ClinVar Miner

Submissions for variant NM_000154.2(GALK1):c.520G>A (p.Glu174Lys)

gnomAD frequency: 0.00001  dbSNP: rs1363497653
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000669565 SCV000794330 uncertain significance Deficiency of galactokinase 2017-11-08 criteria provided, single submitter clinical testing
Baylor Genetics RCV000669565 SCV004197944 likely pathogenic Deficiency of galactokinase 2023-04-05 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000669565 SCV004297549 likely pathogenic Deficiency of galactokinase 2023-06-23 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 174 of the GALK1 protein (p.Glu174Lys). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt GALK1 protein function. ClinVar contains an entry for this variant (Variation ID: 554016). This missense change has been observed in individual(s) with galactokinase deficiency (PMID: 28173647). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is present in population databases (no rsID available, gnomAD 0.04%).
Fulgent Genetics, Fulgent Genetics RCV000669565 SCV005651911 likely pathogenic Deficiency of galactokinase 2024-06-12 criteria provided, single submitter clinical testing

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