. 2020 Jul;22(7):1215-1226.

doi: 10.1038/s41436-020-0792-7. Epub 2020 May 7.

Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7

Laura Castilla-Vallmanya¹, Kaja K Selmer^{2

3}, Clémantine Dimartino^{4

5}, Raquel Rabionet¹, Bernardo Blanco-Sánchez^{4

5}, Sandra Yang⁶, Margot R F Reijnders⁷, Antonie J van Essen⁸, Myriam Oufadem^{4

5}, Magnus D Vigeland^{9

10}, Barbro Stadheim⁹, Gunnar Houge¹¹, Helen Cox¹², Helen Kingston^{13

14}, Jill Clayton-Smith^{13

14}, Jeffrey W Innis¹⁵, Maria Iascone¹⁶, Anna Cereda¹⁶, Sara Gabbiadini¹⁶, Wendy K Chung¹⁷, Victoria Sanders^{18

19}, Joel Charrow¹⁸, Emily Bryant¹⁸, John Millichap¹⁸, Antonio Vitobello^{20

21}, Christel Thauvin^{20

22}, Frederic Tran Mau-Them^{20

21}, Laurence Faivre^{21

22}, Gaetan Lesca^{23

24}, Audrey Labalme²³, Christelle Rougeot²⁵, Nicolas Chatron^{23

24}, Damien Sanlaville^{23

24}, Katherine M Christensen²⁶, Amelia Kirby²⁶, Raymond Lewandowski²⁷, Rachel Gannaway²⁷, Maha Aly^{4

5}, Anna Lehman²⁸, Lorne Clarke²⁸, Luitgard Graul-Neumann²⁹, Christiane Zweier³⁰, Davor Lessel³¹, Bernarda Lozic³², Ingvild Aukrust¹¹, Ryan Peretz³³, Robert Stratton³³, Thomas Smol^{34

35}, Anne Dieux-Coëslier³⁴, Joanna Meira³⁶, Elizabeth Wohler³⁷, Nara Sobreira³⁷, Erin M Beaver³⁸, Jennifer Heeley³⁸, Lauren C Briere³⁹, Frances A High³⁹, David A Sweetser³⁹, Melissa A Walker⁴⁰, Catherine E Keegan¹⁵, Parul Jayakar⁴¹, Marwan Shinawi⁴², Wilhelmina S Kerstjens-Frederikse⁸, Dawn L Earl⁴³, Victoria M Siu⁴⁴, Emma Reesor⁴⁴, Tony Yao⁴⁴, Robert A Hegele⁴⁴, Olena M Vaske⁴⁵, Shannon Rego⁴⁶; Undiagnosed Diseases Network, Care4Rare Canada Consortium; Kevin A Shapiro⁴⁷, Brian Wong⁴⁷, Michael J Gambello⁴⁸, Marie McDonald⁴⁹, Danielle Karlowicz⁴⁹, Roberto Colombo^{50

51}, Alessandro Serretti⁵², Lynn Pais⁵³, Anne O'Donnell-Luria⁵³, Alison Wray⁵⁴, Simon Sadedin⁵⁵, Belinda Chong⁵⁵, Tiong Y Tan^{55

56}, John Christodoulou^{55

56}, Susan M White^{55

56}, Anne Slavotinek⁵⁷, Deborah Barbouth⁵⁸, Dayna Morel Swols⁵⁸, Mélanie Parisot^{59

