RareVarDB

RareVarDB, developed by GeneSpectrum Life Sciences, is a specialized database dedicated to cataloging genetic variants — specifically SNPs and Indels — associated with rare and orphan diseases. The database covers more than 4,000 rare diseases, over 1,000 genes, and more than 1 million variants aggregated from 25 or more data sources. It is intended for researchers, clinicians, and geneticists who require detailed, curated genetic information on rare disorders.

Data in RareVarDB is drawn from multiple authoritative sources including Orphanet, OMIM, ClinVar, dbSNP, and more than 20 additional specialized databases. The database is updated quarterly with new data from integrated sources and curated additions from the scientific literature, with major updates communicated via newsletter.

Search and Discovery

• Supports search by rare disease name (e.g., "Cystic Fibrosis"), gene symbol (e.g., "CFTR"), or genetic variant ID such as an rsID (e.g., "rs121908757").
• Provides example queries within the platform to guide users unfamiliar with the search interface.
• Returns disease-level information including GARD and OMIM identifiers alongside variant-level data.

Variant Annotation

• Each variant record includes chromosomal position, allele frequencies, clinical significance, and pathogenicity predictions.
• Direct links to ClinVar and dbSNP entries are provided for each variant.
• Sample data covers conditions such as Cystic Fibrosis (CFTR, rs121908757), Huntington's Disease (HTT, rs1060505319), Marfan Syndrome (FBN1, rs137854994), Familial Hypercholesterolemia (LDLR, rs121908033), and Retinoblastoma (RB1, rs121913301).

Filtering and Analysis

• Multiple filters can be applied simultaneously to narrow variant results.
• Filterable criteria include clinical significance, chromosome, variant type, minor allele frequency (MAF) threshold, and pathogenicity score.
• Pathogenicity prediction scores from SIFT, PolyPhen, and CADD are available as filter parameters.

Access and Data Contribution

• RareVarDB offers both free and premium access tiers; the free tier includes most features with limitations on data export and API usage.
• Academic researchers may qualify for enhanced access beyond the standard free tier.
• External data contributions from researchers are accepted; all submitted data undergoes quality control review before inclusion.
• Researchers interested in contributing data or collaborating can contact the GeneSpectrum team directly.