Identification and characterization of two novel JARID1C mutations: suggestion of an emerging genotype�Cphenotype correlation

Mental retardation (MR) is characterized by cognitive impairment with an IQ <70. Many of the major causes are genetically determined and the ∼30% male excess suggests that mutations in genes carried on the X chromosome are disproportionably represented. One such gene, jumonji AT-rich interactive domain 1C (JARID1C) on Xp11.2, has been identified in families with X-linked MR (XLMR), with 18 different mutations reported to date. As part of a systematic resequencing of 720 genes in 208 XLMR families of the International Genetic of Learning Disability (IGOLD) consortium, two novel nucleotide changes in the JARID1C coding region were identified, with the nucleotide changes segregating with the disease phenotype in the two families. The first mutation is a single-nucleotide insertion in exon 21 (c.3258_3259insC p.K1087fs^*43) causing a frameshift and resulting in a premature termination codon (PTC). Such PTC-containing mRNAs are generally degraded by nonsense-mediated mRNA decay (NMD) surveillance, but our results show that this is not the case with this mutation. The other change is a single-nucleotide substitution in exon 12 (c.1160C>A) in a published family with nonsyndromic MR, MRX13. This change occurs in a highly conserved amino acid, with proline (P) being substituted by threonine (T) (p.P544T). Functional analysis shows that this amino-acid substitution compromises both tri- and didemethylase activity of the JARID1C protein. We conclude that the two novel changes impair JARID1C protein function and are disease-causing mutations in these families.     

X-linked mental retardation, short stature, microcephaly and hypogonadism maps to Xp22.1-p21.3 in a Belgian family

X-linked mental retardation (XLMR) is a heterogeneous disorder that can be classified as either non-specific (MRX), when mental retardation is the only feature, or as syndromic mental retardation (MRXS). Genetic defects underlying XLMR are being identified at a rapid pace, often starting from X-chromosomal aberrations and XLMR families with a well-defined linkage interval. Here, we present a new family with a syndromic form of XLMR, including mild mental retardation, short stature, microcephaly and hypogonadism. Two-point linkage analysis with 24 polymorphic markers spanning the entire X chromosome was carried out. We could assign the causative gene to a 6 cM interval in Xp22.1-p21.3, with a maximum LOD score of 2.61 for markers DXS989 and DXS1061 at theta = 0.00. No mutations were found in the presented family for two known MRX genes mapping to this interval, ARX and IL1RAPL-1. These data indicate that the interval Xp22.1-p21.3 contains at least one additional MRXS gene.     

X-linked mental retardation: further lumping, splitting and emerging phenotypes

X-linked mental retardation (XLMR) is a very heterogeneous condition, subdivided in two categories mainly based on clinical features: syndromic XLMR (MRXS) and non-syndromic XLMR (MRX). Although it was thought that 20-25% of mental retardation (MR) in males was caused by monogenetic X-linked factors, recent estimations are lower: in the range of 10-12%. The number of identified genes involved in XLMR has been rapidly growing in the past years. Subsequently, an increasing number of patients and families have been reported in which mutations in XLMR genes have been identified. It was observed previously, that mutations in several of XLMR genes can result in syndromic and in non-syndromic phenotypes. This observation has been confirmed for the more recently identified genes. Therefore, in this review, focus has been given on the clinical data and on phenotype-genotype correlations for those genes implicated in both non-syndromic and syndromic XLMR.     

Familial cases and male cases with MECP2 mutations

This is the first report of Chinese familial cases with Rett syndrome (RTT) or X‐linked mental retardation (XLMR). RTT is a neurodevelopmental disorder that almost exclusively affects females. Most RTT cases are sporadic. We have studied eight cases with MECP2 mutations in six Chinese families, including three females and five males with RTT or XLMR. All shared identical MECP2 mutations with their mothers. The three females fulfilled the diagnostic criteria for RTT, while the five males were XLMR. A random X‐chromosome inactive (XCI) pattern was seen in all the three female patients and two mothers while a skewed XCI in the rest four mothers. The clinical manifestations and pathogenic gene spectrum between male and female patients were different. The different MECP2 mutations and different XCI pattern may be the determinants of the phenotypic heterogeneity between the family members.     

