- Letter to Editor
- Open Access
Intragenic MBD5 familial deletion variant does not negatively impact MBD5 mRNA expression
© Mullegama and Elsea; licensee BioMed Central Ltd. 2014
- Received: 18 September 2014
- Accepted: 25 October 2014
- Published: 19 November 2014
2q23.1 deletion syndrome is characterized by intellectual disability, speech impairment, seizures, disturbed sleep pattern, behavioral problems, and hypotonia. Core features of this syndrome are due to haploinsufficiency of MBD5. Deletions that include coding and noncoding exons show reduced MBD5 mRNA expression. We report a patient with a neurological and behavioral phenotype similar to 2q23.1 deletion syndrome with an inherited intronic deletion in the 5-prime untranslated region of MBD5. Our data show that this patient has normal MBD5 mRNA expression; therefore, this deletion is likely not causative for 2q23.1 deletion syndrome. Overall, it is important to validate intronic deletions for pathogenicity.
- 2q23.1 deletion syndrome
- Intronic deletion
- Gene expression
- Familial variant
Comparison of the phenotype of SMS431 to the prominent features of 2q23.1 deletion syndrome
2q23.1 deletion syndrome
Repetitive behaviors (stereotypies)
Short attention span
Infantile feeding difficulties
Heavy arched eyebrows
Thin upper lip
Widely spaced teeth
The Institutional Review Board Baylor College of Medicine approved this study. Fresh blood was collected from SMS431 (proband), SMS432 (father), SMS433 (mother), SMS361 (2q23.1 deletion patient) , and nine normal controls after informed consent was obtained. Total RNA was isolated according to standard methods (Invitrogen, Carlsbad, CA). RNA was quantified using the NanoDrop ® ND-100 Spectrophotometer and reverse transcribed through qSCRIPT cDNA SuperMix (Quanta Biosciences, Inc., Gaithersburg, MD) according to manufacturer’s instructions. To assess MBD5 mRNA expression, quantitative RT-PCR was performed as previously described ,. Briefly, Taqman minor groove binder probes for MBD5 (OMIM 611472, Hs00289233_m1) and GAPDH (OMIM 138400, Hs9999905_m1) were used. GAPDH was used as the endogenous control. All samples of cDNA were run in triplicate in 10 ul reaction volumes. All samples were run and analyzed according to previously published methods using BioRad CFX Connect™ Real-Time PCR Detection System . Three biological replicates were performed. Results are expressed as fold-change relative to the control sample. Standard error was generated for each sample. A paired t- test was used to determine significance. p <0.01 was considered statistically significant.
A survey of the Database of Genomic Variants (DGV) contains no deletions that are identical to that observed in the individuals in this family. DVG lists 14 small deletions in the 5′-noncoding region of MBD5, with nine deletions confined to intronic sequences, which were reported to be nonpathogenic or of unknown significance. Five of the nine small deletions were found in intron 4.
Overall, it is apparent that the intron 4 deletion does not affect expression of MBD5 and likely does not give rise to the features associated with the MBD5 haploinsufficiency that is observed in 2q23.1 deletion syndrome.
Introns in the noncoding region of a gene can play a major role in the transcriptional regulation of a gene and consequently, gene expression. An intron can enhance gene expression through the presence of transcriptional regulatory elements or through structural modulation and splicing . Copy number variants within splice site sequences at the intron-exon junction cause approximately 10% of disease-causing mutations . There are several cases in the medical literature of pathogenic intronic deletions such as NRXN1 deletions (Autism Spectrum Disorder) , SLC34A3 deletions (hereditary hypophosphatemic rickets with hypercalciuria) ,, PKD1 deletions (Rothmund-Thomson syndrome) , and NASE deletions (5-fluorouracil toxicity) .
Since the intronic deletion identified in SMS431 does not delete the splice junctions between exon 4 and exon 5 or create new splice junctions, proper mRNA splicing likely still occurs, without impacting expression. Further, deletions in 5-prime UTR introns could lead to altered expression if transcription factor binding is affected. Whether there are transcription factors, enhancers, or silencers that bind to that specific intronic region of MBD5 remains unclear.
