. 2018 May 3;102(5):985-994.

doi: 10.1016/j.ajhg.2018.03.004. Epub 2018 Apr 12.

Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies

Hanyin Cheng¹, Avinash V Dharmadhikari¹, Sylvia Varland², Ning Ma³, Deepti Domingo⁴, Robert Kleyner⁵, Alan F Rope⁶, Margaret Yoon⁵, Asbjørg Stray-Pedersen⁷, Jennifer E Posey⁸, Sarah R Crews⁹, Mohammad K Eldomery⁸, Zeynep Coban Akdemir⁸, Andrea M Lewis¹⁰, Vernon R Sutton⁸, Jill A Rosenfeld⁸, Erin Conboy¹¹, Katherine Agre¹¹, Fan Xia¹², Magdalena Walkiewicz¹³, Mauro Longoni¹⁴, Frances A High¹⁵, Marjon A van Slegtenhorst¹⁶, Grazia M S Mancini¹⁶, Candice R Finnila¹⁷, Arie van Haeringen¹⁸, Nicolette den Hollander¹⁸, Claudia Ruivenkamp¹⁸, Sakkubai Naidu¹⁹, Sonal Mahida¹⁹, Elizabeth E Palmer²⁰, Lucinda Murray²¹, Derek Lim²², Parul Jayakar²³, Michael J Parker²⁴, Stefania Giusto²⁵, Emanuela Stracuzzi²⁵, Corrado Romano²⁵, Jennifer S Beighley²⁶, Raphael A Bernier²⁶, Sébastien Küry²⁷, Mathilde Nizon²⁷, Mark A Corbett²⁸, Marie Shaw²⁸, Alison Gardner²⁸, Christopher Barnett²⁹, Ruth Armstrong³⁰, Karin S Kassahn³¹, Anke Van Dijck³², Geert Vandeweyer³², Tjitske Kleefstra³³, Jolanda Schieving³³, Marjolijn J Jongmans³³, Bert B A de Vries³³, Rolph Pfundt³³, Bronwyn Kerr³⁴, Samantha K Rojas³⁵, Kym M Boycott³⁵, Richard Person³⁶, Rebecca Willaert³⁶, Evan E Eichler³⁷, R Frank Kooy³², Yaping Yang¹², Joseph C Wu³, James R Lupski³⁸, Thomas Arnesen³⁹, Gregory M Cooper¹⁷, Wendy K Chung⁴⁰, Jozef Gecz⁴¹, Holly A F Stessman⁹, Linyan Meng⁴², Gholson J Lyon⁴³

Affiliations

¹ Baylor Genetics, Houston, TX, 77021, USA.
² Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway.
³ Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
⁴ School of Biological Sciences, Faculty of Genes and Evolution, the University of Adelaide, Adelaide, SA 5000, Australia.
⁵ Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA.
⁶ Department of Medical Genetics, Kaiser Permanente Northwest, Portland, OR 97227, USA.
⁷ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, N-0424 Oslo, and Institute of Clinical Medicine, University of Oslo, N-0318 Oslo, Norway.
⁸ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
⁹ Department of Pharmacology, Creighton University Medical School, Omaha, NE, 68178, USA.
¹⁰ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX 77030, USA.
¹¹ Department of Clinical Genomics, Mayo Clinic, MN 55905, USA.
¹² Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
¹³ Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; The National Institute of Allergy and Infectious Disease, The National Institutes of Health, Bethesda, MD 20892, USA.
¹⁴ Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Harvard Medical School, Boston, MA 02114, USA.
¹⁵ Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA.
¹⁶ Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands.
¹⁷ HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
¹⁸ Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333, The Netherlands.
¹⁹ Kennedy Krieger Institute, 801 North Broadway Baltimore, MD 21205, USA.
²⁰ Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW 2031, Australia.
²¹ Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia.
²² West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Mindelsohn Way, Birmingham B15 2TG, UK.
²³ Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL 33155, USA.
²⁴ Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK.
²⁵ Oasi Research Institute - Istituto di Ricovero e Cura a Carattere Scientifico, Troina 94018, Italy.
²⁶ Department of Psychiatry, University of Washington, Seattle WA, 98195, USA.
²⁷ Department of Medical Genetics, Centre Hospitalier Universitaire, Nantes 44093, France.
²⁸ Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia.
²⁹ Paediatric and Reproductive Genetics, South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), Adelaide, SA 5006, Australia.
³⁰ East Anglian Medical Genetics Service, Clinical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
³¹ Department of Genetics and Molecular Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, SA 5006, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA 5000, Australia.
³² Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium.
³³ Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands.
³⁴ Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9PL, UK; Division of Evolution and Genomic Sciences School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK.
³⁵ Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada.
³⁶ GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA.
³⁷ Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
³⁸ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center of Baylor College of Medicine, Houston, TX 77030, USA.
³⁹ Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway; Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway.
⁴⁰ Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA.
⁴¹ School of Biological Sciences, Faculty of Genes and Evolution, the University of Adelaide, Adelaide, SA 5000, Australia; Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia; Healthy Mothers, Babies and Children, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia.
⁴² Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: lmeng@bcm.edu.
⁴³ Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA. Electronic address: gholsonjlyon@gmail.com.

