ClinVar Miner

Submissions for variant NM_000154.2(GALK1):c.410del (p.Gly137fs)

dbSNP: rs767329054
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000667929 SCV000792456 likely pathogenic Deficiency of galactokinase 2017-06-27 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000667929 SCV001411291 pathogenic Deficiency of galactokinase 2024-01-28 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gly137Valfs*27) in the GALK1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GALK1 are known to be pathogenic (PMID: 7670469, 10790206). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with GALK1-related conditions (PMID: 10570908, 20405025). ClinVar contains an entry for this variant (Variation ID: 552633). For these reasons, this variant has been classified as Pathogenic.
3billion RCV000667929 SCV002058230 pathogenic Deficiency of galactokinase 2022-01-03 criteria provided, single submitter clinical testing Frameshift: 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 (PVS1_VS). The variant has been reported at least twice as pathogenic/likely pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000552633, PMID:10570908). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
CeGaT Center for Human Genetics Tuebingen RCV003326487 SCV004033584 pathogenic not provided 2023-07-01 criteria provided, single submitter clinical testing GALK1: PVS1, PM2, PM3, PP4
Baylor Genetics RCV000667929 SCV004197926 pathogenic Deficiency of galactokinase 2024-01-26 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000667929 SCV004848235 pathogenic Deficiency of galactokinase 2018-09-17 criteria provided, single submitter clinical testing The p.Gly137ValfsX27 variant in GALK1 has been reported in the homozygous state in 6 affected members of one Pakistani family with early-onset cataracts (Yasmeen 2010). It was absent from large population studies. This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 137 and leads to a premature termination codon 27 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. In summary, this variant meets criteria to be classified as pathogenic for galactokinase deficiency in an autosomal recessive manner. ACMG/AMP criteria applied: PVS1_Strong, PP1_Strong, PM2, PM3_Supporting.
Natera, Inc. RCV000667929 SCV002088896 pathogenic Deficiency of galactokinase 2020-03-13 no assertion criteria provided clinical testing

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