The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000162.5(GCK):c.623C>T (p.Ala208Val)

CA4239569

447411 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 6769e16e-1976-4b67-bf42-cbeb1e4c072b

HGVS expressions

NM_000162.5:c.623C>T
NM_000162.5(GCK):c.623C>T (p.Ala208Val)
NC_000007.14:g.44149816G>A
CM000669.2:g.44149816G>A
NC_000007.13:g.44189415G>A
CM000669.1:g.44189415G>A
NC_000007.12:g.44155940G>A
NG_008847.1:g.44608C>T
NG_008847.2:g.53355C>T
ENST00000395796.8:c.*621C>T
ENST00000616242.5:c.623C>T
ENST00000682635.1:n.1109C>T
ENST00000345378.7:c.626C>T
ENST00000403799.8:c.623C>T
ENST00000671824.1:c.623C>T
ENST00000673284.1:c.623C>T
ENST00000345378.6:c.626C>T
ENST00000395796.7:c.620C>T
ENST00000403799.7:c.623C>T
ENST00000437084.1:c.572C>T
ENST00000616242.4:c.620C>T
NM_000162.3:c.623C>T
NM_033507.1:c.626C>T
NM_033508.1:c.620C>T
NM_000162.4:c.623C>T
NM_001354800.1:c.623C>T
NM_033507.2:c.626C>T
NM_033508.2:c.620C>T
NM_033507.3:c.626C>T
NM_033508.3:c.620C>T

Pathogenic

Met criteria codes 6
PS4 PP3 PP2 PP4_Moderate PM2_Supporting PP1_Strong

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GCK Version 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.623C>T variant in the glucokinase gene, GCK, causes an amino acid change of alanine to valine at codon 208 (p.(Ala208Val)) of NM_000162.5. This variant segregated with diabetes/hyperglycemia, with 9 informative meioses in 6 families (PP1_Strong; internal lab contributors). This variant was identified in 16 unrelated individuals with hyperglycemia (PS4; 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% and a 5 generation family history of diabetes) (PP4_Moderate; internal lab contributors). 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 0.851, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant has an incomputable gnomAD v2.1.1 Popmax minor filtering allele frequency due to 1 copy in the European non-Finnish subpopulation and 0 copies in any other subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Popmax FAF <= 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting). In summary, c.623C>T 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): PP1_Strong, PS4, PP4_Moderate, PP2, PP3, PM2_Supporting.
Met criteria codes
PS4
This variant was identified in 16 unrelated individuals with hyperglycemia (PS4; internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.851, which is greater than the MDEP VCEP threshold of 0.70 (PP3).
PP2
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).
PP4_Moderate
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 a 5 generation family history of diabetes) (PP4_Moderate; internal lab contributors).
PM2_Supporting
This variant has an incomputable gnomAD v2.1.1 Popmax minor filtering allele frequency due to 1 copy in the European non-Finnish subpopulation and 0 copies in any other subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Popmax FAF <= 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting).
PP1_Strong
This variant segregated with diabetes/hyperglycemia, with 9 informative meioses in 6 families (PP1_Strong; internal lab contributors).
Approved on: 2024-01-18
Published on: 2024-01-18
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.