Localization of MRX82: a new nonsyndromic X-linked mental retardation locus to Xq24-q25 in a Basque family

Clinical and molecular studies are reported on a Basque family (MRX82) with nonsyndromic X-linked mental retardation (XLMR) in five affected males. A total of 38 microsatellite markers were typed. The XLMR locus has been linked to DXS8067, DXS1001, DXS425, DXS7877, and DXS1183 with a maximum LOD score of 2.4. The haplotype studies and multipoint linkage analysis suggest a localization of the MRX82 locus to an interval of 7.6 Mb defined by markers DXS6805 and DXS7346, in Xq24 and Xq25, respectively. No gene contained in this interval has been so far associated with nonsyndromic mental retardation, except for GRIA3, disrupted by a balanced translocation in a female patient with bipolar affective disorder and mental retardation. However, the search for mutations of this gene did not showed a pathogenic mutation in the present family. Given that there are other eight MRX families overlapping this interval, none of them with known mutation, we conclude that at least one new gene responsible for nonsyndromic mental retardation is located in this region.     

Mutation frequencies of X-linked mental retardation genes in families from the EuroMRX consortium

The EuroMRX family cohort consists of about 400 families with non-syndromic and 200 families with syndromic X-linked mental retardation (XLMR). After exclusion of Fragile X (Fra X) syndrome, probands from these families were tested for mutations in the coding sequence of 90 known and candidate XLMR genes. In total, 73 causative mutations were identified in 21 genes. For 42% of the families with obligate female carriers, the mental retardation phenotype could be explained by a mutation. There was no difference between families with (lod score >2) or without (lod score <2) significant linkage to the X chromosome. For families with two to five affected brothers (brother pair=BP families) only 17% of the MR could be explained. This is significantly lower (P=0.0067) than in families with obligate carrier females and indicates that the MR in about 40% (17/42) of the BP families is due to a single genetic defect on the X chromosome. The mutation frequency of XLMR genes in BP families is lower than can be expected on basis of the male to female ratio of patients with MR or observed recurrence risks. This might be explained by genetic risk factors on the X chromosome, resulting in a more complex etiology in a substantial portion of XLMR patients. The EuroMRX effort is the first attempt to unravel the molecular basis of cognitive dysfunction by large-scale approaches in a large patient cohort. Our results show that it is now possible to identify 42% of the genetic defects in non-syndromic and syndromic XLMR families with obligate female carriers.     

Characterization of novel isoforms and evaluation of <Emphasis Type="Italic">SNF2L/SMARCA1</Emphasis> as a candidate gene for X-linked mental retardation in 12 families linked to Xq25-26

Background  

Mutations in genes whose products modify chromatin structure have been recognized as a cause of X-linked mental retardation (XLMR). These genes encode proteins that regulate DNA methylation (MeCP2), modify histones (RSK2 and JARID1C), and remodel nucleosomes through ATP hydrolysis (ATRX). Thus, genes encoding other chromatin modifying proteins should also be considered as disease candidate genes. In this work, we have characterized the SNF2L gene, encoding an ATP-dependent chromatin remodeling protein of the ISWI family, and sequenced the gene in patients from 12 XLMR families linked to Xq25-26.     

Mutational screening of <Emphasis Type="Italic">ARX</Emphasis> gene in Brazilian males with mental retardation of unknown etiology

ARX gene mutations have been known as important causes of developmental and neurological disorders and are responsible for a large spectrum of abnormal phenotypes, includeing syndromic as well as nonsyndromic forms of mental retardation. We have screened the entire coding and flanking intronic sequences of ARX gene in 143 mentally impaired males in order to investigate the contribution of ARX mutations to mental retardation in the population of Rio de Janeiro, Brazil. Three sequence variants were identified: one patient had the most recurrent mutation already observed in ARX gene, the c.428_451dup(24 bp), two patients presented the c.1347C>T (p.G449G) in exon 4, and one patient had the intronic variant c.1074-3T>C. Although two of these alterations were considered polymorphisms, the known pathogenic variant c.428_451dup(24 bp) was found at a high rate (4.8%) among X-linked mental retardation (XLMR) families. Our results, the first in Latin America, reinforce the idea that ARX mutations are relevant to mental retardation and are indicative that molecular screening of exon 2 should be considered in males with mental retardation of unknown etiology, associated or not with neurological manifestations, especially in familial cases.     

