Molecular and cytogenetic analysis of familial Xp deletions

Five families in which an Xp deletion is segregating and two families in which an X chromosome rearrangement including a deletion of the short arm is segregating were ascertained for study. Normal fertility was seen in all families. Members from 5 of the 7 families manifested short stature (height <5th centile), while normal height was present in two families. Studies of both the FMR-1 and the androgen receptor loci using PCR based X-inactivation analysis demonstrated that in all families analyzed, there is preferential inactivation of one X chromosome. Molecular cytogenetic analysis showed that members of 3 of the 7 families share a common breakpoint in an approximate 2-3 Mb region at Xp22.12, suggesting a possible hotspot for chromatin breakage. Previous genotype-phenotype correlations and deletion mapping have indicated that a gene for stature resides within the pseudoautosomal region in Xp22.33. Our findings indicate that the loss of this region is not always associated with short stature, suggesting that other factors may be involved.     

Two cases of steroid sulfatase deficiency with complex phenotype due to contiguous gene deletions

We report contiguous gene deletions in the distal short arm of the X chromosome in two patients with ichthyosis, due to steroid sulfatase deficiency, and other complex phenotypes. One patient had chondrodysplasia punctata (CDP) and ichthyosis with a normal chromosome constitution. Another patient had a CDP-like phenotype, ichthyosis, and hypogonadism. His karyotype was 46, -X,Y, +der(X)t(X;Y)(p22;q11). DNA from the two patients was analyzed by Southern blotting using cloned fragments mapped in the Xp21-Xpter region to investigate gene deletions. DNA from the patient with CDP showed a gene deletion of the STS, DXS31, and DXS89 loci, and DNA from the patient with X-Y translocation lacked fragments of the STS, DXS31, DXS89, and DXS143 loci. These findings suggest that the common deleted region involving the STS locus might have caused the similar phenotypes in both patients.     

Normal intelligence and social interactions in a male patient despite the deletion of NLGN4X and the VCX genes

Xp22.3 deletion in males can be associated with short stature (SHOX), chondrodysplasia punctata (ARSE), mental retardation (MRX49 locus), ichthyosis (STS), Kallmann syndrome (KAL1) and ocular albinism (OA1), according to the size of the deletion. Studies of terminal and interstitial deletions in male patients with a partial nullisomy of the X chromosome have led to the identification of the VCX-3A gene at the MRX49 locus on Xp22.3. The NLGN4X gene has then been identified less than 350 kb away from VCX-3A. Nonsense mutations in NLGN4X have been associated with autism and/or moderate mental retardation in males. We report a 17-year old male patient presenting with severe ichthyosis and Kallmann syndrome related to a 3.7 Mb interstitial Xp22.3 deletion, encompassing STS and KAL1 genes, respectively. However, despite the deletion of NLGN4X and all VCX genes, including VCX-3A, our patient did not manifest any learning disabilities or behavioural problems. Therefore, our case argues against a major role of NLGN4X and the VCX genes alone in cognitive development and/or communication processes.     

Duchenne muscular dystrophy with adrenal insufficiency and glycerol kinase deficiency: high resolution cytogenetic analysis with molecular, biochemical, and clinical studies.

A syndrome of Duchenne muscular dystrophy (DMD), adrenal hypoplasia, glycerol kinase deficiency, and mental retardation has been recognised. We report a further case ascertained from a history of DMD, severe mental retardation, and an Addison-like disorder. Cytogenetic analysis of the proband revealed an interstitial deletion of the short arm of the X chromosome. from Xp21.1 to Xp22.11, comprising about 9% of the length of the normal X chromosome. His mother was heterozygous for the deletion, but his maternal grandmother and sister both had two normal X chromosomes. DNA probe analysis confirmed the existence of a deletion in the affected boy, as probes 754, C7, XJ1-1, and pERT87 consistently failed to hybridize to his DNA. His sister was heterozygous for the RFLP associated with 754, thus confirming that she had two normal X chromosomes. There was no evidence of chronic granulomatous disease, other immunological defect, or retinitis pigmentosa in this case. Biochemical studies revealed gross glyceroluria and hyperglycerolaemia, indicating glycerol kinase deficiency which has been confirmed enzymatically. We have subsequently screened 21 other boys with DMD for glyceroluria and found one other case. Cytogenetic analysis has also been performed in nine other families, where a boy with DMD has been shown to have a deletion of DNA sequences localised to the region Xp21. None of these cases demonstrated any cytogenetic abnormality, nor has their clinical course been unusual.     

