- Case Report
- Open Access
Microarray based analysis of an inherited terminal 3p26.3 deletion, containing only the CHL1 gene, from a normal father to his two affected children
© Cuoco et al; licensee BioMed Central Ltd. 2011
- Received: 24 August 2010
- Accepted: 1 April 2011
- Published: 1 April 2011
terminal deletions of the distal portion of the short arm of chromosome 3 cause a rare contiguous gene disorder characterized by growth retardation, developmental delay, mental retardation, dysmorphisms, microcephaly and ptosis. The phenotype of individuals with deletions varies from normal to severe. It was suggested that a 1,5 Mb minimal terminal deletion including the two genes CRBN and CNTN4 is sufficient to cause the syndrome.
In addition the CHL1 gene, mapping at 3p26.3 distally to CRBN and CNTN4, was proposed as candidate gene for a non specific mental retardation because of its high level of expression in the brain.
Methods and Results
we describe two affected siblings in which array-CGH analysis disclosed an identical discontinuous terminal 3p26.3 deletion spanning less than 1 Mb. The deletion was transmitted from their normal father and included only the CHL1 gene. The two brothers present microcephaly, light mental retardation, learning and language difficulties but not the typical phenotype manifestations described in 3p- syndrome.
a terminal 3p26.3 deletion including only the CHL1 gene is a very rare finding previously reported only in one family. The phenotype of the affected individuals in the two families is very similar and the deletion has been inherited from an apparently normal parent. As already described for others recurrent syndromes with variable phenotype, these findings are challenging in genetic counselling because of an evident variable penetrance.
- Refseq Gene
- Terminal Deletion
- Abdominal Ultrasound Examination
The 3p deletion syndrome is a rare contiguous gene syndrome caused by deletions in the 3p25-pter region. The deletions are variable in size, ranging from one to several megabases, they don't present common breakpoints and mostly occur de novo, but a few familial cases have been reported [1–4]. The syndrome is characterized by a recognizable phenotype including low birth weight, growth and mental retardation, developmental delay and characteristic facial appearances. The clinical manifestations in individuals with 3p deletions vary from normal to severe. A milder phenotypic effect or a normal intelligence [4, 5] has also been described for larger [3, 6], often inherited, deletions of this region [1–4, 7, 8] and appears to be secondary to the breakpoint's location and the deletion extent [1–3]. Moreover, cases with minimal pathological features despite the presence of a large terminal 3p deletion have been described [3, 4, 9].
Recently, a cohort of 14 patients with visible distal 3p deletions has been studied by SNP array to better define the genetic basis of 3p deletion syndrome . Among the different haploinsufficient genes, CRBN and CNTN4 have been indicated as sufficient to cause the typical clinical features  while the CHL1 gene has been suggested to contribute to mental development [4, 8, 11].
We describe a sub microscopic 3p26.3 terminal deletion transmitted from the normal father to his two affected children. The imbalance is less than 1 Mb in size and includes only the gene CHL1, a member of the L1 family of cell adhesion molecules previously suggested to be responsible for mental defects in patients with 3p- syndrome.
Karyotyping was performed on peripheral blood of the patients and their parents. Screening by Multiplex-ligation-dependent probe amplification method (MLPA) (kit SALSA P036-E1, MRC HOLLAND, Amsterdam, The Netherlands) was used for subtelomeric analysis and fluorescent in situ hybridization (FISH) analysis (ToTel Vysion kit, Vysis, Abbott Molecular, Illinois, U.S.A.) was subsequently used as confirmation method.
To further characterize the rearrangement extent and breakpoints an array-CGH using the Human CGH Microarray Kit 400 K (Agilent Technologies, Palo Alto, CA, USA) covering the whole genome with a 5.3 Kb overall median probe spacing was performed following the manufacturer's protocol.
The patient is the first child of healthy, non-consanguineous parents. Karyotype was normal male. No family history of congenital anomalies or mental retardation was referred. The child was born after 36 weeks of uneventful pregnancy, by caesarean section. At birth, weight was 2.400 kg (10th-25th centile); length and head circumference were not reported. Apgar score was 9 at first minute. He showed a regular physical and psychomotor development (sitting at 6 months, walking at 14 months). At school learning difficulties were observed and a neuropsychological evaluation was performed. A borderline I.Q. level, measured with Wechsler Intelligence Scale for Children-Revised (WISC-R), associated with a deficit in graphic test of Perceptual Organization (Bender-Santucci test) and language disorders with phonological impairment, dyslexia and dyscalculia were noticed.