PMID: 29656860
PMCID: PMC5986698
DOI: 10.1016/j.ajhg.2018.03.004

Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies

Hanyin Cheng et al. Am J Hum Genet. 2018.

. 2018 May 3;102(5):985-994.

doi: 10.1016/j.ajhg.2018.03.004. Epub 2018 Apr 12.

Authors

Affiliations

¹ Baylor Genetics, Houston, TX, 77021, USA.
² Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway.
³ Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
⁴ School of Biological Sciences, Faculty of Genes and Evolution, the University of Adelaide, Adelaide, SA 5000, Australia.
⁵ Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA.
⁶ Department of Medical Genetics, Kaiser Permanente Northwest, Portland, OR 97227, USA.
⁷ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, N-0424 Oslo, and Institute of Clinical Medicine, University of Oslo, N-0318 Oslo, Norway.
⁸ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
⁹ Department of Pharmacology, Creighton University Medical School, Omaha, NE, 68178, USA.
¹⁰ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX 77030, USA.
¹¹ Department of Clinical Genomics, Mayo Clinic, MN 55905, USA.
¹² Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
¹³ Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; The National Institute of Allergy and Infectious Disease, The National Institutes of Health, Bethesda, MD 20892, USA.
¹⁴ Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Harvard Medical School, Boston, MA 02114, USA.
¹⁵ Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA.
¹⁶ Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands.
¹⁷ HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
¹⁸ Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333, The Netherlands.
¹⁹ Kennedy Krieger Institute, 801 North Broadway Baltimore, MD 21205, USA.
²⁰ Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW 2031, Australia.
²¹ Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia.
²² West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Mindelsohn Way, Birmingham B15 2TG, UK.
²³ Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL 33155, USA.
²⁴ Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK.
²⁵ Oasi Research Institute - Istituto di Ricovero e Cura a Carattere Scientifico, Troina 94018, Italy.
²⁶ Department of Psychiatry, University of Washington, Seattle WA, 98195, USA.
²⁷ Department of Medical Genetics, Centre Hospitalier Universitaire, Nantes 44093, France.
²⁸ Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia.
²⁹ Paediatric and Reproductive Genetics, South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), Adelaide, SA 5006, Australia.
³⁰ East Anglian Medical Genetics Service, Clinical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
³¹ Department of Genetics and Molecular Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, SA 5006, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA 5000, Australia.
³² Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium.
³³ Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands.
³⁴ Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9PL, UK; Division of Evolution and Genomic Sciences School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK.
³⁵ Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada.
³⁶ GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA.
³⁷ Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
³⁸ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center of Baylor College of Medicine, Houston, TX 77030, USA.
³⁹ Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway; Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway.
⁴⁰ Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA.
⁴¹ School of Biological Sciences, Faculty of Genes and Evolution, the University of Adelaide, Adelaide, SA 5000, Australia; Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia; Healthy Mothers, Babies and Children, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia.
⁴² Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: lmeng@bcm.edu.
⁴³ Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA. Electronic address: gholsonjlyon@gmail.com.

PMID: 29656860
PMCID: PMC5986698
DOI: 10.1016/j.ajhg.2018.03.004

Abstract

N-alpha-acetylation is a common co-translational protein modification that is essential for normal cell function in humans. We previously identified the genetic basis of an X-linked infantile lethal Mendelian disorder involving a c.109T>C (p.Ser37Pro) missense variant in NAA10, which encodes the catalytic subunit of the N-terminal acetyltransferase A (NatA) complex. The auxiliary subunit of the NatA complex, NAA15, is the dimeric binding partner for NAA10. Through a genotype-first approach with whole-exome or genome sequencing (WES/WGS) and targeted sequencing analysis, we identified and phenotypically characterized 38 individuals from 33 unrelated families with 25 different de novo or inherited, dominantly acting likely gene disrupting (LGD) variants in NAA15. Clinical features of affected individuals with LGD variants in NAA15 include variable levels of intellectual disability, delayed speech and motor milestones, and autism spectrum disorder. Additionally, mild craniofacial dysmorphology, congenital cardiac anomalies, and seizures are present in some subjects. RNA analysis in cell lines from two individuals showed degradation of the transcripts with LGD variants, probably as a result of nonsense-mediated decay. Functional assays in yeast confirmed a deleterious effect for two of the LGD variants in NAA15. Further supporting a mechanism of haploinsufficiency, individuals with copy-number variant (CNV) deletions involving NAA15 and surrounding genes can present with mild intellectual disability, mild dysmorphic features, motor delays, and decreased growth. We propose that defects in NatA-mediated N-terminal acetylation (NTA) lead to variable levels of neurodevelopmental disorders in humans, supporting the importance of the NatA complex in normal human development.

