ClinVar Miner

Submissions for variant NM_006904.6(PRKDC):c.4138G>A (p.Ala1380Thr) (rs56209904)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000768057 SCV000898911 uncertain significance Immunodeficiency 26 with or without neurologic abnormalities 2018-11-02 criteria provided, single submitter clinical testing PRKDC NM_006904.6 (LRG_162) exon 33 p.Ala1380Thr (c.4138G>A): This variant has not been reported in the literature but is present in 0.008% (3/34524) of Latino alleles in the Genome Aggregation Database ( This variant amino acid Threonine (Thr) is present in 3 species (chinese hamster, golden hamster, tenrec) and is not well conserved among evolutionarily distant species; this suggests that this variant may not impact the protein. Additional computational prediction tools do not suggest an impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Invitae RCV000768057 SCV001384434 uncertain significance Immunodeficiency 26 with or without neurologic abnormalities 2019-09-27 criteria provided, single submitter clinical testing This sequence change replaces alanine with threonine at codon 1380 of the PRKDC protein (p.Ala1380Thr). The alanine residue is weakly conserved and there is a small physicochemical difference between alanine and threonine. This variant is present in population databases (rs56209904, ExAC 0.009%). This variant has not been reported in the literature in individuals with PRKDC-related conditions. ClinVar contains an entry for this variant (Variation ID: 625999). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: Tolerated; PolyPhen-2: Not available; Align-GVGD: Class C0. The threonine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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