Evidence Repository - Clinical Genome Resources

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_033508.3:c.878G>A

CA367400147

Gene: GCK (HGNC:2645)

Condition: monogenic diabetes (MONDO:0015967)

Inheritance Mode: Semidominant inheritance

UUID: 3f7c0bfe-c025-4714-a2db-d8534b028c16

Approved on: 2025-01-16

Published on: 2025-01-29

HGVS expressions

NM_033508.3:c.878G>A

NC_000007.14:g.44146601C>T

CM000669.2:g.44146601C>T

NC_000007.13:g.44186200C>T

CM000669.1:g.44186200C>T

NC_000007.12:g.44152725C>T

NG_008847.1:g.47823G>A

NG_008847.2:g.56570G>A

ENST00000395796.8:c.*879G>A

ENST00000616242.5:c.*1G>A

ENST00000683378.1:n.107G>A

ENST00000345378.7:c.884G>A

ENST00000403799.8:c.881G>A

ENST00000671824.1:c.944G>A

ENST00000673284.1:c.881G>A

ENST00000345378.6:c.884G>A

ENST00000395796.7:c.878G>A

ENST00000403799.7:c.881G>A

ENST00000437084.1:c.830G>A

ENST00000473353.1:n.179G>A

ENST00000616242.4:c.878G>A

NM_000162.3:c.881G>A

NM_033507.1:c.884G>A

NM_033508.1:c.878G>A

NM_000162.4:c.881G>A

NM_001354800.1:c.881G>A

NM_001354801.1:c.8+18G>A

NM_033507.2:c.884G>A

NM_033508.2:c.878G>A

NM_000162.5:c.881G>A

NM_033507.3:c.884G>A

Pathogenic

PP4_Moderate PP1 PP3 PP2 PS4 PM2_Supporting

PM1

Evidence Links 0

Expert Panel

Monogenic Diabetes VCEP

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.881G>A variant in the glucokinase gene, GCK, causes an amino acid change of glycine to aspartic acid at codon 294 (p.(Gly294Asp)) 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 absent from gnomAD v2.1.1 (PM2_Supporting). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.793, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant was identified in 11 unrelated individuals with hyperglycemia (PS4; PMIDs: 20337973, 35737141, internal lab contributors). Additonally, one of these individuals had a clinical history highly specific for GCK-hyperglycemia (fasting glucose 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative autoantibodies) (PP4_Moderate; internal lab contributors). This variant segregated with hyperglycemia with 2 informative meioses in 2 families (PP1; internal lab contributors). In summary, c.881G>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, PM2_Supporting, PP1, PP2, PP3.

PP4_Moderate

This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (fasting glucose 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative autoantibodies) (PP4_Moderate; internal lab contributors).

PP1

This variant segregated with hyperglycemia with 2 informative meioses in 2 families (PP1; internal lab contributors).

PP3

This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.793, 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).

PS4

This variant was identified in 11 unrelated individuals with hyperglycemia (PS4; PMIDs: 20337973, 35737141, internal lab contributors).

PM2_Supporting

This variant is absent from gnomAD v2.1.1 (PM2_Supporting).

PM1

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

Curation History

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