Keywords: N-terminal acetylation (NTA); N-terminal acetyltransferases (NATs); NAA10; NAA15; NatA complex; Ogden syndrome; autism; congenital heart defects; intellectual disability; neurodevelopmental disorder.

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Figures

**Figure 1**
Pedigrees, Mild Facial Dysmorphology, and Hands of Individuals with Familial or *de novo NAA15* LGD Variants (A) Pedigrees are shown for the three families with inherited variants. **Family 10, Individual 10-1:** at age 17 years and 6 months, with prominent eyebrows, broad nose, and prominent chin. Hand appears normal. **Individual 10-2:** at 6 years and 6 months, with very well-developed philtral pillars. Hand appears normal. **Individual 10-3:** mother, with long mentum of the chin and relatively thick alae nasi. Hand appears normal. **Family 28, Individual 28-1:** at age 15 years, partial syndactyly in one hand, but otherwise not with particularly notable dysmorphology. **Individual 28-2:** sister, at age 12 years, who was not noted to have any obvious dysmorphology. **Individual 28-3:** Mother at age 45 years, with broad nose but otherwise not with notable dysmorphology. (B) Minor facial dysmorphology was noted in some probands, but there were no reliably consistent features shared among them. **Individual 2:** at 17 years old, noted to have brachycephaly, appearance of ocular hypertelorism with short palpebral fissures, prominent nose tip with a longer columella of the nose, trapezoidal philtrum, and micrognathia without retrognathia. Also noted are small low-set, posteriorly rotated ears, with thickened and overfolded helix; hypoplastic distal phalanges on digits 2, 3, and 4; 5th finger with brachyclinodactyly; and persistence of fetal finger pads on the 3rd and 4th digit. **Individual 8:** at the age 8 years 9 months, noted to have thin philtrum, bulbous nasal tip, and 5th finger with brachyclinodactyly. **Individual 13:** at 4 years old, no facial dysmorphism noted. **Individual 18:** at 4 years and 3 months, with bulbous nose tip, thick alae nasi and anteverted nares, prominent cupid’s bow and philtrum, long mentum of the chin, and simple ears. **Individual 31**: with epicanthus inversus, smooth philtrum, thin vermilion border of the upper lip, and sparse lateral eyebrows.

**Figure 2**
Exonic Localization of *NAA15* LGD Variants Identified in Subjects in This Study Schematic representation of the genomic structure of human *NAA15*. Solid blue rectangles indicate exons, and the horizontal bars represent introns. *NAA15* variants with their relative positions in the gene are shown, and the number of affected individuals with the specific variants is shown in parentheses.

**Figure 3**
Expression Analysis of *NAA15* in Research-Subject-Derived Cell Lines (A and D) Sanger sequencing of genomic DNA (top panel) and reverse-transcribed cDNA (bottom panel) isolated from a lymphoblastoid cell line (LCL) of individual 10-1 (c.239_240delAT) (A) and an induced pluripotent stem cell (iPS) line (passage 16) of individual 19 (c.1009_1012delGAAA) (D). (B and E) Quantification of different cDNA species from cDNA Sanger sequencing showing the relative ratio of WT *NAA15* versus c.239_240delAT (LCL line) (B) and (c.1009_1012delGAAA) (passage 16 iPS cell line) (E). (C and F) *NAA15* mRNA expression level analyzed by qPCR in research subject-derived cell lines (at passage numbers p10, p13, and p16), as compared to control cell lines (at passage 16). Error bars are standard deviation (SD), and the assay was performed three times per sample.

**Figure 4**
Truncation Mutations of Human NAA15 Impair NatA Function and Yeast Viability (A) Serial dilution spot assay depicting the sensitivity of human *NAA15* Thr55Hisfs^∗2 and Lys305^∗ mutants to increased temperature in a *ynaa10Δ*, *ynaa15Δ* double-deletion background (*yNatAΔ*). (B) Confirmation of human NatA expression by immunoblot analysis with anti-hNAA10 and anti-HA (for HA-hNAA15 detection) along with anti-beta Actin as a loading control.

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Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies

Affiliations

Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies

Authors

Affiliations

Abstract

Figures

References

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Grants and funding

LinkOut - more resources

Full Text Sources

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Medical

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