Partial Xp11.23-p11.4 duplication with random X inactivation: clinical report and molecular cytogenetic characterization

Partial duplications of the short arm of the X chromosome are relatively rare and have been described in males and females. We describe a 4 10/12-year-old girl presenting with developmental delay, severe language retardation and minor anomalies with slightly elevated head circumference (+1.8 SD), prominent forehead, wide palpebral fissures and anteverted nares. No pigmentary dysplasia of the skin was present. The external genitalia were normal. The karyotype completed by cytogenetic analysis with the Whole Chromosome Painting probe of chromosome X revealed a de novo partial duplication of the short arm of an X chromosome. In order to further characterize the duplicated segment, we used a series of BAC probes extending from band Xp11.22 to Xp22.1. BACs from Xp11.23 to Xp11.4 were duplicated. The karyotype was finally defined as 46,X,dup(X)(p11p11).ish dup(X)(p11.23p11.4)(WCPX+,RP11-416I6++,RP11-386N14++,RP11-466C12++). The X-inactivation status was studied using the human androgen receptor (HUMARA) and the FRAXA locus methylation assay. Unexpectedly, the two X chromosomes were found to be randomly inactivated, in the proband. Indeed, usually, in women with structurally abnormal X chromosome, the abnormal X chromosome is preferentially inactivated and those patients share an apparent normal phenotype. So, we speculate that in the present case, the phenotype of the patient could be explained by a functional disomy of the genes present in the duplicated region. We will discuss the possible implication of these genes on the observed phenotype.     

Mental retardation locus in Xp21 chromosome microdeletion

Xp21 microdeletion syndrome is associated with variable size Xp21 deletions that usually include the glycerol kinase locus. The clinical phenotypes we studied in this chromosome region include: Xpter – Åland Island eye disease (AIED) -adrenal hypoplasia (AH) -glycerol kinase (GKD) -Duchenne muscular dystrophy (DMD) -retinitis pigmentosa (RP) -ornithine transcarbamylase (OTC) -centromere. In a compilation of 18 individuals in 14 families with the AH, GKD, and DMD loci deleted, 17 were male and all were developmentally delayed. In contrast, we report mentally retarded female carriers in two Xp21 deletion syndrome families with DMD, GKD, and AH in affected males. In the first family with normal karyotypes, a submicroscopic deletion was associated with DMD in the retarded male and with retardation in carrier females. In the second family an X chromosome with a cytogenetically deleted Xp21 distal to the OTC and RP genes segregated in the affected male and retarded female carriers. DNA analysis at the DMD locus verified the cytogenetic findings. This report of mental retardation in otherwise asymptomatic female carriers of Xp21 deletion classifies one form of mental retardation in females. © 1993 Wiley-Liss, Inc.     

Genetic linkage between Becker muscular dystrophy and a polymorphic DNA sequence on the short arm of the X chromosome.

A study of DNA restriction fragment polymorphisms and Becker muscular dystrophy has shown eight families informative for the cloned sequence L1.28, which is located on the short arm of the X chromosome between Xp110 and Xp113. Analysis of these families reveals linkage between the two loci, with the maximum likelihood estimate of the genetic distance being 16 centiMorgans (95% confidence limits between 7 and 32 centiMorgans). Since a study of DNA polymorphisms in Duchenne muscular dystrophy has shown a comparable linkage distance with L1.28, our results suggest that the locus for Becker muscular dystrophy, like that for Duchenne dystrophy, is on the short arm of the X chromosome, and further that these two loci may be closely linked or possibly allelic.     

