Q5: How do I report issues or suggest improvements?

Q6: How do I search a list of genes or a gene panel?

Q1: How do I use Gene Lookup?

Gene Lookup allows you to search by gene name, genomic region, disease name, or phenotype. You can also apply advanced filters for inheritance mode, data source, constraint scores, ClinGen classification, or other structured fields.

Example use cases:

Example #1	Search for a specific gene like SMN1
Example #2	Search for all genes associated with ataxia
Example #3	Search for all disease-associated genes in a genomic region

Q2: What data sources are included?

Gene Lookup aggregates gene-disease association data from the following sources:

OMIM — Online Mendelian Inheritance in Man
ClinGen — Gene-disease validity classifications
GenCC — Gene Curation Coalition
PanelApp UK — Genomics England PanelApp
PanelApp Australia — Australian Genomics PanelApp
DECIPHER — DDG2P gene-disease associations
ClinVar — Pathogenic/likely pathogenic variant annotations
GWAS Catalog — GWAS hits for MONDO rare-disease phenotypes
Fridman et al. 2025 — Autosomal recessive gene-disease associations
gnomAD constraint metrics — pLI, LOEUF, and MOEUF from gnomAD v4.1.1

Q3: What are the constraint scores?

Constraint scores from gnomAD v4.1.1 reflect how tolerant a gene is to different types of variation:

pLI — Probability of loss-of-function intolerance. Values close to 1 indicate the gene is highly intolerant to loss-of-function variants.
LOEUF — Loss-of-function observed/expected upper bound fraction. Lower values indicate greater constraint. A threshold of ≤0.35 is commonly used to identify constrained genes.
MOEUF — Missense observed/expected upper-bound fraction. Lower values suggest the gene is intolerant to missense variation.

Q4: What is the phenotype summary?

The summary is created by aggregating phenotype descriptions from the data sources listed in Q2 and feeding them into a large language model (Gemini Flash) to produce a concise summary.

Q5: How do I report issues or suggest improvements?

Open an issue on the GitHub repository or email weisburd@broadinstitute.org

Q6: How do I search a list of genes or a gene panel?

There are two ways to search many genes at once — useful for reviewing or developing gene panels:

Type a comma-separated list into the search box, e.g. SMN1, CFTR, DMD.
Upload a file using the + button in the search box. Drag & drop or choose a TSV, TXT, or BED file (all optionally gzip-compressed, e.g. .txt.gz):
- TXT / TSV whose first column contains gene symbols, gene IDs (HGNC, ENSG, or RefSeq), or hg38 genomic regions (e.g. chr1:1000000-2000000), one per row. A header row is optional.
- BED whose first 3 columns are the hg38 coordinates chrom, start, end (0-based, half-open). Genes overlapping those regions are returned.

Uploaded genes are matched against gene symbols, aliases, and IDs. After a gene-list search, a summary shows how many of your genes were found in the database and lists any that were not found (with a link to see the full list). Uploaded regions (BED, or regions in a TXT/TSV) report how many overlap a gene and list any with no overlapping gene.

You can also narrow a panel by keyword: upload a gene list, then type a disease or phenotype term (e.g. epilepsy) in the search box before searching to see which of your panel genes are associated with that term.