Probable long-arm deletion of Y chromosome in boy of short stature

Report of a patient with a de novo non-recurrent duplication of 17p11.2p12 and Yq11 deletion

Background

The 17p11.2p12 locus is an unstable region that is predisposed to several known genomic disorders and non-recurrent rearrangements that yield varied and wide-ranging phenotypes. Nearly 1% of male newborns have deletions in the Y chromosome; these events primarily involve the heterochromatic region, but may extend to euchromatic Yq segments containing azoospermia factor regions.

Case presentation

We describe the occurrence of two independent chromosomal rearrangements that originated as de novo events in a single male patient: a 10.8-Mb duplication of 17p11.2p12 and a 14.7-Mb deletion of Yq11. This individual shares some clinical characteristics with previously described patients having one or the other of these rearrangements, including global developmental delay, short stature, hypotonia, delayed puberty, certain facial features and a generalized demyelinating sensory-motor polyneuropathy without clinical manifestation. Our patient also presents some features that were not previously described in relevant individuals, including camptodactyly, preauricular pits and hypertrichosis of the back and elbows.

Conclusions

To our knowledge, this is the first patient to be reported with independent de novo deletion/duplication events involving chromosomes 17 and Y. We discuss possible responsible mechanisms and address the phenotype, particularly in light of the clinical features that were not previously reported for patients bearing a duplication of 17p11.2p12 or a deletion of Yq11. We suggest that some of the previously reported patients with Yq11 deletion and clinical manifestations other than male infertility may have additional chromosomal imbalances that could be identified by chromosome microarray analysis, as illustrated by the present case.

FISH deletion mapping defines a single location for the Y chromosome stature gene, GCY

At least 1 in 1000 males lacks part of the long arm of the Y chromosome. This chromosomal aberration is often associated with short stature and infertility. Deletion mapping and genotype-phenotype analysis have previously defined two non-overlapping critical regions for growth controlling gene(s), GCY(s), on the euchromatic portion of the Y chromosome long arm. These initial mapping assignments were based on the analysis of patients carrying a pure 46,XYq- karyotype as defined by classical cytogenetic karyotyping. Four genes have been assigned to the distal one of the two critical regions. To determine whether one or both of these two critical regions harbours GCY and whether one of the four genes assigned to the distal region is involved in determination of stature, nine adult patients with Yq chromosomal abnormalities were studied in detail. By PCR and FISH analysis, we showed that all patients with a previously defined pure 46,XYq- karyotype are actually mosaics with cells containing an idic(Y) or ring(Y) chromosome in association with 45,X0 cells. This leads us to conclude that (1) FISH is an absolute prerequisite for the correct identification of Y chromosomal rearrangements and (2) only patients with interstitial Y deletions are reliable predictors for the physical location of stature gene(s) on Yq. Our molecular analyses of chromosomes from patients with interstitial Yq deletions finally establishes the proximal interval between markers DYZ3 and DYS11 as the only GCY critical interval. No functional gene has so far been identified in this region adjacent to the centromere.

Clinical features of nine males with molecularly defined deletions of the Y chromosome long arm

Deletions of the long arm of the Y chromosome have previously been associated with azoospermia and short stature. We report the results of a detailed clinical and molecular study of nine males with partial deletions of Yq. Special emphasis was laid on congenital anomalies and dysmorphic features. Some of the patients have developmental problems or distinct facial features, namely a small chin and mouth, a high arched or cleft palate, downward slanting palpebral fissures, high nasal bridge, and dysmorphic ears. As far as we know, similar facial dysmorphism has not been previously described in association with del(Yq). These features are not, however, simply correlated to the size of the deletion. In none of these patients could evidence of aberrant Xq-Yq interchange be found.

Phenotype/karyotype correlations of Y chromosome aneuploidy with emphasis on structural aberrations in postnatally diagnosed cases

Over 600 cases with a Y aneuploidy (other than non-mosaic 47,XYY) were reviewed for phenotype/karyotype correlations. Except for 93 prenatally diagnosed cases of mosaicism 45,X/46,XY (79 cases), 45,X/47,XYY (8 cases), and 45,X/46,XY/47,XYY (6 cases), all other cases were ascertained postnatally. Special emphasis was placed on structural abnormalities. This review includes 11 cases of 46,XYp-; 90 cases of 46,XYq- (52 cases non-mosaic; 38 cases 45,X mosaic); 34 cases of 46,X,r(Y) (9 cases non-mosaic and 25 cases 45,X mosaic); 8 cases of 46,X,i(Yp) (4 non-mosaic and 4 mosaic with 45,X); 12 cases of 46,X,i(Yq) (7 non-mosaic and 5 mosaic); 44 cases of 46,X,idic(Yq); 80 cases of 46,X, idic(Yp) (74 cases had breakpoints at Yq11 and 6 cases had breakpoints at Yq12); 130 cases of Y/autosome translocations (50 cases with a Y/A reciprocal translocation, 20 cases of Y/A translocation in 45,X males, 60 cases of Y/DP or Y/Gp translocations); 52 cases of Y/X translocations [47 cases with der(X); 4 cases with der(Y), and 1 case with 45,X with a der(X)], 7 cases of Y/Y translocations; 151 postnatally diagnosed cases of 45,X/46,XY; 14 postnatally diagnosed cases of 45,X/47,XYY; 18 cases of 45,X/46,XY/47,XYY; and 93 aforementioned prenatally diagnosed cases with a 45,X cell line. It is clear that in the absence of a 45,X cell line, the presence of an entire Yp or a region of it including SRY would lead to a male phenotype in an individual with a Y aneuploidy, whereas the lack of Yp invariably leads to a female phenotype with typical or atypical Ullrich-Turner syndrome (UTS). Once there is a 45,X cell line, regardless of whether there is Yp, Yq, or both Yp and Yq, or even a free Y chromosome in other cell line, there is an increased chance for that individual to be a phenotypic female with UTS manifestations or to have ambiguous external genitalia. This review once again shows a major difference in reported phenotypes between postnatally and prenatally diagnosed cases of 45,X/46,XY, 45,X/47,XYY, and 45,X/46,XY/47,XYY mosaicism. It appears that ascertainment bias can explain the fact that all known patients with postnatal diagnosis are phenotypically abnormal, while over 90% of prenatally diagnosed cases are reported to have a normal male phenotype. Further elucidation of major Y genes and their clinical significance can be expected in the rapidly expanding gene mapping projects. More, consequently better, phenotype/karyotype correlations can be anticipated at both the cytogenetic and the molecular level.

