ClinVar Miner

Submissions for variant NM_006282.5(STK4):c.733C>T (p.Arg245Ter)

gnomAD frequency: 0.00001  dbSNP: rs748660310
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001036103 SCV001199451 pathogenic Combined immunodeficiency due to STK4 deficiency 2023-09-06 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg245*) in the STK4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in STK4 are known to be pathogenic (PMID: 22174160). This variant is present in population databases (rs748660310, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with STK4-related conditions. ClinVar contains an entry for this variant (Variation ID: 835262). For these reasons, this variant has been classified as Pathogenic.
3billion RCV001036103 SCV003842092 pathogenic Combined immunodeficiency due to STK4 deficiency 2023-02-23 criteria provided, single submitter clinical testing The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.001%). This variant was predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported to be associated with STK4 related disorder (ClinVar ID: VCV000835262). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

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