chr7-44145009-GGCCTGGGTCCTGACAAGGCCAGGCCTCCTGCCCCGCCAGGCTGCGAGCACGTGTGGGGAGCACTTCCCCATGGAGCCTGGGTGCTGTGGGGCTGTGGCATCCTCCCTGCGCTTGCGGCCACTGCTCTCACTGGCCCAGCATACAGGCCTTCTTACAGGCCACCGCCG-A
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000162.5(GCK):c.1358_*127delinsT variant causes a stop lost, 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★★). Synonymous variant affecting the same amino acid position (i.e. S453S) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Consequence
GCK
NM_000162.5 stop_lost, 3_prime_UTR
NM_000162.5 stop_lost, 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.862
Genes affected
GCK (HGNC:4195): (glucokinase) This gene encodes a member of the hexokinase family of proteins. Hexokinases phosphorylate glucose to produce glucose-6-phosphate, the first step in most glucose metabolism pathways. In contrast to other forms of hexokinase, this enzyme is not inhibited by its product glucose-6-phosphate but remains active while glucose is abundant. The use of multiple promoters and alternative splicing of this gene result in distinct protein isoforms that exhibit tissue-specific expression in the pancreas and liver. In the pancreas, this enzyme plays a role in glucose-stimulated insulin secretion, while in the liver, this enzyme is important in glucose uptake and conversion to glycogen. Mutations in this gene that alter enzyme activity have been associated with multiple types of diabetes and hyperinsulinemic hypoglycemia. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
Stoplost variant. No alternative stopcodon identified downstream, so we assume a Nonstop Mediated Decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 7-44145009-GGCCTGGGTCCTGACAAGGCCAGGCCTCCTGCCCCGCCAGGCTGCGAGCACGTGTGGGGAGCACTTCCCCATGGAGCCTGGGTGCTGTGGGGCTGTGGCATCCTCCCTGCGCTTGCGGCCACTGCTCTCACTGGCCCAGCATACAGGCCTTCTTACAGGCCACCGCCG-A is Pathogenic according to our data. Variant chr7-44145009-GGCCTGGGTCCTGACAAGGCCAGGCCTCCTGCCCCGCCAGGCTGCGAGCACGTGTGGGGAGCACTTCCCCATGGAGCCTGGGTGCTGTGGGGCTGTGGCATCCTCCCTGCGCTTGCGGCCACTGCTCTCACTGGCCCAGCATACAGGCCTTCTTACAGGCCACCGCCG-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 2571664.Status of the report is reviewed_by_expert_panel, 3 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GCK | NM_000162.5 | c.1358_*127delinsT | stop_lost, 3_prime_UTR_variant | 10/10 | ENST00000403799.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GCK | ENST00000403799.8 | c.1358_*127delinsT | stop_lost, 3_prime_UTR_variant | 10/10 | 1 | NM_000162.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
Monogenic diabetes Pathogenic:1
Likely pathogenic, reviewed by expert panel | curation | ClinGen Monogenic Diabetes Variant Curation Expert Panel | Jun 20, 2023 | The c.1358_*127del168insT variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 453 (NM_000162.5), adding 25 novel amino acids before encountering a stop codon (p.(S453LfsX25)). This variant, located in exon 10 of 10, is predicted to cause loss of a stop codon and result in an elongated protein. The additional residues are expected to cause improper folding, resulting in loss of function in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID 19790256). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). This variant was identified in an individual with diabetes; however, PP4 could not be evaluated due to lack of clinical information (internal lab contributor). PS4_Moderate also cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributor). In summary, c.1358_*127del168insT meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.2.0, approved 6/7/2023): PVS1, PM2_Supporting. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.