Contribution to carrier detection and genetic counselling in X linked retinoschisis.

X linked retinoschisis (RS) is a vitreoretinal disease resulting from microcystic degeneration of the macula associated with peripheral lesions. The disease gene has already been assigned to the distal short arm of the X chromosome (Xp22.2) by linkage studies. In order to contribute both to a better localisation of the RS locus and to genetic counselling in RS families, we have carried out a clinical and genetic analysis in seven pedigrees. We show, first, that in contrast with previous reports, heterozygote carriers frequently express the disease, and display peripheral retinal alterations similar to those found in affected males. Second, while distal markers DXS16, DXS207, and DXS43 are closely linked to the disease locus, a high level of recombination events was found with centromeric markers, namely DXS274, DXS41, and DXS164. These findings must be taken into account for both carrier detection and prenatal diagnosis in X linked RS.     

Prenatal in situ hybridization test for deleted steroid sulfatase gene

X-linked ichthyosis results from steroid sulfatase (STS) deficiency; 90% of affected patients have a complete deletion of the entire 146 kb STS gene on the distal X chromosome short arm (Xp22.3). In these families prenatal diagnosis and carrier testing can be completed in 2 days by hybridizing simultaneously 2 different cosmid probes labeled with fluorescein or Texas red and counterstaining interphase nuclear DNA with DAPI. An STS gene probe labeled with Texas red hybridizes specially to the steroid sulfatase gene on the X chromosome. A second flanking probe labeled with fluorescein hybridizes to both the normal Y chromosome and normal and STS deleted X chromosomes. In this fashion the interphase nuclei of normal males, affected males, normal females, and carrier females can be distinguished unambiguously. Because normal males and carrier females each show two yellow-green fluorescein spots and one Texas red STS spot, use of this test prenatally requires determining fetal sex independently with repetitive X and Y chromosome specific probes. This procedure can be used with lymphocytes, direct and cultured chorionic villus cells, direct and cultured amniocytes, and fibroblasts. Similar methods are anticipated to be useful for rapid diagnostic assessment of other aneuploid gene disorders. © 1993 Wiley-Liss, Inc.     

Inherited interstitial del(Xp) with minimal clinical consequences: with a note on the location of genes controlling phenotypic features.

In a routine cytogenetic investigation of the outpatients of a hospital for the mentally retarded, a 26-year-old women with a presumptive interstitial deletion of the short arm of one of the X chromosomes was found. The same aberration was found in her phenotypically normal mother and in one of her four sisters, all phenotypically normal. By GTG- and QFQ-banding methods, the deletion was interpreted to involve the entire band Xp21 and adjacent parts of p11 and p22. The karyotype is written 46,X,del(X)(pter leads to p22::p11 leads to qter). By autoradiography and Bud R acridine orange technique, the deleted X was the late replicating one in all three affected persons. The deletion apparently causes shortness of stature but no other phenotypic symptoms or signs. Hence a gene or genes controlling stature is located in band Xp21 or regions immediately adjacent to this band. Since the absence of this region does not cause streak gonads, it does not contain genes controlling the formation of the ovaries. This appears to be the first example of a heritable chromosome deletion compatible with a normal phenotype and reproduction.     

A complex rearrangement associated with sex reversal and the Wolf-Hirschhorn syndrome: a cytogenetic and molecular study.

