ClinVar Miner

Submissions for variant NM_000154.2(GALK1):c.611+1G>T

gnomAD frequency: 0.00001  dbSNP: rs982043960
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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 RCV001215181 SCV001386911 pathogenic Deficiency of galactokinase 2023-08-18 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Experimental studies have shown that disruption of this splice site affects GALK1 function (PMID: 10790206). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. ClinVar contains an entry for this variant (Variation ID: 944717). Disruption of this splice site has been observed in individual(s) with galactokinase deficiency (PMID: 10790206). This variant is present in population databases (no rsID available, gnomAD 0.009%). This sequence change affects a donor splice site in intron 4 of the GALK1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in GALK1 are known to be pathogenic (PMID: 7670469, 10790206).
Baylor Genetics RCV001215181 SCV005058779 likely pathogenic Deficiency of galactokinase 2023-12-28 criteria provided, single submitter clinical testing

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