RareVariants Laboratory

The Rare Variants Lab, led by Dr. Mireia Olivella at the University of Vic / Institute for Research and Innovation for Life Sciences and Health, is dedicated to advancing the interpretation of genetic variation through a combination of computational genomics, protein structural biology, and translational rare disease research. The lab focuses on understanding how protein-truncating variants, missense mutations, and other forms of variation disrupt protein function and drive human disease, with a particular emphasis on neurodevelopmental and neurometabolic disorders.

A major line of research in the lab involves developing scalable and interpretable computational frameworks to classify the pathogenicity of genetic variants. These efforts integrate evolutionary constraint, population genomics, structural modeling, and molecular simulations. The lab leads the development of widely used platforms such as TruncPred, HomolVar, GRINdb, and other tools that provide high-resolution, exon-level and protein-level assessments of variant impact.

The Rare Variants Lab places special emphasis on disorders involving the glutamatergic synapse, including GRINpathies and related channelopathies, combining variant databases, structural modeling, and genotype–phenotype analyses to uncover disease mechanisms and improve clinical interpretation. Collaboration is a core principle of the lab. Its members work closely with clinical geneticists, neuroscientists, international research consortia, patient organizations, and translational partners to accelerate diagnostic pipelines, reclassify variants of uncertain significance, and advance precision medicine in rare disease.

Overall, the Rare Variants Lab aims to produce robust, interpretable, and clinically actionable tools that bridge genomic data, molecular mechanisms, and medical decision-making—advancing the understanding and diagnosis of rare genetic disorders.


