A girl with an interstitial deletion of the short arm of chromosome 3 studied with a high-resolution banding technique

Interstitial Chromosome 3p13p14 Deletions: An Update and Review

Deletions of proximal chromosome 3p13p14 are infrequent chromosomal alterations. Variable sizes and breakpoints have been reported in patients with a wide range of phenotypes that are evolving as additional cases are reported. The routine use of high-density chromosomal microarrays (CMA) has allowed the identification of many more cases of this disorder and clinical phenotyping shows evidence for an emerging profile among patients with overlapping deletions of 3p13p14. Here, we review the currently reported cases, their phenotypes and where available, the genomic intervals delineated by CMA. Surprisingly, we found that a significant number of proximal chromosome 3p deletions involve structural rearrangements, especially insertions, that have been identified in balanced parental chromosome complements. This region is historically known as a common human chromosomal fragile site, although an underlying genomic mechanism related to its architecture has not been identified. We conclude that identification of an interstitial 3p deletion in a proband by CMA should prompt consideration of further structural chromosomal evaluation using more traditional cytogenetic techniques. While the variability in breakpoints does not suggest a unifying underlying mechanism for these alterations, identification of the haploinsufficient genes in each patient's deletion interval and their developmental roles can guide genotype-phenotype correlations and impact clinical management.

3p14 deletion is a rare contiguous gene syndrome: report of 2 new patients and an overview of 14 patients

Interstitial deletions of chromosome 3p14p12 are a rare chromosome rearrangement. Twenty-six patients have been reported in the literature to date, however, a specific clinical phenotype has not yet been delineated. We describe three patients (two new) with overlapping chromosome 3p14p12 deletions and review the clinical and molecular data of 11 well-characterized, published cases. These patients had a number of features in common, such as short stature, failure to thrive, facial dysmorphism, congenital heart defects, urogenital abnormalities, neurological problems, hearing loss, and global developmental delay, suggesting that the interstitial chromosome 3p14p12 deletion gives rise to a multiple congenital anomaly syndrome. Some of the patients show clinical overlap with other complex syndromes such as CHARGE syndrome. Genotype-phenotype analysis revealed candidate genes for parts of the clinical features suggesting that the 3p14 deletion is a contiguous gene syndrome.

Delineation of the 3p14.1p13 microdeletion associated with syndromic distal limb contractures

Distal limb contractures (DLC) represent a heterogeneous clinical and genetic condition. Overall, 20-25% of the DLC are caused by mutations in genes encoding the muscle contractile apparatus. Large interstitial deletions of the 3p have already been diagnosed by standard chromosomal analysis, but not associated with a specific phenotype. We report on four patients with syndromic DLC presenting with a de novo 3p14.1p13 microdeletion. The clinical features associated multiple contractures, feeding problems, developmental delay, and intellectual disability. Facial dysmorphism was constant with low-set posteriorly rotated ears and blepharophimosis. Review of previously reported cases with a precise mapping of the deletions, documented a 250 kb smallest region of overlap (SRO) necessary for DLC. This region contained one gene, EIF4E3, the first three exons of the FOXP1 gene, and an intronic enhancer of FOXP1 named hs1149. Sanger sequencing and locus quantification of hs1149, EIF4E3, and FOXP1 in a cohort of 11 French patients affected by DLC appeared normal. In conclusion, we delineate a new microdeletion syndrome involving the 3p14.1p13 locus and associated with DLC and severe developmental delay.

3p interstitial deletion: novel case report and review

3p interstitial deletions have emerged in recent years as a new cause of neurodevelopmental delay and intellectual disability. Since the first report of this condition in 1979, 16 cases have been described in the literature, delineating it as a presumptive syndrome. Here, we add a novel case presenting severely delayed neurodevelopment and psychomotor development; facial dysmorphism (square facies, broad forehead, short palpebral fissures, epicanthic folds, broad nasal bridge, and low-set malformed ears); cerebral, cardiac, and genital malformations; hand and feet anomalies; sacral sinus; and hearing impairment. Genetic investigations revealed a del(3)(p12.3p14.1) of 12.5 Mb, including 31 ORFs, among which ROBO2, PDZRN3, MITF, and FOXP1 are known to act in neurodevelopment. The clinical features of our patient are compared with those previously reported in the literature, thus providing further support for the delineation of the 3p interstitial deletion syndrome.

A 785kb deletion of 3p14.1p13, including the FOXP1 gene, associated with speech delay, contractures, hypertonia and blepharophimosis

We report a child with a 785kb deletion of the 3p14.1p13 region including the genes FOXP1, EIF4E3, PROK2, GPR27 resulting in speech delay, contractures, hypertonia and blepharophimosis. FOXP1 and FOXP2 are transcription factors containing a polyglutamine tract and a forkhead DNA binding domain. They both play a role in the developing human foregut and brain [W. Shu, M.M. Lu, Y. Zhang, P. Tucker, D. Zhou, E.E. Morrisey, Foxp2 and Foxp1 cooperatively regulate lung and esophagus development, Development 134 (2007) 1991-2000, E. Spiteri, G. Konopka, G. Coppola, J. Bomar, M. Oldham, J. Ou, et al. Identification of the transcriptional targets of FOXP2, a gene linked to speech and language, in developing human brain, Am. J. Hum. Genet. 81 (2007) 1144-1157, S. Tamura, Y. Morikawa, H. Iwanishi, T. Hisaoka, E. Senba. Expression pattern of the winged-helix/forkhead transcription factor Foxp1 in the developing central nervous system, Gene Expr. Patterns. 3 (2003) 193-197.]. Mutations in FOXP2 are known to cause severe speech and language abnormalities [C.S.L. Lai, S.E. Fisher, J.A. Hurst, F. Vargha-Khadem, A.P. Monaco, A forkhead-domain gene is mutated in a severe speech and language disorder, Nature 413 (2001) 519-523.] in humans and animals. It has been suggested that overlap of FOXP1 and FOXP2 expression in the songbird and human brain may indicate that mutations in FOXP1 would also result in speech and language abnormalities. The roles of EIF4E3, PROK2 and GPR27 are also evaluated.