60}, Christine Bole-Feysot^{59

60}, Patrick Nitschké^{5

61}, Véronique Pingault^{4

5

62}, Arnold Munnich^{5

62}, Megan T Cho⁶, Valérie Cormier-Daire^{5

62

63}, Susanna Balcells¹, Stanislas Lyonnet^{4

5

62}, Daniel Grinberg¹, Jeanne Amiel^{4

5

62}, Roser Urreizti^#¹, Christopher T Gordon^#^{64

65}

Affiliations

¹ Department of Genetics, Microbiology and Statistics, Faculty of Biology, IBUB, Universitat de Barcelona; CIBERER, IRSJD, Barcelona, Spain.
² Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital and the University of Oslo, Oslo, Norway.
³ The National Center for Epilepsy, Oslo University Hospital, Oslo, Norway.
⁴ Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.
⁵ Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.
⁶ GeneDx, Gaithersburg, MD, USA.
⁷ Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.
⁸ Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands.
⁹ Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
¹⁰ Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
¹¹ Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
¹² West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham Women's Hospital, Edgbaston, Birmingham, UK.
¹³ Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Academic Health Sciences Centre, Manchester, UK.
¹⁴ Division of Evolution and Genomic Sciences, University of Manchester, School of Biological Sciences, Manchester, UK.
¹⁵ Departments of Human Genetics, Pediatrics and Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
¹⁶ Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy.
¹⁷ Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA.
¹⁸ Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA.
¹⁹ Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
²⁰ UF Innovation en diagnostic genomique des maladies rares, CHU Dijon Bourgogne, Dijon, France.
²¹ INSERM UMR1231 GAD, Dijon, France.
²² Centre de Reference maladies rares "Anomalies du Developpement et syndrome malformatifs" de l'Est, Centre de Genetique, Hopital d'Enfants, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France.
²³ Department of Medical Genetics, Lyon Hospices Civils, Lyon, France.
²⁴ Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Université de Lyon, Lyon, France.
²⁵ Hôpital Femme Mère Enfant, Service de Neuropédiatrie, Bron, France.
²⁶ Saint Louis University School of Medicine, St. Louis, MO, USA.
²⁷ Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA.
²⁸ Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada.
²⁹ Institute of Human Genetics, Charité, Universitätsmedizin Berlin, Berlin, Germany.
³⁰ Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
³¹ Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
³² Department of Pediatrics, University Hospital Centre Split; University of Split, School of medicine, Split, Croatia.
³³ Driscoll Children's Hospital, Corpus Christi, TX, USA.
³⁴ Institut de Génétique Médicale, CHU Lille, Lille, France.
³⁵ Université de Lille, EA 7364 - RADEME - Maladies RAres du DEveloppement embryonnaire et du MEtabolisme, Lille, France.
³⁶ Division of Medical Genetics, University Hospital Professor Edgard Santos/ Federal University of Bahia (UFBA), Salvador, Bahia, Brazil.
³⁷ McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
³⁸ Mercy Kids Genetics, Mercy Children's Hospital, St. Louis, MO, USA.
³⁹ Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA, USA.
⁴⁰ Department of Pediatric Neurology, Massachusetts General Hospital for Children, Boston, MA, USA.
⁴¹ Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL, USA.
⁴² Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
⁴³ Seattle Children's Hospital, Seattle, WA, USA.
⁴⁴ University of Western Ontario, London, ON, Canada.
⁴⁵ Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA.
⁴⁶ Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
⁴⁷ Cortica Healthcare, San Diego, CA, USA.
⁴⁸ Department of Human Genetics, Division of Medical Genetics, Emory University School of Medicine, Atlanta, GA, USA.
⁴⁹ Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA.
⁵⁰ Faculty of Medicine, Catholic University, IRCCS Policlinico Gemelli, Rome, Italy.
⁵¹ Center for the Study of Rare Hereditary Diseases (CeSMER), Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy.
⁵² Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy.
⁵³ Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
⁵⁴ Royal Children's Hospital, Melbourne, Australia.
⁵⁵ Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.
⁵⁶ Department of Paediatrics, University of Melbourne, Melbourne, Australia.
⁵⁷ Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
⁵⁸ Dr John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA.
⁵⁹ Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker INSERM UMR1163, Paris, France.
⁶⁰ INSERM US24/CNRS UMS3633, Paris Descartes-Sorbonne Paris Cité University, Paris, France.
⁶¹ Bioinformatics Platform, INSERM UMR 1163, Institut Imagine, Paris, France.
⁶² Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France.
⁶³ Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, Institut Imagine, Paris, France.
⁶⁴ Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France. chris.gordon@inserm.fr.
⁶⁵ Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France. chris.gordon@inserm.fr.

^# Contributed equally.

PMID: 32376980
PMCID: PMC8093014
DOI: 10.1038/s41436-020-0792-7

Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7

Laura Castilla-Vallmanya et al. Genet Med. 2020 Jul.

. 2020 Jul;22(7):1215-1226.

doi: 10.1038/s41436-020-0792-7. Epub 2020 May 7.