Publications

Display all publications
  • Ruiz-Alías G, Soldevila S, Altafaj X, Cordomí A, Olivella M (2025). Missense variants pathogenicity annotation from homologous proteins. Bioinformatics, 41(5), num: 305. DOI: 10.1093/bioinformatics/btaf305
  • Santos-Gómez A, Juliá-Palacios N, Rejano-Bosch A, Marí-Vico R, Miguez-Cabello F, Masana M, Soto D, Olivella M, García-Cazorla À, Altafaj X (2025). Spermidine Treatment Improves GRIN2B Loss-Of-Function, A Primary Disorder of Glutamatergic Neurotransmission Journal of Inherited Metabolic Disease, 48(2), num: 70015 DOI: 10.1002/jimd.70015
  • Jové-Solavera D, Rámila M, Ferrer-Cortés X, Olivella M, Venturi V, Morado M, Sanchez M (2025). The role of genetic testing in accurate diagnosis of X-linked sideroblastic anemia: novel ALAS2 mutations and the impact of X-chromosome inactivation Scientific reports, 15(1), num: 11843 DOI: 10.1038/s41598-025-95590-x
  • Juliá-Palacios N, Olivella M, Bondarenko M S, Ibáñez-Micó S, Muñoz-Cabello B, Alonso-Luengo O, García-Cazorla A (2024). L-serine treatment in patients with GRIN-related encephalopathy: a phase 2A, non-randomized study Brain A Journal Of Neurology DOI: 10.1093/brain/awae041
  • Kumari P, Tarighi S, Fuchshuber E, Li L, Fernández-Duran I, Wang M, Ayoson J, Castelló-García J M, Gámez-García A, Espinosa-Alcantud M, Sreenivasan K, Guenther S, Olivella M, Savai R, Yue S, Vaquero A, Braun T, Ianni A (2024). SIRT7 promotes lung cancer progression by destabilizing the tumor suppressor ARF Proceedings of The National Academy of Sciences of The United States of America, 121(25), num: 2409269121 DOI: 10.1073/pnas.2409269121
  • Julia-Palacios N A, Kuseyri Hübschmann O, Olivella M, Pons R, Horvath G, Lücke T, Fung C-W, Wong S-N, Cortès-Saladelafont E, Rovira-Remisa M M, Yıldız Y, Mercimek-Andrews S, Assmann B, Stevanović G, Manti F, Brennenstuhl H, Jung-Klawitter S, Jeltsch K, Sivri H S, Opladen T (2024). The continuously evolving phenotype of succinic semialdehyde dehydrogenase deficiency Journal of Inherited Metabolic Disease, 47(3), 447-462 DOI: 10.1002/jimd.12723
  • den Hollander B, Veenvliet A R J, Rothuizen-Lindenschot M, van Essen P, Peters G, Santos-Gómez A, Olivella M, van Karnebeek C D (2023). Evidence for effect of L-serine, a novel therapy for GRIN2B-related neurodevelopmental disorder Molecular Genetics and Metabolism, 138(3) DOI: 10.1016/j.ymgme.2023.107523
  • Justel M, Jou C, Sariego-Jamardo A, Juliá-Palacios N A, Ortez C, Poch M L, Olivella M, Natera-de Benito D (2023). Expanding the phenotypic spectrum of TRAPPC11-related muscular dystrophy: 25 Roma individuals carrying a founder variant Journal Of Medical Genetics, 60(10), 965-973 DOI: 10.1136/jmg-2022-109132
  • Illescas S, Diaz-Osorio Y, Serradell A, Toro-Soria L, Musokhranova U, Juliá-Palacios N, Olivella M, Oyarzábal A (2023). Metabolic characterization of neurogenetic disorders involving glutamatergic neurotransmission Journal Of Inherited Metabolic Disease DOI: 10.1002/jimd.12689
  • Rasti G, Becker M, Vazquez B N, Espinosa-Alcantud M, Fernández-Duran I, Gámez-García A, Bosch-Presegué L, Olivella M, Stracker T H, de la Torre C, Vaquero A (2023). SIRT1 regulates DNA damage signaling through the PP4 phosphatase complex Nucleic Acids Research DOI: 10.1093/nar/gkad504
  • Romero-Martín L, Duran-Castells C, Olivella M, Rosás-Umbert M, Ruiz-Riol M, Sanchez J, Mothe B, Olvera A, Brander C (2022). Disruption of the HLA-E/NKG2X axis is associated with uncontrolled HIV infections Frontiers in Immunology, 13(1027855) DOI: 10.3389/fimmu.2022.1027855
  • Santos-Gómez A, García-Recio A, Miguez-Cabello F, Soto D, Altafaj X, Olivella M (2022). Identification of homologous GluN subunits variants accelerates GRIN variants stratification Frontiers in Cellular Neuroscience, 16(998719) DOI: 10.3389/fncel.2022.998719
  • Hübschmann O K, Juliá-Palacios N A, Olivella M, Guder P, Zafeiriou D I, Horvath G, García-Cazorla Á (2022). Integrative approach to predict severity in nonketotic hyperglycinemia Annals of Neurology DOI: 10.1002/ana.26423
  • García-Recio A, Santos-Gómez A, Soto D, Julia-Palacios N, García-Cazorla À, Altafaj X, Olivella M (2021). GRIN database: A unified and manually curated repertoire of GRIN variants Human Mutation, 42(1), 8-18 DOI: 10.1002/humu.24141
