U.S. flag

An official website of the United States government

NM_000162.5(GCK):c.1099G>T (p.Val367Leu) AND Monogenic diabetes

Germline classification:
Uncertain significance (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:
RCV003326018.2

Allele description [Variation Report for NM_000162.5(GCK):c.1099G>T (p.Val367Leu)]

NM_000162.5(GCK):c.1099G>T (p.Val367Leu)

Gene:
GCK:glucokinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p13
Genomic location:
Preferred name:
NM_000162.5(GCK):c.1099G>T (p.Val367Leu)
Other names:
NM_001354803.2:c.133G>T
HGVS:
  • NC_000007.14:g.44145651C>A
  • NG_008847.2:g.57520G>T
  • NM_000162.5:c.1099G>TMANE SELECT
  • NM_001354800.1:c.1099G>T
  • NM_001354801.1:c.88G>T
  • NM_001354802.1:c.-42G>T
  • NM_001354803.2:c.133G>T
  • NM_033507.3:c.1102G>T
  • NM_033508.3:c.1096G>T
  • NP_000153.1:p.Val367Leu
  • NP_001341729.1:p.Val367Leu
  • NP_001341730.1:p.Val30Leu
  • NP_001341732.1:p.Val45Leu
  • NP_277042.1:p.Val368Leu
  • NP_277043.1:p.Val366Leu
  • LRG_1074t1:c.1099G>T
  • LRG_1074t2:c.1102G>T
  • LRG_1074:g.57520G>T
  • LRG_1074p1:p.Val367Leu
  • LRG_1074p2:p.Val368Leu
  • NC_000007.13:g.44185250C>A
Protein change:
V30L
Molecular consequence:
  • NM_001354802.1:c.-42G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000162.5:c.1099G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354800.1:c.1099G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354801.1:c.88G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354803.2:c.133G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033507.3:c.1102G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033508.3:c.1096G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004032115ClinGen Monogenic Diabetes Variant Curation Expert Panel
reviewed by expert panel

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

Citation Link

Help

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, SCV004032115.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.1099G>T variant in the glucokinase gene, GCK, causes an amino acid change of valine to leucine at codon 367 (p.(Val367Leu)) 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 0.813, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). Another missense variant, c.1099G>A p.(Val367Met), has been interpreted as pathogenic by the ClinGen MDEP VCEP and p.Val367Leu has a greater Grantham distance (PM5). This variant was identified in an individual with a phenotype suggestive of GCK-hyperglycemia; however, PP4 is unable to be evaluated due to insufficient clinical information (internal lab contributors). In summary, this variant meets the criteria to be classified as a variant of uncertain significance 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, PM5.

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

Last Updated: Sep 16, 2023