In summary, SMS431 exhibited developmental delay, motor delay, severe language impairment, sleep disturbances and behavioral problems that mimicked 2q23.1 deletion syndrome (Table 1). However, these neurological and behavioral phenotypes are observed in other neurodevelopmental disorders. The 2q23.1 deletion syndrome phenotype overlaps with other neurodevelopmental disorders, including Angelman syndrome, Smith-Magenis syndrome, Pitt-Hopkins syndrome, and Kleefstra syndrome ,. SMS431 likely has a different neurodevelopmental disorder that overlaps phenotypically with 2q23.1 deletion syndrome. Since no other copy number variants were identified for this patient, additional testing will be required to determine a cause for the phenotype. The possibility exists that a gene that is involved in a pathway common to MBD5 may be affected, including a gene downstream of MBD5 or binding partner of MBD5. Finally, whole exome sequencing (WES) may be the best approach toward diagnosis for this child.
In conclusion, we highlight the importance of validating intronic deletions for pathogenicity so that accurate and informed diagnosis can be provided to the patient.
Written informed consent was obtained from the patient’s parents for publication of this paper. A copy of the written consent is available for review by the Editor-in-Chief of this journal.
We are thankful to the family for their willingness to participate in this study. We thank the Fondation Jerome Lejuene for funding portions of this study. This work was supported in part by resources from the Baylor College of Medicine and the Jan and Dan Duncan Neurological Research Institute.
- Shichiji M, Ito Y, Shimojima K, Nakamu H, Oguni H, Osawa M, Yamamoto T: A cryptic microdeletion including MBD5 occurring within the breakpoint of a reciprocal translocation between chromosomes 2 and 5 in a patient with developmental delay and obesity. Am J Med Genet A 2013, 161A: 850–855. 10.1002/ajmg.a.35768View ArticlePubMedGoogle Scholar
- Talkowski ME, Mullegama SV, Rosenfeld JA, van Bon BW, Shen Y, Repnikova EA, Gastier-Foster J, Thrush DL, Kathiresan S, Ruderfer DM, Chiang C, Hanscom C, Ernst C, Lindgren AM, Morton CC, An Y, Astbury C, Brueton LA, Lichtenbelt KD, Ades LC, Fichera M, Romano C, Innis JW, Williams CA, Bartholomew D, Van Allen MI, Parikh A, Zhang L, Wu BL, Pyatt RE, et al.: Assessment of 2q23.1 microdeletion syndrome implicates MBD5 as a single causal locus of intellectual disability, epilepsy, and autism spectrum disorder. Am J Hum Genet 2011, 89: 551–563. 10.1016/j.ajhg.2011.09.011PubMed CentralView ArticlePubMedGoogle Scholar
- Laget S, Joulie M, Le Masson F, Sasai N, Christians E, Pradhan S, Roberts RJ, Defossez PA: The human proteins MBD5 and MBD6 associate with heterochromatin but they do not bind methylated DNA. PLoS One 2010, 5: e11982. 10.1371/journal.pone.0011982PubMed CentralView ArticlePubMedGoogle Scholar
- Bonnet C, Ali Khan A, Bresso E, Vigouroux C, Beri M, Lejczak S, Deemer B, Andrieux J, Philippe C, Moncla A, Giurgea I, Devignes MD, Leheup B, Jonveaux P: Extended spectrum of MBD5 mutations in neurodevelopmental disorders. Eur J Hum Genet 2013, 21: 1457–1461. 10.1038/ejhg.2013.22PubMed CentralView ArticlePubMedGoogle Scholar
