7-44145602-G-C
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2_SupportingPP2PP3PM5PP1_Moderate
This summary comes from the ClinGen Evidence Repository: The c.1148C>G variant in the glucokinase gene, GCK, causes an amino acid change of serine to tryptophan at codon 383 (p. (Ser383Trp)) of NM_000162.5. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). GCK is defined by the ClinGen MDEP as a gene that has a low rate of benign missense variation and has pathogenic missense variants as a common mechanism of disease (PP2) This variant is located in the larger hexokinase domain of the GCK gene (PMID:31638168) but this variant does not reside in an amino acid that directly binds glucose or ATP, which is defined as critical for the protein’s function by the ClinGen MDEP, so it does not meet PM1. This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.85 which is greater than the MDEP VCEP threshold of 0.70 (PP3). Another missense variant, c.1148C>T (p.Ser383Leu), has been interpreted as pathogenic by the ClinGen MDEP, and p.Ser383Trp has an equal or greater Grantham distance (PM5). This variant was found in one family, and segregated with hyperglycemia, with four informative meioses (PP1_Moderate; PMID:3385223). In summary, c.1148C>G meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (VCEP specifications version v1.3.0; approved 8/11/2023): PP3, PP2, PP1_Moderate, PM5, PM2_Supporting LINK:https://erepo.genome.network/evrepo/ui/classification/CA367398735/MONDO:0015967/086
Frequency
Consequence
NM_000162.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Monogenic diabetes Pathogenic:1
The c.1148C>G variant in the glucokinase gene, GCK, causes an amino acid change of serine to tryptophan at codon 383 (p. (Ser383Trp)) of NM_000162.5. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). GCK is defined by the ClinGen MDEP as a gene that has a low rate of benign missense variation and has pathogenic missense variants as a common mechanism of disease (PP2) This variant is located in the larger hexokinase domain of the GCK gene (PMID: 31638168) but this variant does not reside in an amino acid that directly binds glucose or ATP, which is defined as critical for the protein’s function by the ClinGen MDEP, so it does not meet PM1. This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.85 which is greater than the MDEP VCEP threshold of 0.70 (PP3). Another missense variant, c.1148C>T (p.Ser383Leu), has been interpreted as pathogenic by the ClinGen MDEP, and p.Ser383Trp has an equal or greater Grantham distance (PM5). This variant was found in one family, and segregated with hyperglycemia, with four informative meioses (PP1_Moderate; PMID: 3385223). In summary, c.1148C>G meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (VCEP specifications version v1.3.0; approved 8/11/2023): PP3, PP2, PP1_Moderate, PM5, PM2_Supporting -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.