A recent study identified disease-associated variants in the SLC39A7 which encodes the zinc transporter ZIP7 in the B-cell immunodeficiency. Using the whole-exome sequencing, we identified four inherited heterozygous missense variants in the SLC39A7 gene in a Japanese girl with B-cell deficiency of unknown cause. We analyzed the impact of identified variants by the transfected cell lines and found that one variant was unstable due to degradation by the proteasome and the other variant altered the protein‘s properties so that more of it accumulated in the detergent-insoluble fraction. Our findings provide crucial information to uncover the pathogenic mechanisms in B-cell deficiency elicited by variant ZIP7 proteins.