- Williams SR, Mullegama SV, Rosenfeld JA, Dagli AI, Hatchwell E, Allen WP, Williams CA, Elsea SH: Haploinsufficiency of MBD5 associated with a syndrome involving microcephaly, intellectual disabilities, severe speech impairment, and seizures. Eur J Hum Genet 2010, 18: 436–441. 10.1038/ejhg.2009.199PubMed CentralView ArticlePubMedGoogle Scholar
- Hodge JC, Mitchell E, Pillalamarri V, Toler TL, Bartel F, Kearney HM, Zou YS, Tan WH, Hanscom C, Kirmani S, Hanson RR, Skinner SA, Rogers RC, Everman DB, Boyd E, Tapp C, Mullegama SV, Keelean-Fuller D, Powell CM, Elsea SH, Morton CC, Gusella JF, DuPont B, Chaubey A, Lin AE, Talkowski ME: Disruption of MBD5 contributes to a spectrum of psychopathology and neurodevelopmental abnormalities. Mol Psychiatry 2014, 19: 368–379. 10.1038/mp.2013.42View ArticlePubMedGoogle Scholar
- Cenik C, Derti A, Mellor JC, Berriz GF, Roth FP: Genome-wide functional analysis of human 5' untranslated region introns. Genome Biol 2010, 11: R29. 10.1186/gb-2010-11-3-r29PubMed CentralView ArticlePubMedGoogle Scholar
- Krawczak M, Thomas NS, Hundrieser B, Mort M, Wittig M, Hampe J, Cooper DN: Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mRNA splicing. Hum Mutat 2007, 28: 150–158. 10.1002/humu.20400View ArticlePubMedGoogle Scholar
- Dabell MP, Rosenfeld JA, Bader P, Escobar LF, El-Khechen D, Vallee SE, Dinulos MB, Curry C, Fisher J, Tervo R, Hannibal MC, Siefkas K, Wyatt PR, Hughes L, Smith R, Ellingwood S, Lacassie Y, Stroud T, Farrell SA, Sanchez-Lara PA, Randolph LM, Niyazov D, Stevens CA, Schoonveld C, Skidmore D, MacKay S, Miles JH, Moodley M, Huillet A, Neill NJ, et al.: Investigation of NRXN1 deletions: clinical and molecular characterization. Am J Med Genet A 2013, 161A: 717–731. 10.1002/ajmg.a.35780View ArticlePubMedGoogle Scholar
- Ichikawa S, Sorenson AH, Imel EA, Friedman NE, Gertner JM, Econs MJ: Intronic deletions in the SLC34A3 gene cause hereditary hypophosphatemic rickets with hypercalciuria. J Clin Endocrinol Metab 2006, 91: 4022–4027. 10.1210/jc.2005-2840View ArticlePubMedGoogle Scholar
- Ichikawa S, Tuchman S, Padgett LR, Gray AK, Baluarte HJ, Econs MJ: Intronic deletions in the SLC34A3 gene: a cautionary tale for mutation analysis of hereditary hypophosphatemic rickets with hypercalciuria. Bone 2014, 59: 53–56. 10.1016/j.bone.2013.10.018PubMed CentralView ArticlePubMedGoogle Scholar
- Wang LL, Worley K, Gannavarapu A, Chintagumpala MM, Levy ML, Plon SE: Intron-size constraint as a mutational mechanism in Rothmund-Thomson syndrome. Am J Hum Genet 2002, 71: 165–167. 10.1086/341234PubMed CentralView ArticlePubMedGoogle Scholar
- van Kuilenburg AB, Meijer J, Mul AN, Meinsma R, Schmid V, Dobritzsch D, Hennekam RC, Mannens MM, Kiechle M, Etienne-Grimaldi MC, Klumpen HJ, Maring JG, Derleyn VA, Maartense E, Milano G, Vijzelaar R, Gross E: Intragenic deletions and a deep intronic mutation affecting pre-mRNA splicing in the dihydropyrimidine dehydrogenase gene as novel mechanisms causing 5-fluorouracil toxicity. Hum Genet 2010, 128: 529–538. 10.1007/s00439-010-0879-3PubMed CentralView ArticlePubMedGoogle Scholar
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