ClinVar: improvements to accessing data
Open accessAbstract
ClinVar is a freely available, public archive of human genetic variants and interpretations of their relationships to diseases and other conditions, maintained at the National Institutes of Health (NIH). Submitted interpretations of variants are aggregated and made available on the ClinVar website (https://www.ncbi.nlm.nih.gov/clinvar/), and as downloadable files via FTP and through programmatic tools such as NCBI’s E-utilities. The default view on the ClinVar website, the Variation page, was recently redesigned. The new layout includes several new sections that make it easier to find submitted data as well as summary data such as all diseases and citations reported for the variant. The new design also better represents more complex data such as haplotypes and genotypes, as well as variants that are in ClinVar as part of a haplotype or genotype but have no interpretation for the single variant. ClinVar's variant-centric XML had its production release in April 2019. The ClinVar website and E-utilities both have been updated to support the VCV (variation in ClinVar) accession numbers found in the variant-centric XML file. ClinVar's search engine has been fine-tuned for improved retrieval of search results.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Some subtypes of Ehlers-Danlos syndrome have been associated with a pathogenic mutation in the ALB gene and weakly linked to ALDH1AI.
“Furthermore, some subtypes of Ehlers–Danlos syndrome have been associated with a pathogenic mutation in the ALB gene in ref. 42 and weakly linked to ALDH1AI in ref. 43.”
From A foundation model for clinician-centered drug repurposing (2024) · cites this paper as [42]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Richards, S., Aziz, N., Bale, S., Bick, D., Das, S., Gastier-Foster, J., Grody, W. W., Hegde, M., Lyon, E., Spector, E., et al. (2015) · Genetics in Medicine · doi:10.1038/gim.2015.30 · Cited by 32,594 · see citing works
Database resources of the National Center for Biotechnology Information: update
Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,691 · see citing works
Database resources of the National Center for Biotechnology Information
Agarwala, R., Barrett, T., Beck, J., Benson, D., Bollin, C., Bolton, E. E., Bourexis, D., Brister, J., Bryant, S. H., Canese, K., et al. (2017) · Nucleic Acids Res. · doi:10.1093/nar/gkx1095 · Cited by 6,277 · see citing works
Self-citationClinVar: improving access to variant interpretations and supporting evidence
Landrum, M. J., Lee, J. M., Benson, M., Brown, G. R., Chao, C., Chitipiralla, S., Gu, B., Hart, J., Hoffman, D., Jang, W., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1153 · Cited by 4,196 · cited 2× · see citing works
“Similar to ClinVarFullRelease (12), the variant-centric XML is generated and archived monthly.”
BackgroundMethodSelf-citationClinVar: public archive of relationships among sequence variation and human phenotype
Landrum, M. J., Lee, J. M., Riley, G. R., Jang, W., Rubinstein, W. S., Church, D. M., & Maglott, D. R. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1113 · Cited by 3,516 · see citing works
Self-citationDatabase resources of the National Center for Biotechnology Information
Sayers, E. W., Beck, J., Bolton, E. E., Brister, J., Chan, J., Comeau, D. C., Connor, R., DiCuccio, M., Farrell, C., Feldgarden, M., et al. (2014) · Nucleic Acids Res. · doi:10.1093/nar/gku1130 · Cited by 2,584 · see citing works
Self-citationHGVS Recommendations for the Description of Sequence Variants: 2016 Update
den Dunnen, J. T., Dalgleish, R. W. M., Maglott, D. R., Hart, R. K., Greenblatt, M. S., McGowan‐Jordan, J., Roux, A., Smith, T. D., Antonarakis, S. E., & Taschner, P. E. M. (2016) · Human Mutation · doi:10.1002/humu.22981 · Cited by 1,662 · see citing works
Self-citationDatabase resources of the National Center for Biotechnology Information
Coordinators, N. R. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1290 · Cited by 1,459 · see citing works
OMIM.org: leveraging knowledge across phenotype–gene relationships
Amberger, J., Bocchini, C. A., Scott, A., & Hamosh, A. (2018) · Nucleic Acids Res. · doi:10.1093/nar/gky1151 · Cited by 977 · see citing works
Modernizing Reference Genome Assemblies
Church, D., Schneider, V. A., Graves, T., Auger, K., Cunningham, F., Bouk, N., Chen, H.-C., Agarwala, R., McLaren, W., Ritchie, G., et al. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001091 · Cited by 563 · see citing works
Self-citationThe UCSC Genome Browser database: 2018 update
Casper, J., Zweig, A. S., Villarreal, C., Tyner, C., Speir, M. L., Rosenbloom, K. R., Raney, B. J., Lee, C. M., Lee, B. T., Karolchik, D., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1020 · Cited by 475 · see citing works
ClinVar at five years: Delivering on the promise
Landrum, M., & Kattman, B. L. (2018) · Human Mutation · doi:10.1002/humu.23641 · Cited by 210 · see citing works
Self-citationRubinstein, W. S., Maglott, D. R., Lee, J. M., Kattman, B. L., Malheiro, A. J., Ovetsky, M., Hem, V., Gorelenkov, V., Song, G., Wallin, C., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1173 · Cited by 185 · see citing works
Self-citationACMG Board of Directors (2017) · Genetics in Medicine · doi:10.1038/gim.2016.196 · Cited by 110 · see citing works
SPDI: data model for variants and applications at NCBI