Interstitial deletion of a proximal 3p: a clinically recognisable syndrome

Interstitial deletions of the proximal short arm of chromosome 3 occurring as constitutional aberrations are rare and a defined clinical phenotype is not established yet. We report on a 30-months-old girl with distinct facial features (square facies, plagiocephaly, broad forehead, broad nasal bridge, long philtrum and low set ears) and psychomotor/speech delay associated with an interstitial deletion of 3p12 chromosomal band, del(3)(p12p12). Clinical manifestations of our child were compared with those of other eight patients with the same deletion previously described to further delineate the proximal 3p deletion syndrome.

Molecular characterisation of a 15 Mb constitutional de novo interstitial deletion of chromosome 3p in a boy with developmental delay and congenital anomalies

We describe the case of a 22-month-old boy with developmental and psychomotor retardation as well as craniofacial dysmorphism, including a cleft lip. Analysis of G-banded chromosomes of the propositus showed a de novo interstitial deletion of the short arm of chromosome 3, del(3)(p13p11). Fine mapping of the deletion was performed using fluorescence in situ hybridisation analysis with region-specific BAC clones. Eight BACs were absent from one chromosome 3 from the patient. Molecular analyses of eleven polymorphic DNA markers helped to narrow down the breakpoints and demonstrated that the derivative chromosome 3 is of paternal origin. The deleted segment encompasses about 15 Mb between marker D3S3551 and the centromere. Only a small number of known genes, including PROK2, GPR27, RYBP, PPP4R2, ROBO1, and GBE1, which map in the 3p13-p11 region are included in the deletion.

A patient with interstitial deletion of the short arm of chromosome 3 (pter-->p21.2::p12-->qter) and a CHARGE-like phenotype

We report on a 4-month-old boy with a de novo interstitial deletion of the short arm of chromosome 3 (pter-->p21.2::p12-->qter) and clinical findings typical of proximal 3p deletion together with coloboma of iris, heart defect, choanal atresia, retardation of growth and development, genital hypoplasia, and ear anomalies. Family history was unremarkable and parental chromosomes were normal. The clinical manifestations of the patient are compared with those of 10 patients previously described with a proximal 3p deletion. The additional CHARGE-like phenotype is discussed.

Deletion of chromosome 3 and a 3;20 reciprocal translocation demonstrated by chromosome painting

The combined use of high resolution banding and chromosome painting techniques allowed us to identify a reciprocal translocation involving chromosomes 3 and 20 and simultaneous interstitial deletion of chromosome 3 in a patient with several minor anomalies of the face and hands. His karyotype is described as 46,XY,t(3;20) (p14.2;p12.2),del(3)(p11-p14.1).

Insertional translocations: report of two new families and review of the literature

We describe two families with insertional translocations. In the first, a large family ascertained because of repeated pregnancy loss, the insertional translocation, ins(1;3)(q32;p13pter), was found to be segregating through three generations. In the second family, ascertained through a proposita with congenital malformations, multiple spontaneous abortions also occurred. The father had an insertional translocation, inv 4(p14,q21.1)ins(7,4)(q32;q21.1 q23). These cases illustrate that recurrent fetal wastage may be caused by insertional translocations and in fact may be the only clinical manifestation of this unusual type of chromosome rearrangement.

Interstitial deletion of the short arm of chromosome 3 (3p14)

Deletions of 3p usually involve the terminal portion (3p25). An interstitial deletion of a proximal 3p segment (3p14) was detected at amniocentesis. The clinical and cytogenetic characteristics of this case and of three previously published cases are reviewed. Cardiovascular and gastrointestinal malformations have not been reported before in association with this particular chromosome abnormality.

Partial deletion of the short arm of chromosome 3 (3p25----3pter). Further delineation of the clinical phenotype

Clinical descriptions of individuals with partial deletion of the distal short arm of chromosome three have been reported rarely. A characteristic phenotype has been proposed. We present another patient with this cytogenetic abnormality whose physical and developmental features show similarities with, as well as differences from, previously reported cases. This suggests that the clinical phenotype requires further definition. In addition, gene dosage studies were undertaken on several serum proteins in order to try to map the location of the responsible genes on chromosome three.

Interstitial deletion of chromosome 3p: report of a patient and delineation of a proximal 3p deletion syndrome

We report on a patient with a de novo interstitial deletion of the proximal portion of the short arm of chromosome 3 (p12----14.2). The deleted portion excludes the constitutive fragile site assigned to band 3p14. The phenotype of the patient, together with that of three previously reported cases, seems to be sufficiently characteristic to allow the delineation of a proximal 3p deletion syndrome.