At the age of 8 years dropping off to sleep an episode of tonic clonic seizures at right hemi-body occurred for which he was hospitalized.
At physical examination (9 years), weight was 26 kg (50th centile), height 123 cm (10th -25th centile), head circumference 55 cm (>50th centile). In addition epichantal folds, joint hyperlaxity and three abdominal cafè-au-lait spots were noticed. Ophthalmologic evaluation showed divergent strabismus at the right eye, myopia and retinal spots without clinical significance. Cerebral MRI identified mild ectopia of cerebellar tonsilla at the foramen magnum. Abdominal ultrasound examination, cardiological examination and auditory evoked potentials were normal. Electroencephalogram showed aspecific anomalies. At the age of nine years a second episode similar to the precedent (characterized by tonic-clonic seizure at right hemi-body at dropping off to sleep) occurred causing a post-ictal paresis at right hemi-body during 10 minutes. The EEG showed centrotemporal spikes in the left hemisphere, activated by sleep and a treatment with OXC was started.
The brother was born after 36 weeks of uneventful pregnancy, by caesarean section. At birth, weight was 2.080 kg (3rd -10th centile), length 44 cm (3rd -10th centile), head circumference 31.5 cm (10th centile). Apgar score was 7 and 9 at first and fifth minute, respectively. As an infant he presented a regular psychomotor development with a delayed language for which he needed a school support.
At 4 years and 6 months the neuropsychological evaluation revealed normal non-verbal performances at psychometric test but difficulties in both expressive and comprehensive languages, with lexical and syntactic impairment. On examination (7 years), weight was 26 kg (75th centile), height 122 cm (50th centile) and head circumference 52.5 cm (>50th centile). At physical examination he presented straight eyebrows, short and smooth philtrum, right single palmar crease, shallow scrotum, one cafè-au-lait spot at the back, dry skin. Abdominal ultrasound examination, cardiological and ophthalmologic evaluation, electroencephalogram and auditory evoked potentials were normal. Laboratory investigations for metabolic disorders and molecular analysis for fragile-X syndrome were negative.
The father has completed his studies as a dentist, he doesn't present any physical impairment and has been considered healthy and normal all his life.
List of the additional copy number variations (CNVs) identified in the family.
Presence in DGV*
CHL1 has been mapped to 3p26.3, and was proposed as a candidate gene for non specific mental retardation because it is highly expressed in the brain [4, 8, 12–14]. The finding of a balanced translocation disrupting the gene CHL1 in an individual affected by non specific mental retardation further supports this suggestion .
Our findings strongly confirm the evidence that a loss of the more proximal genes is required to cause the typical 3p- syndrome clinical features, moreover the presence of a small terminal 3p deletion including only the CHL1 gene can determine only a mild phenotype or no symptoms at all as we observed in the members of our family.
Since the introduction of array-CGH analysis the finding of a transmitted chromosomal variant from a phenotypically normal parent has became more frequent. Inherited CNVs associated with both abnormal and normal phenotype have been recently reviewed in 200 families. Thrombocytopenia-Absent Radius syndrome , del(1)(q21.1) and deletions and duplications of 16p13.11 region represent only a few examples of genetic variations transmitted from an apparently normal parent to an affected child. A bias of ascertainment, chromosomal non-penetrance and gene modification are hypothesized as possible explanations . Moreover an apparently unaffected parent who carries the deletion could also have subtle phenotypic features consistent with the deletion that would become evident on further clinical evaluation. Other possibilities may account for phenotypic variability including differences in genetic background, epigenetic phenomena, expression or regulatory variation, and the unmasking of recessive variants residing on the other allele. Disease type and severity may be explained by the occurrence of additional rare events and their inheritance within families. The combination of two large CNVs in a single individual would increase or decrease the dosage for different genes creating a sensitized genomic background .
The "two-hit" model, as proposed by Girirajan et al , wherein a secondary rearrangement event is necessary to show the phenotype, could be an alternative explanation for the differences between the father and his sons.
We documented, in fact, the two affected individuals had an additional chromosomal abnormality larger than 500 Kbp and affecting the 1q44 region (Table 1). We can speculate this maternally inherited duplication, which is neutral in the mother, could instead contribute to the differences in the disease outcome observed between the two siblings and their father.
In conclusion, this familial case, characterized by a transmitted 3p deletion containing only the CHL1 gene and associated with a strong phenotypic variability, confirms the hypothesis that the association of terminal 3p deletion, mental retardation and learning disabilities is not casual.