Psychometric assessment of families with X-linked mental retardation

As part of an integrated approach to DNA-linkage analysis in X-linked mental retardation (XLMR), 29 members of five families suspected of having XLMR underwent psychometric assessment. Mental retardation was confirmed in all participants. The range of mental retardation varied from mild to profound within and between families. In addition, these preliminary results indicated family-specific cognitive profiles in MRX45 and MRX46. The fact that two non-overlapping loci were involved provides strong evidence that specific cognitive profiles are linked to specific loci (genes) in mental retardation. We therefore recommend the application of standardised psychometric tests for the assessment of XLMR.     

A new X linked recessive syndrome of mental retardation and mild dysmorphism maps to Xq28.

Efforts to understand the genetic basis of mental retardation are greatly assisted by the identification of families with multiple relatives with mental retardation that clinical geneticists encounter in the routine practice of their profession. Here we describe a linkage study of a four generation family in which X linked recessive mental retardation (XLMR) is associated with minor dysmorphism and premature death of the affected males. Microsatellite based polymorphic loci evenly spaced over the entire X chromosome were used initially to detect linkage to Xq28. Further analysis identified a haplotype of Xq28 markers bounded proximally by locus DXS1113 and distally by DXS1108 that cosegregated with XLMR in this family. Two point lod scores > 3.0 provided strong evidence that the gene locus responsible for XLMR in this family is within this 7 Mb region of Xq28. The minor anomalies noted in some affected males were not distinctive enough to suggest a unique syndrome. None of our patients had features of the Waisman-Laxova syndrome or the PPM-X syndrome. The possibility of allelism with any of the five other non-specific XLMR syndromes (MRX3, MRX16, MRX25, MRX28, and MRX41) mapped to Xq28 could not be excluded. While the recognition of a gene responsible for this disorder needs much additional work, multiple female relatives at risk in this family benefit immediately from knowing their genotype and heterozygotes will have the opportunity to undergo prenatal diagnosis.     

NDP gene mutations in 14 French families with Norrie disease

Norrie disease is a rare X-inked recessive condition characterized by congenital blindness and occasionally deafness and mental retardation in males. This disease has been ascribed to mutations in the NDP gene on chromosome Xp11.1. Previous investigations of the NDP gene have identified largely sixty disease-causing sequence variants. Here, we report on ten different NDP gene allelic variants in fourteen of a series of 21 families fulfilling inclusion criteria. Two alterations were intragenic deletions and eight were nucleotide substitutions or splicing variants, six of them being hitherto unreported, namely c.112C>T (p.Arg38Cys), c.129C>G (p.His43Gln), c.133G>A (p.Val45Met), c.268C>T (p.Arg90Cys), c.382T>C (p.Cys128Arg), c.23479-1G>C (unknown). No NDP gene sequence variant was found in seven of the 21 families. This observation raises the issue of misdiagnosis, phenocopies, or existence of other X-linked or autosomal genes, the mutations of which would mimic the Norrie disease phenotype.     

Monogenic X-linked mental retardation: is it as frequent as currently estimated? The paradox of the ARX (Aristaless X) mutations

Mental retardation affects 30 to 50% more males than females, and X-linked mental retardation (XLMR) is thought to account for the major part of this sex bias. Nonsyndromic XLMR is very heterogeneous, with more than 15 genes identified to date, each of them accounting for a very small proportion of nonsyndromic families. The Aristaless X (ARX) gene is an exception since it was found mutated in 11 of 136 such families, with a highly recurrent mutation (dup24) leading to an expansion of a polyalanine tract in the protein. The rather high frequency of dup24 reported in families with clear X-linked MR (6.6%) contrasts with the very low prevalence of this mutation observed in sporadic male MR (0.13%). We conclude that monogenic XLMR has much lower prevalence in male MR (< 10%) than the 23% that would be required to account for a 30% male excess of mental retardation.     

