Evidence map›Paper›PMID 40169570›Full record

ArticleNature communications2025

A genotype-first approach identifies high incidence of NF1 pathogenic variants with distinct disease associations.

Anton Safonov, Tomoki T Nomakuchi, Elizabeth Chao, Carrie Horton, Jill S Dolinsky, Amal Yussuf, Marcy Richardson, Virginia Speare, Shuwei Li, Zoe C Bogus and 18 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

13 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Review
  6. Article
  7. Article
  8. Article
  9. Article
  10. Neurofibromin Encoded by theInternational journal of molecular sciences · 2025
    Article
  11. Article
  12. Repair of MutatedCancers · 2025
    Article
  13. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

28 authors.

Anton Safonov *Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Tomoki T Nomakuchi *Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Elizabeth ChaoDepartment of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA.ORCID http://orcid.org/0000-0002-4082-371X
Carrie HortonDepartment of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA.ORCID http://orcid.org/0000-0001-5186-6208
Jill S DolinskyDepartment of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA.
Amal YussufDepartment of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA.ORCID http://orcid.org/0000-0002-7876-2713
Marcy RichardsonDepartment of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA.ORCID http://orcid.org/0000-0002-4626-4920
Virginia SpeareDepartment of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA.
Shuwei LiDepartment of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA.
Zoe C BogusDivision of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Maria BonanniDivision of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Anna RaperDivision of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Trust OdiaDivision of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Bradley S WubbenhorstDivision of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Elsa FauldersCollege of Arts and Sciences, Oberlin College, Oberlin, OH, USA.
Elisabeth M SchuthCollege of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA.
Kate LorangerNatera Inc., Austin, TX, USA.
Jingwen ZhangNatera Inc., Austin, TX, USA.
Carly Bess ScaliseNatera Inc., Austin, TX, USA.
Adam ElNaggarNatera Inc., Austin, TX, USA.ORCID http://orcid.org/0000-0003-3409-583X
Youbao ShaNatera Inc., Austin, TX, USA.
Stephanie A FelkerUniversity of Alabama in Birmingham, Heersink School of Medicine, Department of Genetics, Birmingham, AL, USA.ORCID http://orcid.org/0000-0002-1809-1524
Jeffrey WeitzelDivision of Precision Prevention, Department of Medicine, University of Kansas School of Medicine, Kansas City, KS, USA.ORCID http://orcid.org/0000-0001-6714-092X
Staci KallishDivision of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Marylyn D RitchieDepartment of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0002-1208-1720
Penn Medicine BioBank
Katherine L NathansonDivision of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. knathans@upenn.edu.ORCID http://orcid.org/0000-0002-6740-0901
Theodore G DrivasDivision of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. theodore.drivas@pennmedicine.upenn.edu.ORCID http://orcid.org/0000-0002-8717-0111

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026
$347.4M
Technology to Empower Changes in Health (TECH) Network Participant Technologies CenterU24OD023176 · OD · SCRIPPS RESEARCH INSTITUTE, THE · PI TOPOL, ERIC JEFFREY · 2016 to 2022
$204.7M
Precision Medicine Initiative Cohort Program BiobankU24OD023121 · OD · MAYO CLINIC ROCHESTER · PI CEKANOVA, MARIA, CICEK, MINE · 2016 to 2024
$185.5M
Enhancing All of Us Data Resources for Nutrition Precision Health: the All of Us Data and Research CenterU2COD023196 · OD · VANDERBILT UNIVERSITY MEDICAL CENTER · PI GLAZER, DAVID, HARRIS, PAUL A. · 2016 to 2022
$143.7M
Adaptive Platform for Personalized EngagementU24OD023163 · OD · VIGNET, INC. · PI JAIN, PRADUMAN · 2017 to 2020
$102.6M
Phenotypic Diversity in COVID-19UL1TR001878 · NCATS · UNIVERSITY OF PENNSYLVANIA · PI FITZGERALD, GARRET A · 2016 to 2025
$102.4M
University of Arizona-Banner Health All of Us Research Program OT2OD026549 · OD · UNIVERSITY OF ARIZONA · PI MORENO, FRANCISCO A, REIMAN, ERIC MICHAEL · 2018 to 2023
$78.9M
California Precision Medicine Research Program ConsortiumOT2OD026552 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ANTON-CULVER, HODA A, OHNO-MACHADO, LUCILA · 2018 to 2023
$73.4M
All of Us PennsylvaniaOT2OD026554 · OD · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI REIS, STEVEN E, VISWESWARAN, SHYAM · 2018 to 2023
$72.1M
New York City Consortium for Precision MedicineOT2OD026556 · OD · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI BIER, LOUISE E, GHARAVI, ALI G · 2018 to 2023
$67.3M
SouthEast Enrollment Center (SEEC) OT2OD026551 · OD · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI CARRASQUILLO, OLVEEN, COLON, VIVIAN · 2018 to 2023
$62.8M
Southern All of Us NetworkOT2OD026548 · OD · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI FOUAD, MONA N., KORF, BRUCE R · 2018 to 2023
$60.5M
NCATS NIH HHS UL1 TR001878NCI NIH HHS P30 CA008748NCI NIH HHS R01 CA176785NCI NIH HHS R01 CA192393NHGRI NIH HHS T32 HG008961NIAID NIH HHS R01 AI077505NIAID NIH HHS R01 AI116794NIDDK NIH HHS K08 DK127247NIGMS NIH HHS P50 GM115318NIGMS NIH HHS T32 GM008638NIH HHS OT2 OD023205NIH HHS OT2 OD023206NIH HHS OT2 OD025276NIH HHS OT2 OD025277NIH HHS OT2 OD025315NIH HHS OT2 OD025337NIH HHS OT2 OD026548NIH HHS OT2 OD026549NIH HHS OT2 OD026550NIH HHS OT2 OD026551NIH HHS OT2 OD026552NIH HHS OT2 OD026553NIH HHS OT2 OD026554NIH HHS OT2 OD026555NIH HHS OT2 OD026556NIH HHS OT2 OD026557NIH HHS U24 OD023121NIH HHS U24 OD023163NIH HHS U24 OD023176NIH HHS U2C OD023196
6 · The paper itself

Abstract

Loss of function variants in the NF1 gene cause neurofibromatosis type 1, a genetic disorder characterized by complete penetrance, characteristic physical exam findings, and a substantially increased risk for malignancy. However, our understanding of the disorder is based on patients ascertained through phenotype-first approaches, which estimate prevalence at 1 in 3000. Leveraging a genotype-first approach in multiple large patient cohorts including over one million individuals, we demonstrate an unexpectedly high prevalence (1 in 1,286) of NF1 pathogenic variants. Half are identified in individuals lacking clinical features of NF1, with many appearing to have post-zygotic mosaicism for the identified variant. Incidentally discovered variants are not associated with classic neurofibromatosis features but are associated with an increased incidence of malignancy compared to control populations. Our findings suggest that NF1 pathogenic variants are substantially more common than previously thought, often characterized by somatic mosaicism and reduced penetrance, and are important contributors to cancer risk in the general population.

Indexed as

Neurofibromatosis 1Neurofibromin 1AdultFemaleGenetic Association StudiesGenetic Predisposition to DiseaseGenotypeHumansIncidenceMaleMiddle AgedMosaicismNeoplasmsPenetrancePhenotypePrevalenceNeurofibromin 1NF1 protein, human

Identifiers

PMID40169570
PMCPMC11962086

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.