We report a male infant referred with multiple congenital abnormalities consistent with the Wolf-Hirschhorn syndrome. Cytogenetic analysis showed a chromosome complement of 46,XX with a deletion of 4p15.2----4pter and its replacement by material of unknown origin. The patient was positive for a number of Yp probes including SRY, the testis determining factor, and in situ hybridisation localised the Yp material to the tip of the short arm of one X chromosome. Using pDP230, a probe for the pseudoautosomal region, and M27 beta, which recognises a locus in proximal Xp, the material translocated on to 4p was identified as originating from the short arm of the paternal X chromosome. The most reasonable explanation for this complex rearrangement is two separate exchange events involving both chromatids of Xp during paternal meiosis. An aberrant X-Y interchange gave rise to the sex reversal and an X;4 translocation resulted in additional, apparently active Xp material and a deletion of 4p which produced the Wolf-Hirschhorn phenotype.     

Retinitis pigmentosa families showing apparent X linked inheritance but unlinked to the RP2 or RP3 loci.

Three families with retinitis pigmentosa (RP) are described in which the disorder shows apparent X linked inheritance but does not show linkage to the RP2 and RP3 regions of the short arm of the X chromosome. The families are also inconsistent with a localisation of the disease gene between DXS164 and DXS28. In one case, reassessment of the family in the light of these results suggested that the family may have an autosomal dominant form of RP. The remaining two families are consistent with X linkage and suggest the possibility of a new X linked RP (XLRP) locus. These families highlight the difficulties in determining the mode of inheritance on the basis of pedigree structure and clinical data alone. Molecular genetics plays an important role in confirming the mode of inheritance and in detecting potential misclassifications, particularly in a group of disorders as heterogeneous as RP. They emphasise that caution is required in genetic counselling of RP families, particularly in the absence of any molecular genetic analysis.     

Åland Island eye disease (Forsius-Eriksson ocular albinism) and an Xp21 deletion in a patient with duchenne muscular dystrophy,glycerol kinase deficiency,and congenital adrenal hypoplasia

Glycerol kinase deficiency (GKD) has been described in isolation and in complex phenotypes including either congenital adrenal hypoplasia, Duchenne muscular dystrophy, or both. Cytogenetic and molecular studies have localized these defects to a deletion in volving the X chromosome at band Xp21, consistent with its X-linked recessive pattern of inheritance. Other clinical findings in the complex glycerol kinase deficiency (CGKD) patients are mental retardation, short stature, and hypogonadotropic hypogonadisem. We report on a 6-year-old boy who, in addition to the CGKD phenotype described above, had ocular hypopigmentation consistent with Forsius-Eriksson ocular albinism, also known as type 2 ocular albinism or Åland Island eye disease. Cytogenetic analysis shows an interstitial deletion in the short arm of the X-chromosome at Xp21.     

Aland Island eye disease (Forsius-Eriksson ocular albinism) and an Xp21 deletion in a patient with Duchenne muscular dystrophy, glycerol kinase deficiency, and congenital adrenal hypoplasia

Glycerol kinase deficiency (GKD) has been described in isolation and in complex phenotypes including either congenital adrenal hypoplasia, Duchenne muscular dystrophy, or both. Cytogenetic and molecular studies have localized these defects to a deletion involving the X chromosome at band Xp21, consistent with its X-linked recessive pattern of inheritance. Other clinical findings in the complex glycerol kinase deficiency (CGKD) patients are mental retardation, short stature, and hypogonadotropic hypogonadism. We report on a 6-year-old boy who, in addition to the CGKD phenotype described above, had ocular hypopigmentation consistent with Forsius-Eriksson ocular albinism, also known as type 2 ocular albinism or Aland Island eye disease. Cytogenetic analysis shows an interstitial deletion in the short arm of the X-chromosome at Xp21.     

Combined Goltz and Aicardi syndromes in a terminal Xp deletion: are they a contiguous gene syndrome?

We report on 2 girls with a terminal deletion of the short arm of chromosome X. They had microphthalmia, cloudy corneae, mild linear skin lesions, and agenesis of corpus callosum. A comparison of clinical and cytogenetic findings in similar cases suggested that the critical genes for the Goltz and Aicardi syndromes might be contiguous in the region Xp22.31.     

