ClinVar Miner

Submissions for variant NM_005356.5(LCK):c.601G>A (p.Gly201Ser)

gnomAD frequency: 0.00121  dbSNP: rs11567841
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000690357 SCV000818039 likely benign Severe combined immunodeficiency due to LCK deficiency 2024-01-12 criteria provided, single submitter clinical testing
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000690357 SCV001468380 uncertain significance Severe combined immunodeficiency due to LCK deficiency 2021-03-30 criteria provided, single submitter clinical testing LCK NM_001042771.2 exon 7 p.Gly201Ser (c.601G>A): This variant has not been reported in the literature but is present in 0.2% (273/129110) of European alleles, including 1 homozygote in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/1-32741634-G-A?dataset=gnomad_r2_1). This variant is present in ClinVar (Variation ID:569666). This variant amino acid Serine (Ser) is present in >25 species 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. Of note, although this variant occurs in the exon, splice prediction tools suggest that this variant may affect splicing. However, further studies are needed to understand its impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
PreventionGenetics, part of Exact Sciences RCV003907949 SCV004719099 likely benign LCK-related condition 2022-02-20 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV001703233 SCV001931268 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV001703233 SCV001965303 likely benign not provided no assertion criteria provided clinical testing

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