Written consent was obtained from the parents of our two patients for publication of this case report. A copy of the written consent is available for review by the Editor-in-Chief of this journal.
We are grateful to the patients and their family members.
- Cargile CB, Goh DL, Goodman BK, Chen XN, Korenberg JR, Semenza GL, Thomas GH: Molecular cytogenetic characterization of a subtle interstitial del(3)(p25.3p26.2) in a patient with deletion 3p syndrome. Am J Med Genet. 2002, 109: 133-138. 10.1002/ajmg.10323.View ArticlePubMedGoogle Scholar
- Malmgren H, Sahlén S, Wide K, Lundvall M, Blennow E: Distal 3p deletion syndrome: detailed molecular cytogenetic and clinical characterization of three small distal deletions and review. Am J Med Genet A. 2007, 143A: 2143-2149. 10.1002/ajmg.a.31902.View ArticlePubMedGoogle Scholar
- Takagishi J, Rauen KA, Drumheller T, Kousseff B, Sutcliffe M: Chromosome 3p25 deletion in mother and daughter with minimal phenotypic effect. Am J Med Genet A. 2006, 140: 1587-1593.View ArticlePubMedGoogle Scholar
- Pohjola P, de Leeuw N, Penttinen M, Kääriäinen H: Terminal 3p deletions in two families--correlation between molecular karyotype and phenotype. Am J Med Genet A. 2010, 152A: 441-446. 10.1002/ajmg.a.33215.View ArticlePubMedGoogle Scholar
- Knight LA, Yong MH, Tan M, Ng IS: Del(3)(p25.3) without phenotypic effect. J Med Genet. 1995, 32: 994-995. 10.1136/jmg.32.12.994.PubMed CentralView ArticlePubMedGoogle Scholar
- Barber JC: Terminal 3p deletions: phenotypic variability, chromosomal non-penetrance, or gene modification?. Am J Med Genet A. 2008, 146A: 1899-1901. 10.1002/ajmg.a.32387.View ArticlePubMedGoogle Scholar
- Rivera H, Domínguez MG, Matute E: Follow-up of an intelligent odd-mannered teenager with del(3)(p26). Remarks on authorship and ethical commitment. Genet Couns. 2006, 17: 401-405.PubMedGoogle Scholar
- Shrimpton AE, Jensen KA, Hoo JJ: Karyotype-phenotype analysis and molecular delineation of a 3p26 deletion/8q24.3 duplication case with a virtually normal phenotype and mild cognitive deficit. Am J Med Genet A. 2006, 140A: 388-391. 10.1002/ajmg.a.31066.View ArticleGoogle Scholar
- Dijkhuizen T, van Essen T, van der Vlies P, Verheij JB, Sikkema-Raddatz B, van der Veen AY, Gerssen-Schoorl KB, Buys CH, Kok K: FISH and array-CGH analysis of a complex chromosome 3 aberration suggests that loss of CNTN4 and CRBN contributes to mental retardation in 3pter deletions. Am J Med Genet A. 2006, 140: 2482-2487.View ArticlePubMedGoogle Scholar
- Shuib S, McMullan D, Rattenberry E, Barber RM, Rahman F, Zatyka M, Chapman C, Macdonald F, Latif F, Davison V, Maher ER: Microarray based analysis of 3p25-p26 deletions (3p- syndrome). Am J Med Genet A. 2009, 149A: 2099-2105. 10.1002/ajmg.a.32824.View ArticlePubMedGoogle Scholar
- Frints SG, Marynen P, Hartmann D, Fryns JP, Steyaert J, Schachner M, Rolf B, Craessaerts K, Snellinx A, Hollanders K, D'Hooge R, De Deyn PP, Froyen G: CALL interrupted in a patient with non-specific mental retardation: gene dosage-dependent alteration of murine brain development and behavior. Hum Mol Genet. 2003, 12: 1463-1474. 10.1093/hmg/ddg165.View ArticlePubMedGoogle Scholar
- Angeloni D, Lindor NM, Pack S, Latif F, Wei M-H, Lerman MI: CALL gene is haploinsufficient in a 3p- syndrome patient. Am J Med Genet. 1999, 86: 482-485. 10.1002/(SICI)1096-8628(19991029)86:5<482::AID-AJMG15>3.0.CO;2-L.View ArticlePubMedGoogle Scholar
