NM_000162.5:c.118G>A

Variant names:

• chr7-44153391-C-T
• rs794727236
• NM_000162.5:c.118G>A

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PP4_Moderate PM2_Supporting PS3_Moderate PP2 PP3 PS4 PP1_Strong PM3_Supporting

This summary comes from the ClinGen Evidence Repository: The c.118G>A variant in the glucokinase gene, GCK, causes an amino acid change of glutamic acid to lysine at codon 40 (p.(Glu40Lys)) of NM_000162.5. 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 predicted to be deleterious by computational evidence, with a REVEL score of 0.967, which is greater than the MDEP VCEP threshold of 0.70 (PP3). It is absent from gnomAD v2.1 and v4.1 (PM2_Supporting). MDEP wild type quality control measures were met, and the relative activity Index (RAI) of this variant was found to be 0.069, which is below the MDEP cutoff (<0.5) (PS3_Moderate; PMID:25015100). This variant was identified in at least 33 unrelated individuals with hyperglycemia (PS4; PMID:22332836, 29207974, 25015100, Internal lab contributors). This variant segregated with hyperglycemia, with four informative meioses in three families (PP1_Strong; PMID:24804978, Internal lab contributors). This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%, antibody negative) (PP4_Moderate; Internal lab contributor). This variant has been detected in the homozygous state in one individual with neonatal diabetes (PM3_Supporting; PMID:25015100). In summary, c.118G>A meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PS4, PP4_Moderate, PS3_Moderate, PP1_Strong, PP2, PP3, PM2_Supporting, PM3_Supporting LINK:https://erepo.genome.network/evrepo/ui/classification/CA201503/MONDO:0015967/086

• Frequency: Genomes: not found (cov: 32)
• Consequence: GCK NM_000162.5 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:3
• Conservation: PhyloP100: 7.88

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]

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PS4: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP1: For more information check the summary or visit ClinGen Evidence Repository.
• PP2: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GCK	NM_000162.5	c.118G>A	p.Glu40Lys	missense_variant	Exon 2 of 10	ENST00000403799.8	NP_000153.1
GCK	NM_033507.3	c.121G>A	p.Glu41Lys	missense_variant	Exon 2 of 10		NP_277042.1
GCK	NM_033508.3	c.115G>A	p.Glu39Lys	missense_variant	Exon 3 of 11		NP_277043.1
GCK	NM_001354800.1	c.118G>A	p.Glu40Lys	missense_variant	Exon 2 of 11		NP_001341729.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GCK	ENST00000403799.8	c.118G>A	p.Glu40Lys	missense_variant	Exon 2 of 10	1	NM_000162.5	ENSP00000384247.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: reviewed by expert panel

Submissions by phenotype

Maturity-onset diabetes of the young type 2 Pathogenic:1

Oct 16, 2023

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PS4,PM2_SUP,PP2,PP3 -

Monogenic diabetes Pathogenic:1

Jan 29, 2025

ClinGen Monogenic Diabetes Variant Curation Expert Panel

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

The c.118G>A variant in the glucokinase gene, GCK, causes an amino acid change of glutamic acid to lysine at codon 40 (p.(Glu40Lys)) of NM_000162.5. 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 predicted to be deleterious by computational evidence, with a REVEL score of 0.967, which is greater than the MDEP VCEP threshold of 0.70 (PP3). It is absent from gnomAD v2.1 and v4.1 (PM2_Supporting). MDEP wild type quality control measures were met, and the relative activity Index (RAI) of this variant was found to be 0.069, which is below the MDEP cutoff (<0.5) (PS3_Moderate; PMID: 25015100). This variant was identified in at least 33 unrelated individuals with hyperglycemia (PS4; PMID: 22332836, 29207974, 25015100, Internal lab contributors). This variant segregated with hyperglycemia, with four informative meioses in three families (PP1_Strong; PMID: 24804978, Internal lab contributors). This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%, antibody negative) (PP4_Moderate; Internal lab contributor). This variant has been detected in the homozygous state in one individual with neonatal diabetes (PM3_Supporting; PMID: 25015100). In summary, c.118G>A meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PS4, PP4_Moderate, PS3_Moderate, PP1_Strong, PP2, PP3, PM2_Supporting, PM3_Supporting -

not provided Pathogenic:1

Nov 22, 2014

Eurofins Ntd Llc (ga)

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.95
BayesDel_addAF	Pathogenic	0.53	D
BayesDel_noAF	Pathogenic	0.52
CADD	Pathogenic	33
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.93	.;D;.;.;.
Eigen	Pathogenic	0.90
Eigen_PC	Pathogenic	0.84
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.94	D;D;.;D;D
M_CAP	Pathogenic	0.74	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	2.9	.;M;.;.;.
PrimateAI	Uncertain	0.79	T
PROVEAN	Uncertain	-3.0	.;D;D;D;D
REVEL	Pathogenic	0.97
Sift	Uncertain	0.017	.;D;D;D;D
Sift4G	Uncertain	0.038	D;D;D;D;D
Polyphen		1.0	D;D;D;D;.
Vest4		0.97
MutPred		0.86		.;Gain of glycosylation at E40 (P = 0.0322);.;.;Gain of glycosylation at E40 (P = 0.0322);
MVP		1.0
MPC		2.4
ClinPred		0.99	D
GERP RS		5.1
Varity_R		0.94
gMVP		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs794727236; hg19: chr7-44192990;