Research workflows

Which Pax2 mouse models have kidney phenotypes?

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

Ask your AI client

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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The result

MGI resolved Pax2 to MGI:97486 and returned 30 of 68 renal/urinary annotations. The selected rows show why zygosity and genetic background belong next to the phenotype.

Selected renal annotations · one row per genotype–phenotype observation
Allelic compositionAnnotated phenotypeGenetic backgroundGenotype / reference
Pax2<tm1Pgr>/Pax2<+>Decreased nephron number · MP:0011290Involves 129S1/Sv × 129X1/SvJMGI:3694692 · PMID:8575306
Pax2<tm1Pgr>/Pax2<tm1Pgr>Absent kidney · MP:0000520Involves 129S1/Sv × 129X1/SvJMGI:2677317 · PMID:8575306
Pax2<1Neu>/Pax2<+>Abnormal kidney development · MP:0000527Involves 102 × C57BL/6MGI:3841044 · PMID:14603255
Pax2<1Neu>/Pax2<1Neu>Abnormal kidney development · MP:0000527Involves 102 × C3HMGI:3841029 · PMID:8943028
Allele records for those genotypes
AlleleMGI identifierRecorded type
Pax2<tm1Pgr>MGI:1857673Targeted · null/knockout
Pax2<1Neu>MGI:1857114Spontaneous

The first two rows use the same recorded mixed background but different allelic compositions. The two 1Neu rows have different recorded backgrounds as well as different zygosity; they are not a controlled comparison.

These selected annotations do not report penetrance, effect size, age or sex. Open the genotype records and cited experiments before interpreting severity or selecting a model.

Thirty rows are a bounded sample. A complete renal query would need a larger limit while retaining the renal/urinary filter.

Retrieved through Claude Code 2.1.261 · Claude Opus 5.

Original source records
How GeneFoundry got this

  1. Resolve the mouse marker

    Look up Pax2 and verify the current mouse symbol and human ortholog before collecting model annotations.

    mgi_get_marker

    {
  "query": "Pax2",
  "response_mode": "standard"
}

  2. Retrieve renal annotations with their genotypes

    Filter to the renal/urinary system. Read phenotype annotations as statements about the specified genotype and background, rather than about every mouse carrying a Pax2 allele.

    mgi_get_marker_phenotypes

    {
  "query": "Pax2",
  "mp_system": "renal/urinary system",
  "response_mode": "full",
  "limit": 30
}

  3. Check how the alleles were made

    Join each selected phenotype row to the allele inventory by MGI allele ID. Distinguish a targeted null allele from a spontaneous mutation before choosing records to read next.

    mgi_get_marker_alleles

    {
  "query": "Pax2",
  "limit": 50,
  "response_mode": "compact"
}

This connector’s phenotype report covers single-locus, non-conditional genotypes. It excludes conditional/Cre-driven and multi-genic models; consult MGI for those records.

An annotated mouse phenotype supports model discovery. It does not validate a human candidate variant or establish that a selected model reproduces a patient’s disease.

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