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Quick Guide to Nomenclature for Alleles and Mutations

A note on gene and allele assignments:

A new heritable phenotypic allele may be an allele of a known gene or an allele of a previously unknown gene.

Example: You discover a new spontaneous phenotypic allele that looks "shaker like," but with a somewhat milder phenotype.

Basic rules for naming alleles

For designating mutants that are alleles of new genes (Case 2 above), see Quick Guide to Nomenclature for Genes.

For designating mutants that are alleles of known genes, the basic guidelines are:

  1. Allele designations begin with a letter and contain alphanumeric characters. Punctuation marks occur in certain cases where they convey meaning.
  2. Allele designations appear as superscripted short alphanumeric strings following the gene symbol of which they are an allele and serve as an acronym for the allele name. Example: Atp7aMo or Egfrtm1Mag.
  3. For allele designations for spontaneous and induced alleles of known genes...
    • Allele designations begin with a lower case letter if the allele is a recessive and begin with a capital letter otherwise. Example: Wnt3avt is the allele symbol for the recessive vestigial tail allele of the Wnt3a gene, while Atp7aMo is the allele symbol for the dominant mottled allele of the Atp7a gene.
    • If an allele is part of an allelic series, a serial number and lab code are part of its designation. Each laboratory has its own numbering series. Example: Tyrc-4J is the 4th albino allele in the series discovered at The Jackson Laboratory (J) for the Tyr gene; T39H is the 39th mutation of T from Harwell (H). This particular T allele was discovered in Harwell's ENU mutagenesis program.
  4. Allele designations for transgenic and targeted alleles of known genes...
    • Tg(YYY)#Zzz for transgenic alleles, where YYY is the inserted gene, # is the serial number, and Zzz the lab code for the laboratory. Example: VcanTg(Hoxa1)1Chm, the Tg(Hoxa1)1Chm allele of Vcan. A construct containing the mouse homeobox a1 (Hoxa1) was inserted by microinjection, the first reported by Corey H. Mjaatvedt (Chm). This transgene was found before it was associated with any known gene. Later, it was identified as an allele of Versican (chondroitin sulfate proteoglycan).
    • tm#Zzz for targeted alleles by homologous recombination, where tm indicates targeted mutation, # is the serial number, and Zzz the lab code for the laboratory. Example: Egfrtm1Mag where this is the 1st targeted mutation of Egfr created by Terry Magnuson (Mag).

The Mouse Genomic Nomenclature Committee (MGNC) provides assistance in assigning nomenclature. Please contact us at nomen@jax.org.

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Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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