Interpreting the molecular mechanisms of disease variants in human transmembrane proteins
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Abstract
Next-generation sequencing of human genomes reveals millions of missense variants, some of which may lead to loss of protein function and ultimately disease. Here, we investigate missense variants in membrane proteins-key drivers in cell signaling and recognition. We find enrichment of pathogenic variants in the transmembrane region across 19,000 functionally classified variants in human membrane proteins. To accurately predict variant consequences, one fundamentally needs to understand the underlying molecular processes. A key mechanism underlying pathogenicity in missense variants of soluble proteins has been shown to be loss of stability. Membrane proteins, however, are widely understudied. Here, we interpret variant effects on a larger scale by performing structure-based estimations of changes in thermodynamic stability using a membrane-specific energy function and analyses of sequence conservation during evolution of 15 transmembrane proteins. We find evidence for loss of stability being the cause of pathogenicity in more than half of the pathogenic variants, indicating that this is a driving factor also in membrane-protein-associated diseases. Our findings show how computational tools aid in gaining mechanistic insights into variant consequences for membrane proteins. To enable broader analyses of disease-related and population variants, we include variant mappings for the entire human proteome.
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Tesei, G., Trolle, A. I., Jonsson, N., Betz, J., Knudsen, F. E., Pesce, F., Johansson, K. E., & Lindorff‐Larsen, K. (2024) · Nature · doi:10.1038/s41586-023-07004-5 · Cited by 318 · see citing works
Self-citationRapid protein stability prediction using deep learning representations
Blaabjerg, L. M., Kassem, M. M., Good, L. L., Jonsson, N., Cagiada, M., Johansson, K. E., Boomsma, W., Stein, A., & Lindorff-Larsen, K. (2023) · eLife · doi:10.7554/elife.82593 · Cited by 177 · see citing works
Self-citationExpert-guided protein language models enable accurate and blazingly fast fitness prediction
Marquet, C., Schlensok, J., Abakarova, M., Rost, B., & Laine, E. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae621 · Cited by 33 · see citing works
Decoding molecular mechanisms for loss-of-function variants in the human proteomePreprint
Cagiada, M., Jonsson, N., & Lindorff‐Larsen, K. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.21.595203 · Cited by 33 · see citing works
Self-citationGeneralizable and scalable protein stability prediction with rewired protein generative models
Li, Z., & Luo, Y. (2025) · Nature Communications · doi:10.1038/s41467-025-67609-4 · Cited by 22 · see citing works
Tesei, G., Trolle, A. I., Jonsson, N., Betz, J., Pesce, F., Johansson, K. E., & Lindorff‐Larsen, K. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.08.539815 · Cited by 21 · see citing works
Self-citationMAVISp: A Modular Structure-Based Framework for Protein Variant Effects
Arnaudi, M., Utichi, M., Degn, K., Tiberti, M., Beltrame, L., Krzesińska, K., Sánchez-Izquierdo Besora, P., Kiachaki, E., Scrima, S., Bauer, L., et al. (2022) · doi:10.1101/2022.10.22.513328 · Cited by 20 · see citing works
Alignment-based Protein Mutational Landscape Prediction: Doing More with Less
Abakarova, M., Marquet, C., Rera, M., Rost, B., & Laine, E. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad201 · Cited by 14 · see citing works
A small molecule stabilizer rescues the surface expression of nearly all missense variants in a GPCR
Mighell, T. L., & Lehner, B. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01659-6 · Cited by 13 · see citing works
Allostery is a widespread cause of loss-of-function variant pathogenicity
Liao, X., & Lehner, B. (2026) · Nature Communications · doi:10.1038/s41467-026-74517-8 · Cited by 12 · see citing works
Nordquist, E. B., Zhang, G., Barethiya, S., Ji, N., White, K. M., Han, L., Jia, Z., Shi, J., Cui, J., & Chen, J. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011460 · Cited by 8 · see citing works
Mighell, T. L., & Lehner, B. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.28.625821 · Cited by 7 · see citing works
Decoding molecular mechanisms for loss-of-function variants in the human proteomePreprint
Cagiada, M., Jonsson, N., & Lindorff‐Larsen, K. (2025) · eLife · doi:10.7554/elife.108160.1 · Cited by 8 · see citing works
Self-citationHarnessing Chimeric Degrader Technologies for Antimicrobial Innovation
