# 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](tel:+16507236858)

Fax: (650) 498-4555

## Locations

[Mary L. Johnson Specialty Services](/content/en/location/730-welch-road.html)

Medical Genetics

730 Welch Road

Palo Alto, CA 94304

Phone : [(650) 723-6858](tel:(650) 723-6858)

Fax : (650) 498-4555

## Services

[Cleft and Craniofacial Center](/content/en/services/cleft-and-craniofacial-center.html)

[Genetics Services](/content/en/services/genetics.html)

[Microtia and Ear Canal Atresia](/content/en/services/microtia.html)

## 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](https://doi.org/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](https://doi.org/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](https://doi.org/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](https://doi.org/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](https://doi.org/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](https://doi.org/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](https://doi.org/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](https://doi.org/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](https://doi.org/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](https://healthier.stanfordchildrens.org/)