PenCards: a global and community-contributed public archive of variant penetrance

Zhaopo Zhu; Ling Shang; Chuhan Shao; Zheng Wang; Xinxin Mao; Yuanfeng Huang; Pei Yu; Bin Li; Jinchen Li; Guihu Zhao

doi:10.1016/j.jgg.2025.07.001

PenCards: a global and community-contributed public archive of variant penetrance

doi: 10.1016/j.jgg.2025.07.001

a. Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, and National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China;
b. Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China;
c. Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China;
d. Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China

基金项目:

We thank the members of the National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University. We are grateful for technical support from Furong Laboratory, Central South University. This work was supported by the National Key R&D Program of China (2021YFC2502100), the Hunan Innovative Province Construction Project (2021SK1010), the National Natural Science Foundation of China (32070591, 82371552), the Scientific Research Program of FuRong Laboratory (2023SK2093-1), the Central South University Research Programme of Advanced Interdisciplinary Study (2023QYJC010), the Natural Science Foundation of Hunan Province (2023JJ30975), and the Fundamental Research Funds for the Central Universities of Central South University (2025ZZTS0834).

详细信息

通讯作者:
Bin Li,E-mail:lebin001@csu.edu.cn

Jinchen Li,E-mail:lijinchen@csu.edu.cn

Guihu Zhao,E-mail:ghzhao@csu.edu.cn

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出版历程
- 收稿日期: 2025-04-10
- 录用日期: 2025-07-01
- 修回日期: 2025-06-30
- 网络出版日期: 2025-07-11

PenCards: a global and community-contributed public archive of variant penetrance

Zhaopo Zhu^a,
Ling Shang^b,
Chuhan Shao^b,
Zheng Wang^c,
Xinxin Mao^c,
Yuanfeng Huang^c,
Pei Yu^a,
Bin Li^{a,c
, ,},
Jinchen Li^{a,c,d
, ,},
Guihu Zhao^{a,c
, ,}

a. Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, and National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China;
b. Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China;
c. Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China;
d. Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China

Funds:

摘要

摘要:
Penetrance is a crucial indicator for accurately assessing disease risk and plays a vital role in disease research, gene therapy, and genetic counseling. However, with penetrance data dispersed across various sources, efficiently accessing and consolidating this information becomes a challenge. A comprehensive platform that integrates penetrance is urgently needed. Here, we present PenCards, a global, community-contributed public archive of variant penetrance, by first collecting penetrance data from all published literature and then using large international cohorts to specifically calculate the penetrance of autism-related variants. PenCards contains a total of 244,531 variants—including 239,244 single nucleotide variants, 4,994 insertions and deletions, and 293 copy number variants, covering approximately 300 phenotypes. We also provide a submission portal for the dynamic updating of penetrance. Additionally, to help users efficiently access genetic information, we comprehensively integrate over 150 variant- and gene-level resources. In summary, PenCards is a powerful platform designed to advance genetic research and diagnostics. PenCards is publicly available at https://genemed.tech/pencards/.
- Penetrance /
- Disease risk /
- Genetic research and diagnostics /
- Secondary findings /
- Human genomics
Abstract:
Penetrance is a crucial indicator for accurately assessing disease risk and plays a vital role in disease research, gene therapy, and genetic counseling. However, with penetrance data dispersed across various sources, efficiently accessing and consolidating this information becomes a challenge. A comprehensive platform that integrates penetrance is urgently needed. Here, we present PenCards, a global, community-contributed public archive of variant penetrance, by first collecting penetrance data from all published literature and then using large international cohorts to specifically calculate the penetrance of autism-related variants. PenCards contains a total of 244,531 variants—including 239,244 single nucleotide variants, 4,994 insertions and deletions, and 293 copy number variants, covering approximately 300 phenotypes. We also provide a submission portal for the dynamic updating of penetrance. Additionally, to help users efficiently access genetic information, we comprehensively integrate over 150 variant- and gene-level resources. In summary, PenCards is a powerful platform designed to advance genetic research and diagnostics. PenCards is publicly available at https://genemed.tech/pencards/.
- Penetrance /
- Disease risk /
- Genetic research and diagnostics /
- Secondary findings /
- Human genomics

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PenCards: a global and community-contributed public archive of variant penetrance

doi: 10.1016/j.jgg.2025.07.001

通讯作者:
Bin Li,E-mail:lebin001@csu.edu.cn

Jinchen Li,E-mail:lijinchen@csu.edu.cn

Guihu Zhao,E-mail:ghzhao@csu.edu.cn

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PenCards: a global and community-contributed public archive of variant penetrance

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PenCards: a global and community-contributed public archive of variant penetrance

doi: 10.1016/j.jgg.2025.07.001

通讯作者: Bin Li,E-mail:lebin001@csu.edu.cn Jinchen Li,E-mail:lijinchen@csu.edu.cn Guihu Zhao,E-mail:ghzhao@csu.edu.cn

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出版历程

PenCards: a global and community-contributed public archive of variant penetrance

计量

出版历程

目录

通讯作者:
Bin Li,E-mail:lebin001@csu.edu.cn

Jinchen Li,E-mail:lijinchen@csu.edu.cn

Guihu Zhao,E-mail:ghzhao@csu.edu.cn