Research workflows | GeneFoundry

What do gnomAD and ClinVar show for HNF1B?

One question brings together gene constraint and five source-linked variant records.

Use GeneFoundry to look up HNF1B in gnomAD on GRCh38. Show its gene-level constraint metrics, then get five ClinVar variants sorted by review status. Include variant names, classifications, review stars and links to the original records.

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Which genes link renal cysts and diabetes?

Two phenotype searches found 13 shared genes. A ClinGen lookup added curated evidence for HNF1B.

Use GeneFoundry to find genes associated with renal cyst and diabetes mellitus in HPO, using exact terms without descendants. Retrieve every page and show the genes shared by both lists. Then check the ClinGen gene–disease validity evidence for HNF1B and link to the original curation.

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What does CFTR p.Phe508del change?

Normalize an allele, compare transcript consequences and separate VEP annotation from ClinVar classification.

Use GeneFoundry to annotate NM_000492.4:c.1521_1523del in CFTR on GRCh38. Show the returned VCF, genomic HGVS and SPDI representations. Identify the MANE Select transcript, consequence term and protein change, then compare one alternative transcript. Find the matching ClinVar record and report its classification, review status and transcript version separately. Flag identifier or normalization differences before joining records; do not turn VEP impact labels into an ACMG classification.

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What do three studies show about HNF1B in kidney development?

A focused literature search turns three primary-study abstracts into a comparison of models, mechanisms and findings.

Use GeneFoundry to find three primary studies of HNF1B in kidney development. Retrieve their full abstracts and compare the experimental models, the main findings and what each study adds. Cite every finding with its PMID and distinguish experimental mechanisms from evidence in patients.

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Draft a source-backed HNF1B gene summary

GeneReviews passages and ClinGen curation become a concise report draft that separates HNF1B-related disease from the broader 17q12 deletion syndrome.

Use GeneFoundry to draft a short HNF1B gene summary for a research report. Check GeneReviews and ClinGen, cover the renal and diabetes associations, and distinguish intragenic HNF1B variants from the broader 17q12 deletion syndrome. Cite the supporting chapter and curation. Do not make a patient diagnosis or classify an individual variant.

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How strong is the MYH7 link to different heart and muscle diseases?

Compare five ClinGen relationships with GenCC assertions without turning one definitive association into a claim about every condition.

Use GeneFoundry to assess MYH7 gene-disease validity. List each ClinGen disease, inheritance, evidence strength, curator and date; compare GenCC submissions for the same disease identifiers. Explain which relationships are definitive and which remain limited, without classifying a patient variant.

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What evidence supports HNF1B p.Arg177Ter—and what is still missing?

Build an ACMG/AMP research worksheet from an exact allele, a PVS1 suggestion and an unsuccessful population-frequency lookup.

Use GeneFoundry to build an ACMG/AMP evidence worksheet for HNF1B NM_000458.4:c.529C>T (p.Arg177Ter), ClinVar VCV000012635, in autosomal dominant renal cysts and diabetes syndrome. Resolve the GRCh38 allele, retrieve its ClinVar record and gnomAD frequency, inspect AutoPVS1 and VEP, and confirm ClinGen validity and dosage context. Separate source classifications from candidate criteria, identify missing evidence and avoid double counting. Do not produce an autonomous final classification.

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Which Pax2 mouse models have kidney phenotypes?

Find annotated renal phenotypes, then keep the allele, genotype and genetic background together.

Use GeneFoundry to find mouse Pax2 models with renal or urinary phenotypes in MGI. Resolve the mouse marker, retrieve 30 phenotype annotations, and look up the alleles. Compare a heterozygous and homozygous Pax2 mutation, preserving genotype IDs, genetic backgrounds and source references. State whether the response is complete and whether conditional models are included.

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Where are HNF1B, PAX2 and GATA3 expressed?

Compare three genes across adult kidney cortex, kidney medulla and pancreas in GTEx.

Use GeneFoundry to compare HNF1B, PAX2 and GATA3 expression in GTEx v10 adult kidney cortex, kidney medulla and pancreas. Report median TPM, sample counts and the returned versioned gene IDs. Explain what bulk adult tissue expression can and cannot tell me about a developmental disease candidate.

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