The ARX mutations: a frequent cause of X-linked mental retardation

The ARX gene mutations have been demonstrated to cause different forms of mental retardation (MR). Beside FMR1, in families with X-linked mental retardation (XLMR), the ARX dysfunction was demonstrated to be among the most frequent causes of this heterogeneous group of disorders. Nevertheless, in sporadic cases of MR, ARX mutations are extremely rare. In order to evaluate the frequency of ARX mutation in XLMR, we performed mutational analysis of ARX in 165 mentally retarded probands negative for FRAXA and belonging to families in which the condition segregates as an X-linked condition. The same recurrent mutation, an in frame 24 bp insertion (c.428-451 dup (24 bp)), was identified in five patients. In one family, the mother of two affected boys was found not to carry the mutation detected in her sons. These data suggest the presence of germline mosaicism for the mutation in the mother. Our results confirm the significant contribution of ARX mutations in the etiology of MR, especially in this group of patients selected for XLMR (3%). These data, together with those reported in the literature, imply that screening for c.428-451 dup (24 bp) mutation should be recommended in all patients with suspected XLMR.     

XLMR genes: update 1998

Since the Seventh Fragile X and XLMR Mental Retardation (XLMR) Workshop in 1995, the genes for Coffin-Lowry, Mohr-Tranebjaerg, and Opitz G/BBB syndromes have been cloned. Jensen syndrome has been found to be allelic to Mohr-Tranebjaerg. Twenty new XLMR syndromes and metabolic or neuromuscular disorders have been reported. Twenty-four new localizations have been established, including five in previously reported conditions (FG, Carpenter, Arts, OPA2, and OFD1). The number of families with nonspecific XLMR that have been reported has continued to increase; 58 families or loci are now known. Eighteen new families with nonspecific mental retardation (MRX) have been reported. Two of them, however, were subsequently found to have mutations in the RABGDIA gene, which codes for a GDP-dissociation inhibitor for RAB proteins. In total, 41 more entries have been added to the X chromosome map of XLMR. The total number of known syndromes and MRX families has increased to 178. Of the 120 known XLMR disorders, 53 have been mapped, and 22 have been cloned. Assuming that at least 10 loci are necessary to account for the 58 families with MRX, the total number of XLMR loci counted so far would be 130. Although it is likely that many of the disorders will eventually prove to be allelic, it is not possible at present to determine the precise number of loci for nonspecific XLMR.     

X‐chromosome duplications in males with mental retardation: pathogenic or benign variants?

Gijsbers ACJ, den Hollander NS, Helderman‐van de Enden ATJM, Schuurs‐Hoeijmakers JHM, Vijfhuizen L, Bijlsma EK, van Haeringen A, Hansson KBM, Bakker E, Breuning MH, Ruivenkamp CAL. X‐chromosome duplications in males with mental retardation: pathogenic or benign variants? Studies to identify copy number variants (CNVs) on the X‐chromosome have revealed novel genes important in the causation of X‐linked mental retardation (XLMR). Still, for many CNVs it is unclear whether they are associated with disease or are benign variants. We describe six different CNVs on the X‐chromosome in five male patients with mental retardation that were identified by conventional karyotyping and single nucleotide polymorphism array analysis. One deletion and five duplications ranging in size from 325 kb to 12.5 Mb were observed. Five CNVs were maternally inherited and one occurred de novo. We discuss the involvement of potential candidate genes and focus on the complexity of X‐chromosomal duplications in males inherited from healthy mothers with different X‐inactivation patterns. Based on size and/or the presence of XLMR genes we were able to classify CNVs as pathogenic in two patients. However, it remains difficult to decide if the CNVs in the other three patients are pathogenic or benign.     

Splitting and lumping in the nosology of XLMR.

Although it is assumed that genes that influence cognitive function are ubiquitous in the human genome, to date, more such genes have been found on the X chromosome than on any other comparable segment of the autosomes. This is in large measure because of the power of hemizygosity in exposing mutations of X-linked genes in males. Clinical manifestations, mapping of gene loci by linkage analysis or chromosome rearrangements, and gene identification by positional cloning or mutational analysis of candidate genes have permitted extensive lumping and splitting within the large and heterogeneous category of X-linked mental retardation (XLMR). Approximately 130 XLMR syndromes have been identified, 25 gene loci have been mapped and cloned, and 55 other loci have been mapped but not cloned. Well-recognized syndromes (e.g., Fragile X and Coffin-Lowry syndromes) and syndromes represented by only a single family (e.g., Arena and monoamine oxidase-A syndromes) are among these more or less well-defined entities. In addition, more than 75 families with nonsyndromal XLMR have been regionally mapped and 7 causative genes have been identified.