Prenatal identification of a Y-chromosome deletion by Y-specific single copy DNA probes

A sex chromosome deletion was identified in the course of prenatal diagnosis for maternal age. Ultrasound pictures revealed male fetal sex and a comparison with the father's Y chromosome suggested that the altered chromosome might be a de novo deletion of the Y chromosome. DNA hybridization with five human Y-specific probes shows that, among the Y-specific sequences recognized by the probes, only two of them are absent. The normal infant, at birth, was mosaic 46, XYq-/46,XY.

Deletion of the long arm of the Y chromosome and review of Y chromosome abnormalities

We report on a patient whose karyotype is 45,X/46,X,del(Y) (pter----q11.212). We also present a review of literature on the Y chromosome in which evidence is presented that there are genes on the Y chromosome that prevent Ullrich-Turner syndrome manifestations; aid in testes maturation and spermatogenesis; and affect height, tooth size, and bone maturation.

Yq- in a child with livedo reticularis, snub nose, microcephaly, and profound mental retardation

A child with terminal deletion of the long arm of the Y chromosome (Yq--) presented with marked livedo reticularis, snub nose, microcephaly, short stature, and other dysmorphic features. He was profoundly mentally retarded. Most of the patients with Yq- have been reported as having varying dysmorphic features, mental retardation, and short stature. This child, in addition to the above, has livedo reticularis and microcephaly. He was of normal birthweight and, therefore, does not come into the syndrome of microcephaly, snub nose, livedo reticularis, and low birthweight dwarfism. Further information on Yq- should be obtained to ascertain if consistent patterns of abnormalities exist.

Localisation of male determining factors in man: a thorough review of structural anomalies of the Y chromosome

It is widely accepted that male determination in man depends on the presence of a factor or factors on the Y chromosome. These factors may be localised within the Y chromosome through the study of structural anomalies of the Y. A thorough review of seven different structural anomalies of the Y is presented: dicentric Y chromosomes, Y isochromosomes, ring Y chromosomes, Y; autosome, Y;X, and Y;Y translocations, and Y deletions. The evidence from these studies indicates that a gene or genes on the short arm or the Y near the centromere play a crucial role in the development of the testes. A few studies indicate that one or more factors on the long arm of the Y may also influence testicular development. If such a factor is present on the long arm, then it too must be very near the centromere. The theory that separate genes independently control the initial development and maturation of the tests (on the long and short arms of the Y, respectively) may be premature. Recently proposed arguments in its favour are examined. Some evidence also indicates the presence of a fertility factor on the non-fluorescent segment of the long arm. Relevant information on the H-Y antigen is discussed.

A synopsis of the human Y chromosome

Phenotypic features and functions known to depend on the presence of the Y chromosome or the H-Y antigen are discussed in relation to structural anomalies of the Y chromosome and other abnormalities of sexual and somatic development. Recent knowledge about molecular organization of constitutive heterochromatin in relation to the human Y is presented. An attempt is made at assigning different functions, genes and DNA sequences to different regions of the Y chromosome.

Yq deletion, aspermia, and short stature

A large Yq deletion involving both the fluorescent and part of the non-fluorescent segment in a 36-year-old phenotypic normal male is presented. His short stature and aspermia gives strong support, after a complete review of the literature, to the existence of factors involved in the control of both characteristics in the non-fluorescent segment of the long arm of chromosome Y, distally within band 11.

Localization of factors controlling spermatogenesis in the nonfluorescent portion of the human Y chromosome long arm

A deletion of the Y chromosome at the distal portion of band q11 was found in 6 men with normal male habitus but with azoospermia. Five of them were found during a survey of 1170 subfertile males while the sixth was karyotyped because of slight bone abnormalities. These findings, together with a review of the literature, suggest that on the distal portion of the nonfluoresecent segment of the long arm of the Y, factors are located controlling spermatogenesis.

45,XO/46,XYg dic mosaicism in a patient with ambiguous genitalia

45,XO/46,XYq dic mosaicism was found in a patient with ambiguous genitalia. The patient had dysgenetic testis and gonadoblastoma. The same mosaicism was found in skin and gonadal tissue cultured fibroblasts. Localization of the genes related to height and male determination is discussed.

Deletion of the long arms of the Y chromosome with normal male development and intelligence

Normal male development was found in a man with a proven deletion of the long arms of the Y chromosome. The only phenotypic effect was on his build. This study offers additional proof that all, or most of the long arms of the Y chromosome are not primarily concerned with the determination of male sexual characteristics.