X-linked retinoschisis is closely linked to DXS41 and DXS16 but not DXS85

A linkage study was carried out in nine families with 24 males affected by X-linked recessive retinoschisis (RS), using three polymorphic DNA probes from the distal segment of Xp. Close linkage of the disease locus with markers DXS41 (probe p99-6) and DXS16 (pXUT23) was found, confirming the location of the RS gene on the distal short arm of the X chromosome. Lod scores for linkage with DXS85 (probe 782) were negative.     

Inherited interstitial del(Xp) with minimal clinical consequences: With a note on the location of genes controlling phenotypic features

In a routine cytogenetic investigation of the outpatients of a hospital for the mentally retarded, a 26-year-old woman with a presumptive interstitial deletion of the short arm of one of the X chromosomes was found. The same aberration was found in her phenotypically normal mother and in one of her four sisters, all phenotypically normal. By GTG- and QFQ-banding methods, the deletion was interpreted to involve the entire band Xp21 and adjacent parts of p11 and p22. The karyotype is written 46,X,del(X)(pter→p22::p11→qter). By autoradiography and Bud R acridine orange technique, the deleted X was the late replicating one in all three affected persons. The deletion apparently causes shortness of stature but no other phenotypic symptoms or signs. Hence a gene or genes controlling stature is located in band Xp21 or regions immediately adjacent to this band. Since the absence of this region does not cause streak gonads, it does not contain genes controlling the formation of the ovaries. This appears to be the first example of a heritable chromosome deletion compatible with a normal phenotype and reproduction.     

Inherited duplication Xq27-qter at Xp22.3 in severely affected males: Molecular cytogenetic evaluation and clinical description in three unrelated families

We describe the clinical phenotype in four males from three families with duplication (X)(qter→q27::p22.3→qter). This is an unusual duplication of the distal long arm segment, Xq27-qter, onto the distal short arm of the X chromosome at Xp22.3, as shown by fluorescent in situ hybridization analysis with multiple X-specific probes. The patients are young male offspring of three unrelated, phenotypically normal carrier women. The affected males have similar clinical manifestations including severe growth retardation and developmental delay, severe axial hypotonia, and minor anomalies. Such clinical similarity in three unrelated families demonstrates that this chromosome abnormality results in a new and distinct clinical phenotype. Replication studies, performed on two of the mothers, provided evidence that inactivation of the abnormal X chromosome permitted the structural abnormality to persist in these families for a generation or more in females without phenotypic expression. Am. J. Med. Genet. 80:377–384, 1998. © 1998 Wiley-Liss, Inc.     

Contiguous gene syndrome due to a maternally inherited 8.41 Mb distal deletion of chromosome band Xp22.3 in a boy with short stature, ichthyosis, epilepsy, mental retardation, cerebral cortical heterotopias and Dandy-Walker malformation

Microdeletions of Xp22.3 are associated with contiguous gene syndromes, the extent and nature of which depend on the genes encompassed by the deletion. Common symptoms include ichthyosis, mental retardation and hypogonadism. We report on a boy with short stature, ichthyosis, severe mental retardation, cortical heterotopias and Dandy-Walker malformation. The latter two abnormalities have so far not been reported in terminal Xp deletions. MLPA showed deletion of SHOX and subsequent analysis using FISH and SNP-arrays revealed that the patient had an 8.41 Mb distal deletion of chromosome region Xp22.31 --> Xpter. This interval contains several genes whose deletion can partly explain our patient's phenotype. His cortical heterotopias and DWM suggest that a gene involved in brain development may be in the deleted interval, but we found no immediately obvious candidates. Interestingly, further analysis of the family revealed that the patient had inherited his deletion from his mother, who has a mos 46,X,del(X)(p22)/45,X/46, XX karyotype.