Jonathan Bernstein, MD, PhD

Division Chief, Medical Genetics | Professor

Clinical Genetics and Genomics

Mary L. Johnson Specialty Services

Medical Genetics

730 Welch Road

Palo Alto, CA 94304

Phone: (650) 723-6858

Fax: (650) 498-4555

Locations

Mary L. Johnson Specialty Services

Medical Genetics

730 Welch Road

Palo Alto, CA 94304

Phone : (650) 723-6858 723-6858)

Fax : (650) 498-4555

Services

Cleft and Craniofacial Center

Genetics Services

Microtia and Ear Canal Atresia

Conditions

• Autism
• Autism and Developmental Disorders
• Cardiovascular Genetic Issues
• Cleft Lip Cleft Palate
• Craniofacial Disorders and Craniosynostosis
• Development Delays and Disorders

Work and Education

• Professional Education: Stanford University School of Medicine, Palo Alto, CA, 06/30/2003
• Residency: Lucile Packard Children's Hospital, Palo Alto, CA, 06/30/2006
• Fellowship: Lucile Packard Children's Hospital, Palo Alto, CA, 06/30/2008
• Board Certifications:
  • Clinical Genetics and Genomics, American Board of Medical Genetics and Genomics, 2020
  • Pediatrics, American Board of Pediatrics, 2006

Publications

• BHLHE22 monoallelic and biallelic variants cause a neurodevelopmental disorder with agenesis of the corpus callosum, intellectual disability, abnormal muscle tone and movement abnormalities. Journal of medical genetics

  • Authors: Le, C., Kalayci, T., Uyguner, Z., Karaman, B. ... Bernstein, J. A., ... DOI 10.1136/jmg-2025-111432
  • PubMedID: 42586785

• Cognitive Decline, Neurologic Involvement, and Neonatal Crisis in ABCC9-Related Intellectual Disability and Myopathy Syndrome. Neurology. Genetics

  • Authors: Nagaraj, V., Thomas, Q. H., Nóbrega, P. R., ... Bernstein, J. A., ... DOI 10.1212/NXG.0000000000200385
  • PubMedID: 42290677

• "It didn't feel like anything unusual because we had already been through so much": Disability-Related Research Experiences of Families with Children Enrolled in the Undiagnosed Diseases Network. Genetics in medicine : official journal of the American College of Medical Genetics

  • Authors: Mintz, K. T., Altamirano, E. N., Halley, M. C., ... Bernstein, J. A., ... DOI 10.1016/j.gim.2026.102663
  • PubMedID: 42439107

• Autonomous biomedical research with an artificial intelligence agent. Science (New York, N.Y.)

  • Authors: Huang, K., Zhang, S., Wang, H., ... Bernstein, J. A., ... DOI 10.1126/science.adz4351
  • PubMedID: 42424436

• RNU4ATAC-opathy: Clinical, molecular and transcriptomic insights from a large cohort. Genetics in medicine : official journal of the American College of Medical Genetics

  • Authors: Matalon, D. R., Duker, A. L., Arriaga, T. M., ... Bernstein, J. A., ... DOI 10.1016/j.gim.2026.102633
  • PubMedID: 42322193

• Psychotic Features in Myhre Syndrome: Evidence for Broader Neuropsychiatric Surveillance. American journal of medical genetics. Part C, Seminars in medical genetics

  • Authors: Ebuen, M., Krishnan, V., Irby, K., ... Bernstein, J. A., ... DOI 10.1002/ajmg.c.70011
  • PubMedID: 42267964

• De Novo Variants Associated With Autosomal Recessive Conditions: Case Series and Implications for Genetic Testing and Counseling. American journal of medical genetics. Part A

  • Authors: Niehaus, A. D., Bonner, D. E., Carter, J., ... Bernstein, J. A., ... DOI 10.1002/ajmg.a.70162
  • PubMedID: 42002855

• Biallelic variants in the noncoding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes. Nature genetics

  • Authors: Rius, R., Blakes, A. J., Chen, Y., ... Bernstein, J. A., ... DOI 10.1038/s41588-026-02554-6
  • PubMedID: 41951959

• Biallelic variants in RNU2-2 cause the most prevalent known recessive neurodevelopmental disorder. Nature genetics

  • Authors: Greene, D., Mendez, R., Lees, J., ... Bernstein, J. A., ... DOI 10.1038/s41588-026-02539-5
  • PubMedID: 41912932

Blog

August 26, 2014
Two Generations Turn to Lucile Packard Children’s Hospital Stanford for Cleft Lip and Palate Care
View our blog posts