  • Santos-Gómez A, Miguez-Cabello F, Juliá-Palacios N, García-Navas D, Soto-Insuga V, García-Peñas J J, Olivella M, Altafaj X (2021). Paradigmatic de novo grin1 variants recapitulate pathophysiological mechanisms underlying grin1-related disorder clinical spectrum International Journal of Molecular Sciences, 22(23) DOI: 10.3390/ijms222312656
  • Garcia-Recio A, Gomez-Tamayo J C, Reina I, Campillo M, Cordomi A, Olivella M (2021). TMSNP: a web server to predict pathogenesis of missense mutations in the transmembrane region of membrane proteins NAR Genomics and Bioinformatics, 3(1) DOI: 10.1093/nargab/lqab008
  • García-Recio A, Navarro G, Franco R, Olivella M, Guixà-González R, Cordomí A (2020). DIMERBOW: exploring possible GPCR dimer interfaces Bioinformatics Oxford, 36(10), 3271-3272 DOI: 10.1093/bioinformatics/btaa117
  • Santos-Gomez A, Miguez-Cabello F, Garcia-Recio A, Locubiche-Serra S, Garcia-Diaz R, Soto-Insuga V, Olivella M, et al. (2020). Disease-associated GRIN protein truncating variants trigger NMDA receptor loss-of-function Human Molecular Genetics, 29(4), 3859-3871 DOI: 10.1093/hmg/ddaa220
  • Rodríguez-Espigares I, Torrens-Fontanals M, Tiemann J K S, Aranda-García D, Ramírez-Anguita J M, Stepniewski T M, Worp N, Varela-Rial A, Morales-Pastor A, Medel-Lacruz B, Pándy-Szekeres G, Mayol E, Giorgino T, Carlsson J, Deupi X, Filipek S, Filizola M, Gómez-Tamayo J C, Gonzalez A, Gutiérrez-de-Terán H, Jiménez-Rosés M, Jespers W, Kapla J, Khelashvili G, Kolb P, Latek D, Marti-Solano M, Matricon P, Matsoukas M T, Miszta P, Olivella M, et al. (2020). GPCRmd uncovers the dynamics of the 3D-GPCRome Nature Methods, 17, 777-787 DOI: 10.1038/s41592-020-0884-y
  • Mayol E, García-Recio A, Tiemann J K S, Hildebrand P W, Guixà-González R, Olivella M, Cordomí A (2020). HomolWat. A web server tool to incorporate «homologous» water molecules into GPCR structures Nucleic Acids Research, 48(1), 54-59 DOI: 10.1093/nar/gkaa440
  • Simonet N G, Thackray J K, Vazquez B N, Ianni A, Espinosa-Alcantud M, Morales-Sanfrutos J, Olivella M, et al. (2020). SirT7 auto-ADP-ribosylation regulates glucose starvation response through mH2A1 Science advances, 6(30) DOI: 10.1126/sciadv.aaz2590
  • Mayol E, Campillo M, Cordomi A, Olivella M (2019). Inter-residue interactions in alpha-helical transmembrane proteins Bioinformatics, 35(15), 2578-2584 DOI: 10.1093/bioinformatics/bty978
  • Soto D, Olivella M, Grau C, Armstrong J, Alcon C, Gasull X, Altafaj X (2019). l-Serine dietary supplementation is associated with clinical improvement of loss-of-function GRIN2B -related pediatric encephalopathy Science Signaling, 12(586) DOI: 10.1126/scisignal.aaw0936
  • Soto D, Olivella M, Grau C, Armstrong J, Alcon C, Gasull X, et al. (2018). Rett-like severe encephalopathy caused by a de novo GRIN2B mutation is attenuated by D-serine dietary supplement Biological Psychiatry, 83(2), 160-172 DOI: 10.1016/j.biopsych.2017.05.028
  • Gómez Tamayo J C, Olivella M, Ríos S, Hoogstraat M, Gonzalez A, Mayol E, Cordomí A (2018). GPCR-SAS: A web application for statistical analyses on G protein-coupled receptors sequences PLoS ONE, 13(7) DOI: 10.1371/journal.pone.0199843
  • Gratacos-Batlle E, Olivella M, Sanchez-Fernandez N, Yefimenko N, Miguez-Cabello F, Fado R, et al. (2018). Mechanisms of CPT1C-dependent AMPAR trafficking enhancement Frontiers in Molecular Neuroscience, 11(275) DOI: 10.3389/fnmol.2018.00275
  • Soto D, Olivella M, Grau C, Ciruela F, Bayes A, Sindreu C, et al. (2017). Rett-like severe encephalopathy caused by a de novo Grin2b mutation is attenuated by D-serine dietary supplement Basic & clinical pharmacology & toxicology, 121, 62-63 DOI:
  • Gómez-Tamayo J C, Cordomí A, Olivella M, Mayol E, Fourmy D, Pardo L (2016). Analysis of the interactions of sulfur-containing amino acids in membrane proteins Protein Science, 25(8), 1517-1524 DOI:
  • Perea M, Lugtenburg I, Mayol E, Cordomí A, Deupí X, Pardo L, Olivella M (2015). TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and ß-barrel domains of membrane proteins BMC Bioinformatics, 16(266) DOI: 10.1186/s12859-015-0699-5

