ClinVar Miner

Submissions for variant NM_016734.3(PAX5):c.253G>A (p.Gly85Arg)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
St. Jude Clinical Genomics Lab, St. Jude Children's Research Hospital RCV001526820 SCV001737471 likely pathogenic Leukemia, acute lymphoblastic, susceptibility to, 3 2021-05-20 criteria provided, single submitter clinical testing The PAX5 c.253G>A (p.Gly85Arg) missense change replaces glycine with arginine at codon 85 of the PAX5 gene and is absent in population databases including gnomAD v2.1.1 (PM2_supporting; https://gnomad.broadinstitute.org/). The glycine residue is highly conserved across species and the glycine and arginine substitution is a non-conservative amino acid change, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Seven of seven in silico tools predict a deleterious effect of this variant on protein function (PP3). Experimental data indicates that this variant likely plays a role in leukemogenesis. In a mutagenesis experiment, multiple ENU treated Pax5+/- mice acquired p.Gly85Arg mutations (PS3; PMID: 25855603). In a mouse model of BCR-ABL1 leukemia, a Pax5+/+ mouse was found to be homozygous for this variant and exhibited a pre-pro B leukemic phenotype (https://doi.org/10.1182/blood.V112.11.293.293; https://dc.uthsc.edu/dissertations/186/). This variant has been identified in an individual with B cell acute lymphoblastic leukemia in which the tumor exhibited loss of the wild-type PAX5 allele (internal data). This is consistent with literature reports of individuals with B cell acute lymphoblastic leukemia and pathogenic germline variants in PAX5 (PMID: 24013638, 24287434). Additionally, expression analysis showed that this tumor sample clustered with the PAX5 altered p.Pro80Arg subtype (internal data). In summary, this variant meets criteria to be classified as of likely pathogenic based on the ACMG/AMP criteria and additional internal data: PS3, PM2_supporting, PP3.

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