Holmes, J. B., Moyer, E., Phan, L. D., Maglott, D. R., & Kattman, B. L. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz856 · Cited by 58 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
A joint NCBI and EMBL-EBI transcript set for clinical genomics and research
Morales, J., Pujar, S., Loveland, J. E., Astashyn, A., Bennett, R., Berry, A., Cox, E., Davidson, C., Ermolaeva, O., Farrell, C. M., et al. (2022) · Nature · doi:10.1038/s41586-022-04558-8 · Cited by 571 · see citing works
The next-generation Open Targets Platform: reimagined, redesigned, rebuilt
Ochoa, D., Hercules, A., Carmona, M., Suveges, D., Baker, J., Malangone, C., Lopez, I., Miranda, A., Cruz-Castillo, C., Fumis, L., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1046 · Cited by 432 · see citing works
A foundation model for clinician-centered drug repurposing
Huang, K., Chandak, P., Wang, Q., Havaldar, S., Vaid, A., Leskovec, J., Nadkarni, G. N., Glicksberg, B. S., Gehlenborg, N., & Zitnik, M. (2024) · Nature Medicine · doi:10.1038/s41591-024-03233-x · Cited by 249 · see citing works
AlphaFold heralds a data-driven revolution in biology and medicine
Thornton, J. M., Laskowski, R. A., & Borkakoti, N. (2021) · Nature Medicine · doi:10.1038/s41591-021-01533-0 · Cited by 185 · see citing works
Precision genome editing using cytosine and adenine base editors in mammalian cells
Huang, T. P., Newby, G. A., & Liu, D. R. (2021) · Nature Protocols · doi:10.1038/s41596-020-00450-9 · Cited by 175 · see citing works
An atlas of protein homo-oligomerization across domains of life
Schweke, H., Pacesa, M., Levin, T., Goverde, C. A., Kumar, P., Duhoo, Y., Dornfeld, L. J., Dubreuil, B., Georgeon, S., Ovchinnikov, S., et al. (2024) · Cell · doi:10.1016/j.cell.2024.01.022 · Cited by 144 · see citing works
The structural coverage of the human proteome before and after AlphaFold
Porta-Pardo, E., Ruiz-Serra, V., Valentini, S., & Valencia, A. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009818 · Cited by 131 · see citing works
A natural mutator allele shapes mutation spectrum variation in mice
Sasani, T. A., Ashbrook, D. G., Beichman, A. C., Lu, L., Palmer, A. A., Williams, R. W., Pritchard, J. K., & Harris, K. (2022) · Nature · doi:10.1038/s41586-022-04701-5 · Cited by 64 · see citing works
McCafferty, C. L., Pennington, E. L., Papoulas, O., Taylor, D. W., & Marcotte, E. M. (2023) · Communications Biology · doi:10.1038/s42003-023-04773-7 · Cited by 35 · see citing works
GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction
Benegas, G., Albors, C., Aw, A. J., Ye, C., & Song, Y. S. (2023) · doi:10.1101/2023.10.10.561776 · Cited by 118 · see citing works
“For evaluation, we first consider the classification of ClinVar [22] pathogenic vs. common mis-sense variants in gnomAD [23].”
Onisiforou, A., & Spyrou, G. M. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab141 · Cited by 23 · see citing works
“Disease data can be collected from databases such as the STRING: disease query app in Cytoscape [77], MalaCards [74], DisGeNET [75], OMIM [114] and ClinVar [115].”
MethodCRISPRmap: Sequencing-free optical pooled screens mapping multi-omic phenotypes in cells and tissue
Gu, J., Iyer, A., Wesley, B., Taglialatela, A., Leuzzi, G., Hangai, S., Decker, A., Gu, R., Klickstein, N., Shuai, Y., et al. (2023) · doi:10.1101/2023.12.26.572587 · Cited by 10 · see citing works
Dirvanskyte, P., Gurram, B., Bolton, C., Warner, N., Jones, K. D. J., Griffin, H. R., Genomics England Research Consortium, Park, J. Y., Keller, K.-M., Gilmour, K. C., et al. (2023) · Journal of Crohn s and Colitis · doi:10.1093/ecco-jcc/jjac103 · Cited by 6 · see citing works
InpherNet accelerates monogenic disease diagnosis using patients’ candidate genes’ neighbors
Yoo, B., Birgmeier, J., Bernstein, J. A., & Bejerano, G. (2021) · Genetics in Medicine · doi:10.1038/s41436-021-01238-2 · Cited by 4 · see citing works
Liu, X., Chen, Y.-W., Xu, X., Smith, D., & Fan, F. (2026) · Toxicological Sciences · doi:10.1093/toxsci/kfag021 · Cited by 1 · see citing works
- Authors
- Landrum, M. J., Chitipiralla, S., Brown, G. R., Chen, C., Gu, B., Hart, J., Hoffman, D., Jang, W., Kaur, K., Liu, C., Lyoshin, V., Maddipatla, Z., Maiti, R., Mitchell, J., O’Leary, N., Riley, G. R., Shi, W., Zhou, G., Schneider, V., Maglott, D., Holmes, J. B., & Kattman, B. L.
- Affiliations
- National Institutes of Health (US)
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- Corresponding author
- Landrum, Melissa J
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-11-28
- Volume
- 48
- Issue
- D1
- Pages
- D835-D844
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC6943040
- OpenAlex
- W2990435446
- Cited by
- 994
- References
- 15
- Citations by year
- 2026: 114 · 2025: 171 · 2024: 240 · 2023: 166 · 2022: 170 · 2021: 100 · 2020: 31 · 2019: 2
- FWCI
- 48.21
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Health Sciences › Health Professions › Health Information Management › Electronic Health Records Systems
- Keywords
- ClinVar, human genetic variants, variant interpretation, disease association, website redesign, haplotypes, genotypes, search engine optimization, data access
- MeSH terms
- Disease, Haplotypes, Humans, National Library of Medicine (U.S.), United States, Genetic Variation, Genome, Human, Internet, Genomics, Databases, Genetic, Search Engine
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.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
