Homozygous paracentric inversion 12 in a mentally retarded boy: a case report and review of the literature

Genome sequencing identifies a homozygous inversion disrupting QDPR as a cause for dihydropteridine reductase deficiency

Background

Dihydropteridine reductase (DHPR) is one of the key enzymes for maintaining in the organism the supply of tetrahydrobiopterin (BH₄), an essential cofactor for aromatic amino acid hydroxylases. Its dysfunction causes the condition of hyperphenylalaninemia together with the lack of neurotransmitters.

Methods

We report a patient with biochemically diagnosed DHPR deficiency, with extensive molecular investigations undertaken to detect variations in quinoid dihydropteridine reductase (QDPR) gene. Sanger sequencing of QDPR coding regions, exome sequencing, QDPR mRNA PCR, and karyotyping were followed by trio genome sequencing.

Results

Short‐read genome sequencing revealed a homozygous 9‐Mb inversion disrupting QDPR. Structural variant breakpoints in chromosome 4 were located to intron 2 of QDPR at Chr4(GRCh38):g.17505522 and in intron 8 of the ACOX3 gene, Chr4(GRCh38):g.8398067). Both nonrelated parents carried the variant in heterozygous state. The inversion was not present in gnomAD structural variant database.

Conclusion

Identification of the exact breakpoints now allows further straightforward molecular genetic testing of potential carriers of the inversion. This study extends the pathogenic variant spectrum of DHPR deficiency and highlights the role of structural variants in recessive metabolic disorders. To our knowledge, this is the first report on a large, canonical (rather than complex) homozygous pathogenic inversion detected by genome sequencing.

Cerebellar ataxia and mental retardation in a child with an inherited satellited chromosome 4q

We identified a case of familial satellited chromosome 4q through a child with cerebellar ataxia and mental retardation. No loss of genetic material could be demonstrated at the molecular level but other possible mechanisms of this association are discussed. We conclude that in these cases genetic counselling should be reassuring.

Development of acute lymphoblastic leukemia with translocation (4;11) in a young girl with familial pericentric inversion 12

We report a case of a 1-year-old girl with familial pericentric inv(12) who developed acute lymphoblastic leukemia (ALL) with t(4;11) 1 month after recovery from idiopathic hemophagocytic lymphohistiocytosis (HLH). The inv(12)(p13q15) was first found in bone marrow (BM) cells when she was diagnosed as having HLH, and then detected in the BM blasts together with t(4;11)(q21;q23) when she developed ALL. The inv(12) was retained in the BM cells after she achieved complete remission. Cytogenetic analysis on the PHA-stimulated peripheral lymphocytes revealed inv(12) in all of the 30 cells examined. Because the data that ALL with t(4;11) predicts an extremely poor prognosis, she received an allogeneic BM transplantation from an HLA-matched sibling at 10 months from the onset of ALL. She is now at 26 months post transplantation and maintains in a state of complete remission. Familial cytogenetic study demonstrated that 4 of 8 maternal members examined had the inv(12), but they showed no family history of a higher risk of development of hematological and other types of malignancies, suggesting that pericentric inv(12) itself might not be directly involved in the development of ALL in this case.

Paracentric inversions: a review

This review of paracentric inversions in man includes what we know of the behaviour and reproductive consequences of paracentric inversions from other species. Observations of naturally occurring inversions in several species of plants and animals and results of experiments with mutagenically induced inversions in the mouse are discussed. From a review of 184 cases, it is concluded that most of the paracentric inversions in man are harmless and that the risk of heterozygotes having a child with an unbalanced karyotype is low. However, in some cases, it is difficult, if not impossible, to distinguish between a paracentric inversion and a paracentric insertion, the risk in the latter case being about 15%. Caution is also necessary in interpreting the results of prenatal diagnosis for heterozygotes of paracentric inversions, because of the possibility of a variety of unpredictable unbalanced chromosome products.

