ClinVar Miner

Submissions for variant NM_000162.5(GCK):c.863+1G>A

dbSNP: rs1376796469
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics Inc RCV000711787 SCV000842184 pathogenic not provided 2020-10-14 criteria provided, single submitter clinical testing This variant is expected to severely impact normal RNA splicing, and consequently, protein structure and/or function. The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). This variant has been identified in at least one individual with clinical features associated with this gene.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001420913 SCV001623362 likely pathogenic Maturity-onset diabetes of the young type 2 2021-04-21 criteria provided, single submitter clinical testing Variant summary: GCK c.863+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5 splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4.1e-06 in 241310 control chromosomes (gnomAD). c.863+1G>A has been reported in the literature in one individual affected with maturity-onset diabetes of the young (Alkorta-Aranburu_2014). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One ClinVar submitter (evaluation after 2014) cites the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Invitae RCV000711787 SCV002235594 pathogenic not provided 2022-10-29 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. ClinVar contains an entry for this variant (Variation ID: 585928). Disruption of this splice site has been observed in individual(s) with maturity-onset diabetes of the young (PMID: 19790256, 21696527, 25306193). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change affects a donor splice site in intron 7 of the GCK 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 GCK are known to be pathogenic (PMID: 7553875, 9867845, 14578306, 24323243, 25015100).
Geisinger Clinic, Geisinger Health System RCV001420913 SCV002562196 pathogenic Maturity-onset diabetes of the young type 2 2022-08-02 criteria provided, single submitter research PVS1, PM2, PS4_Supporting, PS1_Moderate, PP4

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