Projects

Display all projects
  • Repurposing glutamatergic synapse therapies across rare neurodevelopmental disorders Research team: - Code: JTC25-99 Institutions: - Funding: ERDERA Duration: 2026-01-01 → 2028-12-31
  • Interacciones Estocásticas y Heterogéneas de Receptores de Membrana exploradas con Inteligencia Artificial basada en principios Físicos Research team: MANZO, CARLO (IP), OLIVELLA GARCÍA, MIREIA, CULLELL DALMAU, MARTA, Bertran Muñoz, Joan Code: PID2024-156712NB-I00 Institutions: Universitat de Vic - Universitat Central de Catalunya Funding: I+D Duration: 2025-09-01 → 2028-08-31
  • Ajut FI-SDUR Sergi Soldevila (3 anualitats) Research team: OLIVELLA GARCÍA, MIREIA (IP) Code: 2024 FISDU 00156 Institutions: Universitat de Vic - Universitat Central de Catalunya Funding: Agència de Gestió d'Ajuts Universitaris i de Recerca Duration: 2025-03-01 → 2028-02-29
  • MEDICINA PERSONALIZADA PARA EL ESTUDIO DE LAS VARIANTES GRIN HUERFANAS - Retraso del desarrollo, discapacidad intelectual y trastorno del espectro autista asociado al gen GRIN2B Research team: OLIVELLA GARCÍA, MIREIA (IP) Code: OTH23015 Institutions: IRIS-CC Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central, Universitat de Vic - Universitat Central de Catalunya Funding: Fundación FEDER para la investigación Duration: 2024-04-01 → 2025-04-01
  • Medicina personalizada para las Grinpatías y sinaptopatías glutamatérgicas asociadas a encefalopatías del Desarrollo Research team: Xavier Altafaj (IP), OLIVELLA GARCÍA, MIREIA Code: PI22/00515 Institutions: Universitat de Barcelona Funding: Instituto de Salud Carlos III Duration: 2023-01-01 → 2025-12-31
  • Organización de las proteínas de la unión estrecha a escala nanométrica Research team: MANZO, CARLO (IP), MASO ORRIOLS, SERGI, SANDINO VELASQUEZ, CLARA INÉS, OLIVELLA GARCÍA, MIREIA, CULLELL DALMAU, MARTA, BERTRAN COMULADA, JOAN, MASOLIVER, MONTSE, GARCÍA RECIO, ADRIÁN Code: PID2021-125386NB-I00 Institutions: Funding: Ministerio de Ciencia e Innovación Duration: 2022-09-01 → 2025-08-31
  • Mutaciones de novo de los receptores NMDA asociadas a discapacidad intelectual y epilepsia: impacto patofisiológico, estratificación y farmacoterapia personalizada Research team: OLIVELLA GARCÍA, MIREIA Code: PI16/00851 Institutions: IDIBELL Funding: Instituto de Salud Carlos III Duration: 2017-01-01 → 2019-12-31
  • Modulación de los receptores acoplados a proteínas G por ligandos y porteínas Research team: Leonardo Pardo (IP), OLIVELLA GARCÍA, MIREIA Code: SAF2016-77830-R Institutions: Universitat Autònoma de Barcelona Funding: AGAUR Duration: 2017-01-01 → 2020-12-31
  • 2014SGR-596: Bioinformàtica i Estadística Mèdica Research team: CALLE, M. LUZ (IP), OLIVELLA GARCÍA, MIREIA, CAPELLAS HERMS, MONTSERRAT, CULLELL DALMAU, MARTA, BERTRAN COMULADA, JOAN, BAU MACIÀ, JOSEP, SERRAT JURADO, JOSEP M., VILLÀ-FREIXA, JORDI, AGULLÓ, LUIS Code: 2014SGR-596 Institutions: Universitat de Vic - Universitat Central de Catalunya Funding: AGAUR Duration: 2014-01-01 → 2017-01-31
  • Nuevas dianas y estrategias terapéuticas Research team: Leonardo Pardo (IP), OLIVELLA GARCÍA, MIREIA Code: SAF2013-48271-C2-2-R Institutions: Universitat Autònoma de Barcelona Funding: Ministerio de Ciencia y Tecnología Duration: 2013-01-01 → 2015-12-31

Theses

Display all theses
  • Sergi Soldevila Gálvez (Ongoing). Study the relation between genotype and phenotype in grinpathies. Director: OLIVELLA GARCÍA, MIREIA. Universitat de Vic - Universitat Central de Catalunya
  • Gabriel Ruiz Alías (Ongoing). Studying the relation between genotype and clinical phenotye through protein structure and function. Director: OLIVELLA GARCÍA, MIREIA. Universitat de Vic - Universitat Central de Catalunya
  • Adrián García Recio (2022). Relation between sequence and structure in membrane proteins. Director: OLIVELLA GARCÍA, MIREIA. Universitat de Vic - Universitat Central de Catalunya
  • Luis Eduardo Mayol (2019). Desenvolupament d'eines bioinformàtiques per a l'estudi de proteïnes de membrana. Director: OLIVELLA GARCÍA, MIREIA. Universitat Autònoma de Barcelona