Variant: NM_000162.5(GCK):c.1020-1G>A

CA367399428

447378 (ClinVar)

Gene: GCK

Condition: monogenic diabetes

Inheritance Mode: Semidominant inheritance

UUID: 765c2ee2-101a-45d7-894e-7f0aeaa1633c

Approved on: 2024-03-31

Published on: 2024-03-31

HGVS expressions

NM_000162.5:c.1020-1G>A
NM_000162.5(GCK):c.1020-1G>A
NC_000007.14:g.44145731C>T
CM000669.2:g.44145731C>T
NC_000007.13:g.44185330C>T
CM000669.1:g.44185330C>T
NC_000007.12:g.44151855C>T
NG_008847.1:g.48693G>A
NG_008847.2:g.57440G>A
ENST00000395796.8:c.*1018-1G>A
ENST00000616242.5:c.*140-1G>A
ENST00000683378.1:n.246-1G>A
ENST00000336642.9:c.54-1G>A
ENST00000345378.7:c.1023-1G>A
ENST00000403799.8:c.1020-1G>A
ENST00000671824.1:c.1083-1G>A
ENST00000672743.1:n.32-1G>A
ENST00000673284.1:c.1020-1G>A
ENST00000336642.8:c.72-1G>A
ENST00000345378.6:c.1023-1G>A
ENST00000395796.7:c.1017-1G>A
ENST00000403799.7:c.1020-1G>A
ENST00000437084.1:c.969-1G>A
ENST00000459642.1:n.399G>A
ENST00000473353.1:n.318-1G>A
ENST00000616242.4:c.1017-1G>A
NM_000162.3:c.1020-1G>A
NM_033507.1:c.1023-1G>A
NM_033508.1:c.1017-1G>A
NM_000162.4:c.1020-1G>A
NM_001354800.1:c.1020-1G>A
NM_001354801.1:c.9-1G>A
NM_001354802.1:c.-121-1G>A
NM_001354803.1:c.54-1G>A
NM_033507.2:c.1023-1G>A
NM_033508.2:c.1017-1G>A
NM_033507.3:c.1023-1G>A
NM_033508.3:c.1017-1G>A
NM_001354803.2:c.54-1G>A

Pathogenic

• Met criteria codes: PVS1 PP4_Moderate PM2_Supporting

• Not Met criteria codes: PS4 PP1

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

Evidence submitted by expert panel

Monogenic Diabetes VCEP

The c.1020-1G>A variant in the glucokinase gene, GCK, is predicted to remove a canonical splice acceptor site in intron 8 of NM_000162.5. This variant is predicted to cause skipping of biologically-relevant exon 9 of 10, resulting in deletion of >10% of a protein encoded by a gene in which loss-of-function is an established disease mechanism (PVS1; PMID: 19790256). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in 3 apparently unrelated individuals with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors). Two of these individuals had a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative antibodies or 2 hour OGTT increment < 3 mmol/L)(PP4_Moderate, internal lab contributors). This variant segregated with hyperglycemia with 2 informative meioses in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMID: 27236918, internal lab contributors). In summary, c.1020-1G>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, approved 8/11/2023): PVS1, PP4_Moderate, PM2_Supporting.

Met criteria codes

• PVS1: This variant is predicted to cause skipping of biologically-relevant exon 9 of 10, resulting in deletion of >10% of a protein encoded by a gene in which loss-of-function is an established disease mechanism (PVS1; PMID: 19790256).
• PP4_Moderate: This variant was identified in 2 individuals with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative antibodies or 2 hour OGTT increment < 3 mmol/L)(PP4_Moderate, internal lab contributors).
• PM2_Supporting: This variant is absent from gnomAD v2.1.1 (PM2_Supporting).

Not Met criteria codes

• PS4: This variant was identified in 3 apparently unrelated individuals with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors).
• PP1: This variant segregated with hyperglycemia with 2 informative meioses in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMID: 27236918, internal lab contributors).