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NM_000162.5(GCK):c.1121T>A (p.Val374Glu) AND Monogenic diabetes

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 9, 2023
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003326074.2

Allele description [Variation Report for NM_000162.5(GCK):c.1121T>A (p.Val374Glu)]

NM_000162.5(GCK):c.1121T>A (p.Val374Glu)

Gene:
GCK:glucokinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p13
Genomic location:
Preferred name:
NM_000162.5(GCK):c.1121T>A (p.Val374Glu)
Other names:
NM_001354803.2:c.155T>A
HGVS:
  • NC_000007.14:g.44145629A>T
  • NG_008847.2:g.57542T>A
  • NM_000162.5:c.1121T>AMANE SELECT
  • NM_001354800.1:c.1121T>A
  • NM_001354801.1:c.110T>A
  • NM_001354802.1:c.-20T>A
  • NM_001354803.2:c.155T>A
  • NM_033507.3:c.1124T>A
  • NM_033508.3:c.1118T>A
  • NP_000153.1:p.Val374Glu
  • NP_001341729.1:p.Val374Glu
  • NP_001341730.1:p.Val37Glu
  • NP_001341732.1:p.Val52Glu
  • NP_277042.1:p.Val375Glu
  • NP_277043.1:p.Val373Glu
  • LRG_1074t1:c.1121T>A
  • LRG_1074t2:c.1124T>A
  • LRG_1074:g.57542T>A
  • LRG_1074p1:p.Val374Glu
  • LRG_1074p2:p.Val375Glu
  • NC_000007.13:g.44185228A>T
Protein change:
V373E
Molecular consequence:
  • NM_001354802.1:c.-20T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000162.5:c.1121T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354800.1:c.1121T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354801.1:c.110T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354803.2:c.155T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033507.3:c.1124T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033508.3:c.1118T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Monogenic diabetes
Identifiers:
MONDO: MONDO:0015967; MedGen: C3888631

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004032075ClinGen Monogenic Diabetes Variant Curation Expert Panel
reviewed by expert panel

(ClinGen Monogenic Diabetes ACMG Specifications GCK V1.3.0)		Likely pathogenic
(Aug 9, 2023) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen Monogenic Diabetes Variant Curation Expert Panel, SCV004032075.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.1121T>A variant in the glucokinase gene, GCK, causes an amino acid change of valine to glutamic acid at codon 374 (p.(Val374Glu)) of NM_000162.5. GCK is defined by the ClinGen MDEP VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.968, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). 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% and negative antibodies) (PP4_Moderate; internal lab contributors). Another missense variant, c.1120G>A p.(Val374Met), has been classified as likely pathogenic by the ClinGen MDEP VCEP (PM5_Supporting). This variant was identified in two unrelated individuals with hypglycemia; however, this number does not meet the MDEP cutoff for PS4_Moderate (Solano et al. 2019. Rev Esp Endocrinol Pediatr 10(2):69-73, internal lab contributors). In summary, this variant meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.2.0, approved 6/7/2023): PP2, PP3, PM2_Supporting, PP4_Moderate, PM5_Supporting .

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 16, 2023