Authors

Affiliations

¹ Department of Genetics, Microbiology and Statistics, Faculty of Biology, IBUB, Universitat de Barcelona; CIBERER, IRSJD, Barcelona, Spain.
² Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital and the University of Oslo, Oslo, Norway.
³ The National Center for Epilepsy, Oslo University Hospital, Oslo, Norway.
⁴ Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.
⁵ Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.
⁶ GeneDx, Gaithersburg, MD, USA.
⁷ Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.
⁸ Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands.
⁹ Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
¹⁰ Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
¹¹ Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
¹² West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham Women's Hospital, Edgbaston, Birmingham, UK.
¹³ Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Academic Health Sciences Centre, Manchester, UK.
¹⁴ Division of Evolution and Genomic Sciences, University of Manchester, School of Biological Sciences, Manchester, UK.
¹⁵ Departments of Human Genetics, Pediatrics and Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
¹⁶ Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy.
¹⁷ Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA.
¹⁸ Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA.
¹⁹ Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
²⁰ UF Innovation en diagnostic genomique des maladies rares, CHU Dijon Bourgogne, Dijon, France.
²¹ INSERM UMR1231 GAD, Dijon, France.
²² Centre de Reference maladies rares "Anomalies du Developpement et syndrome malformatifs" de l'Est, Centre de Genetique, Hopital d'Enfants, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France.
²³ Department of Medical Genetics, Lyon Hospices Civils, Lyon, France.
²⁴ Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Université de Lyon, Lyon, France.
²⁵ Hôpital Femme Mère Enfant, Service de Neuropédiatrie, Bron, France.
²⁶ Saint Louis University School of Medicine, St. Louis, MO, USA.
²⁷ Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA.
²⁸ Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada.
²⁹ Institute of Human Genetics, Charité, Universitätsmedizin Berlin, Berlin, Germany.
³⁰ Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
³¹ Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
³² Department of Pediatrics, University Hospital Centre Split; University of Split, School of medicine, Split, Croatia.
³³ Driscoll Children's Hospital, Corpus Christi, TX, USA.
³⁴ Institut de Génétique Médicale, CHU Lille, Lille, France.
³⁵ Université de Lille, EA 7364 - RADEME - Maladies RAres du DEveloppement embryonnaire et du MEtabolisme, Lille, France.
³⁶ Division of Medical Genetics, University Hospital Professor Edgard Santos/ Federal University of Bahia (UFBA), Salvador, Bahia, Brazil.
³⁷ McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
³⁸ Mercy Kids Genetics, Mercy Children's Hospital, St. Louis, MO, USA.
³⁹ Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA, USA.
⁴⁰ Department of Pediatric Neurology, Massachusetts General Hospital for Children, Boston, MA, USA.
⁴¹ Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL, USA.
⁴² Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
⁴³ Seattle Children's Hospital, Seattle, WA, USA.
⁴⁴ University of Western Ontario, London, ON, Canada.
⁴⁵ Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA.
⁴⁶ Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
⁴⁷ Cortica Healthcare, San Diego, CA, USA.
⁴⁸ Department of Human Genetics, Division of Medical Genetics, Emory University School of Medicine, Atlanta, GA, USA.
⁴⁹ Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA.
⁵⁰ Faculty of Medicine, Catholic University, IRCCS Policlinico Gemelli, Rome, Italy.
⁵¹ Center for the Study of Rare Hereditary Diseases (CeSMER), Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy.
⁵² Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy.
⁵³ Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
⁵⁴ Royal Children's Hospital, Melbourne, Australia.
⁵⁵ Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.
⁵⁶ Department of Paediatrics, University of Melbourne, Melbourne, Australia.
⁵⁷ Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
⁵⁸ Dr John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA.
⁵⁹ Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker INSERM UMR1163, Paris, France.
⁶⁰ INSERM US24/CNRS UMS3633, Paris Descartes-Sorbonne Paris Cité University, Paris, France.
⁶¹ Bioinformatics Platform, INSERM UMR 1163, Institut Imagine, Paris, France.
⁶² Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France.
⁶³ Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, Institut Imagine, Paris, France.
⁶⁴ Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France. chris.gordon@inserm.fr.
⁶⁵ Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France. chris.gordon@inserm.fr.

^# Contributed equally.

PMID: 32376980
PMCID: PMC8093014
DOI: 10.1038/s41436-020-0792-7

Abstract

Purpose: Somatic variants in tumor necrosis factor receptor-associated factor 7 (TRAF7) cause meningioma, while germline variants have recently been identified in seven patients with developmental delay and cardiac, facial, and digital anomalies. We aimed to define the clinical and mutational spectrum associated with TRAF7 germline variants in a large series of patients, and to determine the molecular effects of the variants through transcriptomic analysis of patient fibroblasts.