Paracentric inversions in humans: a review of 446 paracentric inversions with presentation of 120 new cases

We present a large review of 446 cases of paracentric inversions (PAI), including 120 new cases, to assess their incidence, distribution, inheritance, modes of ascertainment, interchromosomal effects, viable recombinant offspring, and clinical relevance. All 23 autosomes and sex chromosomes had inversions. However, none were identified in chromosome arms 18p, 19q, 20q, and Yp. PAI were most commonly reported in chromosomes 1, 3, 5, 6, 7, 11, and 14 and less frequently in chromosomes 4, 16, 17, 18, 19, 20, 21, 22, and Y. Inversions were most common in chromosome arms 6p, 7q, 11q, and 14q and observed least in chromosome arms 2p, 2q, 3q, 4q, and 6q. Frequently encountered breakpoints included 3(p13p25), 6(p12p23), 6(p12p25), 7(q11q22), and 11(q21q23). Ascertainment was primarily incidental (54.5%), mental retardation and/or congenital anomalies (22.2%), spontaneous abortions (11.4%), associations with syndromes (3.0%), and infertility (2.0%) accounted for the remainder. Ascertainment was neither related to the length of the inverted segment nor to specific inversions except for PAI of Xq which often presented with manifestations of Ullrich-Turner syndrome. Sixty-six percent of PAI were inherited while 8.5% were de novo. Recombination was observed in 17 cases, 15 of which resulted in a monocentric chromosomal deletion or duplication. No common factors were identified that suggested a tendency towards recombination. The incidence of viable recombinants was estimated to be 3.8%. This review documents that PAI are perhaps more commonly identified than suggested in previous reviews. Despite the possible bias of ascertainment in some cases, there may be associated risks with PAI that require further examination. Our data suggest that PAI carriers do not appear to be free of risks of abnormalities or abnormal progeny and caution is recommended when counseling.

Three unrelated cases of paracentric inversions of 1p in individuals with abnormal phenotypes

Paracentric inversions, involving a rearrangement within one chromosome arm, are rare. Although carriers of balanced paracentric inversions should theoretically not be at risk for abnormal offspring, such cases have been reported. We report on 2 unrelated cases of inherited paracentric inversions of 1p with breakpoints at p32 and p36.1 and p32.3 and p36.22 in individuals with abnormal phenotypes. Another case of 2 abnormal monozygotic twins with a de novo paracentric inversion of 1p with breakpoints at p22 and p34 is presented as well.

Complementation by two non-homologous recombinant chromosomes 3

The first example known to us of complementation by two non-homologous chromosomes 3 is present in the karyotype of a phenotypically normal brother of an inv(3)(p25q21) carrier. The normal chromosomes 3 are replaced by two complementary recombinant chromosomes 3. The longer recombinant duplicates 3q21-qter and is deficient for 3p25-pter. It is identical to the recombinant inherited by infants born with multiple congenital anomalies to inv(3)(p25q21) carriers. The shorter recombinant duplicates 3p25-pter and is deficient for 3q21-qter. This recombinant has previously been observed only in prometaphase spreads from sperm of an inv(3) carrier from the same kindred. Theoretically it is possible for the carrier of these complementary recombinant chromosomes 3 to produce sperm carrying either a normal 3, or the inversion 3, which could then fertilize an egg carrying a normal 3 followed by normal fetal development. However, the spouse of our propositus reported one first trimester spontaneous abortion, followed by no recognized pregnancy over the next 12 years of marriage.

Developmental arrest at early stages of Chinese hamster embryos homozygous for chromosomal rearrangements

Forty-three Chinese hamster stocks with autosomal rearrangements produced by X-irradiation were used. These rearrangements, 38 reciprocal translocations and 5 inversions, were chromosomally balanced. Heterozygotes for these rearrangements were all fertile and morphologically normal in both sexes except for one line with growth retardation. By crossing male and female heterozygotes for the same rearrangements, homozygotes were obtained in 37 lines. In the remaining 6 lines (5 with reciprocal translocations and 1 with an inversion), no homozygotes were viable. These 6 lines revealed arrested development of homozygous embryos at the two-cell stage, around the eight-cell stage, and after implantation, respectively. The bands of the breakpoints of rearrangements associated with lethality of homozygous embryos were different for each rearrangement. These results suggest that abnormal expression including embryonic lethality in homozygotes may be due to an influence of genes at the breakpoints.

Genetic causes of mental handicap and opportunities for prevention

Prior to 1970 nearly one half of severe mental handicap (IQ less than 50) was unexplained and genetic causes were recognized in one third of all patients. In recent years the genetic contribution has risen to 50%, with the decline in importance of environmental causes and the growing recognition of X-linked forms of mental retardation and chromosomal microdeletion syndromes. Recognition of genetic conditions is vital for accurate assessment of recurrence risks and in order, in some instances, to provide specific prenatal diagnosis. With full utilization of existing prenatal screening procedures and a more detailed family history, severe mental handicap due to genetic conditions should be reduced by 30-40%.