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A biallelic loss-of-function variant in TMEM147 causes profound intellectual disability and spasticity

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Abstract

Intellectual disability (ID), occurring in syndromic or non-syndromic forms, is the most common neurodevelopmental disorder. Although many cases are caused by single gene defects, ID is highly genetically heterogeneous. Biallelic variants in the transmembrane protein TMEM147 have recently been linked to intellectual disability with dysmorphic facial features. TMEM147 is believed to localize to the endoplasmic reticulum membrane and nuclear envelope and also involved in biogenesis of multi-pass membrane proteins. Here, we report two patients born to a consanguineous family with a novel loss-of-function variant; (NM_001242597.2:c.193-197del) in TMEM147 causing intellectual disability and spasticity. Whole exome sequencing and validating Sanger sequencing were utilized to confirm the identified causal variant. Our findings were in line with the previously described patients with TMEM147 variants manifesting intellectual disability as a major clinical sign but also featured spasticity as a phenotypic expansion. This study provides additional evidence for the pathogenicity of TMEM147 mutations in intellectual disability and expands the phenotypic and variant spectrum linked to this gene.

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  • 20 September 2023

    A non-academic email was mistakenly used by Dr. Hossein Mazdarani (co-corresponding author) in the proof. This has been replaced with his academic email.

References

  1. Harripaul R, Noor A, Ayub M, Vincent JB (2017) The use of next-generation sequencing for research and diagnostics for intellectual disability. Cold Spring Harb Perspect Med 7(3). https://doi.org/10.1101/cshperspect.a026864

  2. Hu H, Kahrizi K, Musante L, Fattahi Z, Herwig R, Hosseini M, Oppitz C, Abedini SS, Suckow V, Larti F, Beheshtian M (2019) Genetics of intellectual disability in consanguineous families. Mol Psychiatry 24(7):1027–1039. https://doi.org/10.1038/s41380-017-0012-2

    Article  CAS  PubMed  Google Scholar 

  3. Reuter MS et al (2017) Diagnostic yield and novel candidate genes by exome sequencing in 152 consanguineous families with neurodevelopmental disorders. JAMA Psychiatry 74(3):293–299. https://doi.org/10.1001/jamapsychiatry.2016.3798

    Article  PubMed  Google Scholar 

  4. Dettmer U, Kuhn PH, Abou-Ajram C et al (2010) Transmembrane protein 147 (TMEM147) is a novel component of the Nicalin-NOMO protein complex. J Biol Chem 285(34):26174–26181. https://doi.org/10.1074/jbc.M110.132548

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Rosemond E, Rossi M, McMillin SM, Scarselli M, Donaldson JG, Wess J (2011) Regulation of M3 muscarinic receptor expression and function by transmembrane protein 147. Mol Pharmacol 79(2):251–261. https://doi.org/10.1124/mol.110.067363

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Christodoulou A, Maimaris G, Makrigiorgi A et al (2020) TMEM147 interacts with lamin B receptor, regulates its localization and levels, and affects cholesterol homeostasis. J Cell Sci 133(16). https://doi.org/10.1242/jcs.245357

  7. Duband-Goulet I, Courvalin JC, Buendia B (1998) LBR a chromatin and lamin binding protein from the inner nuclear membrane, is proteolyzed at late stages of apoptosis. J Cell Sci 111(10):1441–1451. https://doi.org/10.1242/jcs.111.10.1441

    Article  CAS  PubMed  Google Scholar 

  8. Koczok K, Gurumurthy CB, Balogh I, Korade Z, Mirnics K (2019) Subcellular localization of sterol biosynthesis enzymes. J Mol Histol 50(1):63–73. https://doi.org/10.1007/s10735-018-9807-y

    Article  PubMed  Google Scholar 

  9. McGilvray PT, Anghel SA, Sundaram A et al (2020) An ER translocon for multi-pass membrane protein biogenesis. Elife 9. https://doi.org/10.7554/eLife.56889

  10. Thomas Q, Motta M, Gautier T et al (2022) Bi-allelic loss-of-function variants in TMEM147 cause moderate to profound intellectual disability with facial dysmorphism and pseudo-Pelger-Huët anomaly. Am J Hum Genet 109(10):1909–1922. https://doi.org/10.1016/j.ajhg.2022.08.008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Sundaram A, Yamsek M, Zhong F, Hooda Y, Hegde RS, Keenan RJ (2022) Substrate-driven assembly of a translocon for multipass membrane proteins. Nature 611(7934):167–172. https://doi.org/10.1038/s41586-022-05330-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26(5):589–595. https://doi.org/10.1093/bioinformatics/btp698

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38(16):e164. https://doi.org/10.1093/nar/gkq603

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Karczewski KJ, Francioli LC, Tiao G et al (2021) The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 590(7846):E53. https://doi.org/10.1038/s41586-020-2308-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Richards S, Aziz N, Bale S et al (2015) Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 17(5):405–424. https://doi.org/10.1038/gim.2015.30

    Article  PubMed  PubMed Central  Google Scholar 

  16. Oosterwijk JC, Mansour S, van Noort G, Waterham HR, Hall CM, Hennekam RC (2003) Congenital abnormalities reported in Pelger-Huët homozygosity as compared to Greenberg/HEM dysplasia: highly variable expression of allelic phenotypes. J Med Genet 40(12):937–941. https://doi.org/10.1136/jmg.40.12.937

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Hoffmann K, Dreger CK, Olins AL et al (2002) Mutations in the gene encoding the lamin B receptor produce an altered nuclear morphology in granulocytes (Pelger-Huët anomaly). Nat Genet 31(4):410–414. https://doi.org/10.1038/ng925

    Article  CAS  PubMed  Google Scholar 

  18. Bolar NA, Golzio C, Živná M et al (2016) Heterozygous loss-of-function SEC61A1 mutations cause autosomal-dominant tubulo-interstitial and glomerulocystic kidney disease with anemia. Am J Hum Genet 99(1):174–187. https://doi.org/10.1016/j.ajhg.2016.05.028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Graham HK et al (2015) Cerebral palsy. Nat Rev Dis Prim 2(1):15082. https://doi.org/10.1038/nrdp.2015.82

    Article  Google Scholar 

  20. Korzeniewski SJ, Slaughter J, Lenski M, Haak P, Paneth N (2018) The complex aetiology of cerebral palsy. Nat Rev Neurol 14(9):528–543. https://doi.org/10.1038/s41582-018-0043-6

    Article  PubMed  Google Scholar 

  21. Michael-Asalu A, Taylor G, Campbell H et al (2019) Cerebral palsy: diagnosis, epidemiology, genetics, and clinical update. Adv Pediatr 66:189–208. https://doi.org/10.1016/j.yapd.2019.04.002

    Article  PubMed  Google Scholar 

  22. Radio FC, Pang K, Ciolfi A et al (2021) SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females. Am J Hum Genet 108(3):502–516. https://doi.org/10.1016/j.ajhg.2021.01.015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank all family members for their participation.

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Correspondence to Michael C. Kruer or Hossein Mozdarani.

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The study was approved by the Student Research Committee (SRC) of the Faculty of Medical Sciences, Tarbiat Modares University.

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Ghorashi, T., Darvish, H., Bakhtiari, S. et al. A biallelic loss-of-function variant in TMEM147 causes profound intellectual disability and spasticity. Neurogenetics 24, 311–316 (2023). https://doi.org/10.1007/s10048-023-00734-8

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