Poddar, S. K., Dey, K., & Zheng, G. (2025) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5c01479 · Cited by 5 · see citing works
Cao, L., Quan, L., Chen, Q., Zhang, B. X., Zhang, Z., Peng, L., Wang, J., Jiang, Y., Nie, L., Li, G., et al. (2025) · Communications Biology · doi:10.1038/s42003-025-08452-7 · Cited by 5 · see citing works
Energetic and structural control of polyspecificity in a multidrug transporter
Miller, S. T., Henzler‐Wildman, K. A., & Raman, S. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2511892122 · Cited by 4 · see citing works
Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates
Yee, S. W., Ferrández-Peral, L., Alentorn-Moron, P., Fontsere, C., Ceylan, M., Koleske, M. L., Handin, N., Artegoitia, V. M., Lara, G., Chien, H.-C., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48569-7 · Cited by 4 · see citing works
Ridha, F., Frishman, D., & Gromiha, M. M. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.148290 · Cited by 2 · see citing works
Sezgin, E., & Levental, I. (2023) · Biophysical Journal · doi:10.1016/j.bpj.2023.05.005 · Cited by 2 · see citing works
Destabilization and Degradation of a Disease-Linked PGM1 Protein Variant
Gouliaev, F., Jonsson, N., Gersing, S. K., Lisby, M., Lindorff‐Larsen, K., & Hartmann‐Petersen, R. (2024) · Biochemistry · doi:10.1021/acs.biochem.4c00042 · Cited by 2 · see citing works
Self-citationVarLand: A pipeline to map the structural landscape of missense variants at the proteome scale
Guzmán‐Vega, F. J., Cardona‐Londoño, K. J., González‐Álvarez, A. C., Peña‐Guerra, K. A., Althagafi, A., Khan, T., Hoehndorf, R., & Arold, S. T. (2025) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2025.111071 · Cited by 1 · see citing works
Carbone, A., Laine, É., & Lombardi, G. (2012) · Methods in molecular biology · doi:10.1007/978-1-0716-4828-5_7 · Cited by 1 · see citing works
Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates
Giacomini, K., Yee, S. W., Ferrández-Peral, L., Alentorn, P., Fontsere, C., Ceylan, M., Koleske, M., Handin, N., Artegoitia, V., Lara, G., et al. (2023) · doi:10.21203/rs.3.rs-3263845/v1 · Cited by 1 · see citing works
Decoding molecular mechanisms for loss-of-function variants in the human proteomePreprint
Cagiada, M., Jonsson, N., & Lindorff‐Larsen, K. (2025) · eLife · doi:10.7554/elife.108160 · Cited by 1 · see citing works
Self-citationBao, Y., Liu, Z., Zhao, F., Li, W., Jin, H., & Lin, G. N. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.18.654712
Weidling, C., Harms, H., Ameen, A. O., Panfilova, A., Gloystein, T., Stein, A., Chua, H. C., & Pless, S. A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.15.676065
Self-citationChang-Gonzalez, A. C., Bell, E. W., Vanoye, C. G., Guadarrama, E., Desai, R. R., DeKeyser, J., Butcher, K. R., Scott, T., Sanders, C. R., George, A. L., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.31.685955
Bao, Y., Liu, Z., Zhao, F., Li, W., Jin, H., & Lin, G. N. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag352
Chang-Gonzalez, A. C., Bell, E. W., Vanoye, C. G., Guadarrama, E., Desai, R. R., DeKeyser, J., Butcher, K. R., Scott, J., Sanders, C. R., George, A. L., et al. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2537217123 · Cited by 1 · see citing works
Bursch, K. L., Chi, Y., Licklider, J., Jensen, D. R., Catlin, A. E., Zimmermann, M. T., Lomberk, G. A., Urrutia, R. A., & Smith, B. C. (2026) · Human Molecular Genetics · doi:10.1093/hmg/ddag094
- Authors
- Tiemann, J. K. S., Zschach, H., Lindorff-Larsen, K., & Stein, A.
- Affiliations
- University of Copenhagen (DK)
- Corresponding author
- Stein, Amelie
- Venue
- Biophysical Journal
- Publisher
- Elsevier BV
- Published
- 2023-06
- Volume
- 122
- Issue
- 11
- Pages
- 2176-2191
- ISSN
- 0006-3495 (ISSN-L)
- PMC
- PMC10257119
- OpenAlex
- W4313530868
- Cited by
- 35
- References
- 92
- Citations by year
- 2026: 5 · 2025: 12 · 2024: 6 · 2023: 8 · 2022: 3 · 2012: 1
- FWCI
- 5.15
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Biophysical Journal (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- PubMed (publishedVersion)
- Funders
- Lundbeck Foundation (R272-2017-4528)
- Novo Nordisk Fonden (NNF18OC0033950)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- missense mutations, transmembrane proteins, membrane proteins, pathogenic variants, thermodynamic stability, sequence conservation, protein evolution, variant pathogenicity prediction, human proteome
- MeSH terms
- Humans, Membrane Proteins, Signal Transduction, Mutation, Missense
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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