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.1148C>T (p.Ser383Leu)

CA10581499

236014 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 585d0bc1-7940-4c9b-aa3c-faf9a98a90a8

HGVS expressions

NM_000162.5:c.1148C>T
NM_000162.5(GCK):c.1148C>T (p.Ser383Leu)
NC_000007.14:g.44145602G>A
CM000669.2:g.44145602G>A
NC_000007.13:g.44185201G>A
CM000669.1:g.44185201G>A
NC_000007.12:g.44151726G>A
NG_008847.1:g.48822C>T
NG_008847.2:g.57569C>T
ENST00000395796.8:c.*1146C>T
ENST00000616242.5:c.*268C>T
ENST00000683378.1:n.374C>T
ENST00000336642.9:c.182C>T
ENST00000345378.7:c.1151C>T
ENST00000403799.8:c.1148C>T
ENST00000671824.1:c.1211C>T
ENST00000672743.1:n.160C>T
ENST00000673284.1:c.1148C>T
ENST00000336642.8:c.200C>T
ENST00000345378.6:c.1151C>T
ENST00000395796.7:c.1145C>T
ENST00000403799.7:c.1148C>T
ENST00000437084.1:c.1097C>T
ENST00000459642.1:n.528C>T
ENST00000616242.4:c.1145C>T
NM_000162.3:c.1148C>T
NM_033507.1:c.1151C>T
NM_033508.1:c.1145C>T
NM_000162.4:c.1148C>T
NM_001354800.1:c.1148C>T
NM_001354801.1:c.137C>T
NM_001354802.1:c.8C>T
NM_001354803.1:c.182C>T
NM_033507.2:c.1151C>T
NM_033508.2:c.1145C>T
NM_033507.3:c.1151C>T
NM_033508.3:c.1145C>T
NM_001354803.2:c.182C>T

Pathogenic

Met criteria codes 7
PS4 PP3 PP2 PM2_Supporting PS3_Moderate PP4_Moderate PP1_Strong
Not Met criteria codes 1
PM1

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.1148C>T variant in the glucokinase gene, GCK, causes an amino acid change of serine to leucine at codon 383 (p. (Ser383Leu)) of NM_000162.5. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). 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 located in the larger hexokinase domain of the GCK gene (PMID: 31638168) but this variant does not reside in an amino acid that directly binds glucose or ATP, which is defined as critical for the protein’s function by the ClinGen MDEP, so it does not meet PM1. This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.831 which is greater than the MDEP VCEP threshold of 0.70 (PP3). MDEP wild type quality control measures were met, and the relative activity Index (RAI) of this variant was found to be 0.20, which is below the MDEP cutoff (<0.5) (Matschinsky FM, Magnuson MA (eds): Glucokinase and Glycemic Disease: From Basics to Novel Therapeutics. Front. Diabetes. Basel, Karger, 2004, vol 16, pp 92–109). This variant has been identified in at least 53 unrelated individuals with hyperglycemia and segregated with the phenotype, with 30 informative meioses in 49 families (PS4, PP1_Strong; PMID: 28555465, 30663027, 34462253, 34746319, internal lab contributors). At least of of these patients had a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%, negative GAD-65 (PP4_Moderate; PMID: 28555465). In summary, c.1148C>T meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (VCEP specifications version v1.3.0; approved 8/11/2023): PP3, PS4, PP4_Moderate, PP2, PP1_Strong, PM2_Supporting
Met criteria codes
PS4
This variant was identified in at least 53 unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4; PMIDs: 28555465, 30663027, 34462253, 34746319, Internal lab contributors).
PP3
REVEL 0.831
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).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PS3_Moderate
MDEP wild type quality control measures were met, and the relative activity Index (RAI) of this variant was found to be 0.20, which is below the MDEP cutoff (<0.5) (Matschinsky FM, Magnuson MA (eds): Glucokinase and Glycemic Disease: From Basics to Novel Therapeutics. Front. Diabetes. Basel, Karger, 2004, vol 16, pp 92–109).
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%, negative GAD-65 (PP4_Moderate; PMID: 28555465).
PP1_Strong
PP1_strong This variant segregated with hyperglycemia, with 30 informative meioses in 49 families (PP1_Strong; PMID: 28555465, internal lab contributors).
Not Met criteria codes
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2024-02-28
Published on: 2024-02-28
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