Locus Specific, HGMD) to which links are provided, click here.Table B. OMIM Entries for Kleefstra Syndrome (View All in OMIM) View in own window 607001EUCHROMATIC HISTONE METHYLTRANSFERASE 1; EHMT1 610253KLEEFSTRA SYNDROMENormal allelic variants. The previously defined EHMT1 transcript (NM_024757.3) contained 26 exons, the translation start site being located in exon 2. The 'updated' NM_024757.4 version varies significantly, and contains an extra 5' exon. The novel open reading frame comprises 27 coding exons. The translation start site is located in the "novel" exon 1, 97.6 kb proximal to the ‘old’ ATG start codon. Diagnostic testing so far has been directed towards the 25 coding exons of the EHMT1 NM_024757.3 sequence. Since three individuals with Kleefstra syndrome harbor interstitial 9q microdeletions encompassing only this novel EHMT1 sequence in addition to several proximally located genes [Author, personal observation], routine diagnostic testing should be adjusted to the novel transcript.All normal variants reported to date are listed in Table 2 [Kleefstra et al 2006a]. Note: The nomenclature has been adjusted for the ‘updated’ NM_024757.4 sequence.Pathologic allelic variants. EHMT1 sequence variants include nonsense, splice site, and missense mutations. All intragenic EHMT1 mutations reported to date are listed in Table 2 [Kleefstra et al 2006a, Kleefstra et al 2009]. Note: The nomenclature has been adjusted for the ‘updated’ NM_024757.4 sequence.Table 2. Selected EHMT1 Allelic VariantsView in own windowClass of Variant AlleleDNA Nucleotide ChangeProtein Amino Acid Change 1Reference SequencesNormalc.444T>Cp.=NM_024757.4 NP_079033.4c.1044G>Ap.=c.1089T>Cp.=c.1368C>Tp.=c.1806G>Ap.=Pathologicc.871C>Tp.Arg291* c.1413_1425delp.Pro473fsc.1533_1536delp.Asp512fsc.1810C>Tp.Gln604*c.1858C>Tp.Arg620*c.2029insGp.Pro677fsc.2193-1G>Cp.?c.2863_2864delp.Val955fsc.2868-1G>Ap.?c.2878_2881p.Ser929fsc.3181-80_3233delp.Tyr1061fsc.3180+1G>Tp.?c.3229C>Tp.Gln1077*c.3218G>Ap.Cys1073Tyr c.3502C>Tp.Arg1168* c.3589C>Tp.Arg1197TrpSee Quick Reference for an explanation of nomenclature. GeneReviews follows the standard naming conventions of the Human Genome Variation Society (www.hgvs.org). 1. p.= designates that protein has not been analyzed, but no change is expected. p.? designates that protein has not been analyzed; an effect is expected but difficult to predict.Normal gene product. The NM_024757.4 transcript encodes a protein of 1298 amino acid residues. EHMT1 encodes euchromatin histone-lysine N-methyl transferase 1, a protein involved in histone methylation. DNA is wrapped around histones, and histone tails have an important role in folding of chromatin fibers. Methylation of these histone tails is thought to regulate this folding process, hereby altering the accessibility of DNA to proteins mediating transcription [Martin & Zhang 2005]. The restricted expression of EHMT1 in the mouse brain (olfactory bulb, the anterior/ventral ventricular wall, hippocampus, and piriform cortex) supports a role of epigenetic histone modification in normal brain development [Kleefstra et al 2005].Abnormal gene product. Haploinsufficiency resulting from deletion or inactivation of one EHMT1 allele is the cause of Kleefstra syndrome. The majority of mutations that have been described disrupt the open reading frame of EHMT1 and are predicted to lead to nonsense-mediated decay (NMD). The one missense change described to date is predicted to have an influence on the local conformation of the pre-SET domain of the EHMT1 protein, thereby reflecting a null allele [Kleefstra et al 2009]. Besides EHMT1, other genes associated with intellectual disability (e.g., MECP2, RSK2, and XNP) appear to play a role in chromatin remodeling [Ausio et al 2003]. Loss of proper regulation of chromatin structure can result in deregulation of gene transcription and inappropriate protein expression. This can in turn contribute to complex genetic disorders including intellectual disability.