Methods: We performed exome, targeted capture, and Sanger sequencing of patients with undiagnosed developmental disorders, in multiple independent diagnostic or research centers. Phenotypic and mutational comparisons were facilitated through data exchange platforms. Whole-transcriptome sequencing was performed on RNA from patient- and control-derived fibroblasts.

Results: We identified heterozygous missense variants in TRAF7 as the cause of a developmental delay-malformation syndrome in 45 patients. Major features include a recognizable facial gestalt (characterized in particular by blepharophimosis), short neck, pectus carinatum, digital deviations, and patent ductus arteriosus. Almost all variants occur in the WD40 repeats and most are recurrent. Several differentially expressed genes were identified in patient fibroblasts.

Conclusion: We provide the first large-scale analysis of the clinical and mutational spectrum associated with the TRAF7 developmental syndrome, and we shed light on its molecular etiology through transcriptome studies.

Keywords: TRAF7; blepharophimosis; craniofacial development; intellectual disability; patent ductus arteriosus.

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Figures

**Figure 1.**
TRAF7 variants. Domain boundaries drawn approximately to scale, based on ref. Variants causing the *TRAF7* syndrome are indicated in red (reported here) or grey (previously reported). In pink, variants of unknown significance reported here. Beneath the protein, the most recurrent somatic variants (ie, in greater than five samples) are indicated; in black, those reported in meningiomas^, and in blue, those in adenomatoid tumors of the genital tract. CC; coiled-coil.

**Figure 2.**
Facial features of patients with variants in *TRAF7*. Patient numbers are indicated at the top of each panel. See text for description of the major features.

**Figure 3.**
Anomalies of the extremities (A) and upper body appearance (B) of patients with variants in *TRAF7*. Patient numbers are indicated at the top of each panel. See text for description of the major features.

**Figure 4.**
qRT-PCR quantification of mRNA levels in *TRAF7* syndrome patient fibroblasts. (A) qRT-PCR of *BCL2*, *PTGS2*, *IGFBP7*, *NOTCH3*, *TRAF7* and *FLNB* in fibroblasts from three patients, with or without TNFα treatment. Relative mRNA level was normalized to the mean of six controls in each treatment condition (dotted line). *GAPDH* was used as a reference gene (the use of *PPIA* gave similar results). Data shown represents the mean ± SEM of the three patients, in six independent experiments. Asterisks indicate significant differences (p<0.05) between patients and controls in the corresponding condition (treated or untreated). (B) qRT-PCR validation of DEGs identified by RNA-Seq: *ANGPT1*, *CASK*, *KIF26B*, *KRAS*, *RIT1*, *WNT5A*, *CFD*, *GPC6* and *KAZALD1*. Relative mRNA level was normalized to the mean of six controls in each treatment condition (dotted line). *GAPDH* was used as a reference gene (the use of *PPIA* gave similar results). Data shown represents the mean ± SEM of the four patients, in two independent experiments. Asterisks indicate significant differences (p<0.05) between patients and controls in the corresponding condition (treated or untreated).

**Figure 5.**
Transcriptome analysis of fibroblasts bearing missense *TRAF7* variants. (A) Volcano plots representing differentially expressed genes (DEGs) in each condition (untreated or treated with TNFα (10 ng/ml) for 6 hours), measuring changes in expression (log₂ fold change) and their significance (FDR; -log₁₀ adjusted p-value). (B) Proportions of up- and down-regulated transcripts in untreated or treated patient fibroblasts. (C) Venn diagrams representing overlapping up- and down-regulated DEGs. (D and E) Ingenuity Pathway Analysis of DEGs in *TRAF7* syndrome patient fibroblasts. (D) Selected over-represented Canonical Pathways. The number of DEGs included in each pathway is specified and a −log₁₀ p-value >1.3 was considered significant. (E) Selected over-represented categories of “Cellular Functions and Physiological System Development”. The number of DEGs associated with each category is specified and a −log₁₀ p-value >1.3 was considered significant.

See this image and copyright information in PMC

References

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Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7

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Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7

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