- Barber JC: Directly transmitted unbalanced chromosome abnormalities and euchromatic variants. J Med Genet. 2005, 42: 609-629. 10.1136/jmg.2004.026955.PubMed CentralView ArticlePubMedGoogle Scholar
- Wei MH, Karavanova I, Ivanov SV, Popescu NC, Keck CL, Pack S, Eisen JA. Lerman MI: In silico-initiated cloning and molecular characterization of a novel human member of the L1 gene family of neural cell adhesion molecules. Hum Genet. 1998, 103: 355-364. 10.1007/s004390050829.View ArticlePubMedGoogle Scholar
- Klopocki E, Schulze H, Strauss G, Ott CE, Hall J, Trotier F, Fleischhauer S, Greenhalgh L, Newbury-Ecob RA, Neumann LM, Habenicht R, König R, Seemanova E, Megarbane A, Ropers HH, Ullmann R, Horn D, Mundlos S: Complex inheritance pattern resembling autosomal recessive inheritance involving a microdeletion in thrombocytopenia-absent radius syndrome. Am J Hum Genet. 2007, 80: 232-240. 10.1086/510919.PubMed CentralView ArticlePubMedGoogle Scholar
- Mefford HC, Sharp AJ, Baker C, Itsara A, Jiang Z, Buysse K, Huang S, Maloney VK, Crolla JA, Baralle D, Collins A, Mercer C, Norga K, de Ravel T, Devriendt K, Bongers EM, de Leeuw N, Reardon W, Gimelli S, Bena F, Hennekam RC, Male A, Gaunt L, Clayton-Smith J, Simonic I, Park SM, Mehta SG, Nik-Zainal S, Woods CG, Firth HV, Parkin G, Fichera M, Reitano S, Lo Giudice M, Li KE, Casuga I, Broomer A, Conrad B, Schwerzmann M, Räber L, Gallati S, Striano P, Coppola A, Tolmie JL, Tobias ES, Lilley C, Armengol L, Spysschaert Y, Verloo P, De Coene A, Goossens L, Mortier G, Speleman F, van Binsbergen E, Nelen MR, Hochstenbach R, Poot M, Gallagher L, Gill M, McClellan J, King MC, Regan R, Skinner C, Stevenson RE, Antonarakis SE, Chen C, Estivill X, Menten B, Gimelli G, Gribble S, Schwartz S, Sutcliffe JS, Walsh T, Knight SJ, Sebat J, Romano C, Schwartz CE, Veltman JA, de Vries BB, Vermeesch JR, Barber JC, Willatt L, Tassabehji M, Eichler EE: Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med. 2008, 359: 1685-1699. 10.1056/NEJMoa0805384.PubMed CentralView ArticlePubMedGoogle Scholar
- Hannes FD, Sharp AJ, Mefford HC, de Ravel T, Ruivenkamp CA, Breuning MH, Fryns JP, Devriendt K, Van Buggenhout G, Vogels A, Stewart H, Hennekam RC, Cooper GM, Regan R, Knight SJ, Eichler EE, Vermeesch JR: Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant. J Med Genet. 2009, 46: 223-232. 10.1136/jmg.2007.055202.PubMed CentralView ArticlePubMedGoogle Scholar
- Girirajan S, Eichler EE: Phenotypic variability and genetic susceptibility to genomic disorders. Hum Mol Genet. 2010, 19 (R2): R176-187. 10.1093/hmg/ddq366.PubMed CentralView ArticlePubMedGoogle Scholar
- Girirajan S, Rosenfeld JA, Cooper GM, Antonacci F, Siswara P, Itsara A, Vives L, Walsh T, McCarthy SE, Baker C, Mefford HC, Kidd JM, Browning SR, Browning BL, Dickel DE, Levy DL, Ballif BC, Platky K, Farber DM, Gowans GC, Wetherbee JJ, Asamoah A, Weaver DD, Mark PR, Dickerson J, Garg BP, Ellingwood SA, Smith R, Banks VC, Smith W, McDonald MT, Hoo JJ, French BN, Hudson C, Johnson JP, Ozmore JR, Moeschler JB, Surti U, Escobar LF, El-Khechen D, Gorski JL, Kussmann J, Salbert B, Lacassie Y, Biser A, McDonald-McGinn DM, Zackai EH, Deardorff MA, Shaikh TH, Haan E, Friend KL, Fichera M, Romano C, Gécz J, DeLisi LE, Sebat J, King MC, Shaffer LG, Eichler EE: A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. Nat Genet. 2010, 42: 203-209. 10.1038/ng.534.PubMed CentralView ArticlePubMedGoogle Scholar
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