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.106C>T (p.Arg36Trp)

CA4239720

431973 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 2bd76ae9-5b63-4964-b20a-1ac96ac6e398

HGVS expressions

NM_000162.5:c.106C>T
NM_000162.5(GCK):c.106C>T (p.Arg36Trp)
NC_000007.14:g.44153403G>A
CM000669.2:g.44153403G>A
NC_000007.13:g.44193002G>A
CM000669.1:g.44193002G>A
NC_000007.12:g.44159527G>A
NG_008847.1:g.41021C>T
NG_008847.2:g.49768C>T
ENST00000395796.8:c.*104C>T
ENST00000616242.5:c.106C>T
ENST00000682635.1:n.592C>T
ENST00000345378.7:c.109C>T
ENST00000403799.8:c.106C>T
ENST00000671824.1:c.106C>T
ENST00000673284.1:c.106C>T
ENST00000345378.6:c.109C>T
ENST00000395796.7:c.103C>T
ENST00000403799.7:c.106C>T
ENST00000437084.1:c.106C>T
ENST00000476008.1:n.541C>T
ENST00000616242.4:c.103C>T
NM_000162.3:c.106C>T
NM_033507.1:c.109C>T
NM_033508.1:c.103C>T
NM_000162.4:c.106C>T
NM_001354800.1:c.106C>T
NM_033507.2:c.109C>T
NM_033508.2:c.103C>T
NM_033507.3:c.109C>T
NM_033508.3:c.103C>T

Likely Pathogenic

Met criteria codes 5
PP4 PP3 PP2 PP1_Strong PS2_Moderate
Not Met criteria codes 7
PS3 PS4 PM2 BA1 BS3 BS1 BP4

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 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.106G>T variant in the glucokinase gene,GCK, causes an amino acid change of arginine to tryptophan at codon 36 (p.(Arg36Trp)) of NM_000162.5. While the Popmax filtering allele frequency is 0.000002920 (European non-Finnish population), which is less than the MDEP cutoff for PM2_Supporting, there are two copies of the variant in the African/African American subpopulation; therefore, PM2_Supporting cannot be applied, and PS4 cannot be applied regardless of the number of cases. 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 0.911, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant was identified in an individual with a clinical history highly specific for GCK-MODY (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%) (PP4; PMID: 16965331). This variant was identified as a de novo occurrence with confirmed parental relationships in an individual with diabetes, but whose clinical picture is not highly specific for GCK-MODY (PS2_Moderate; PMID:8168652). This variant segregated with diabetes, with five informative meioses in three families with MODY (PP1_Strong; PMIDs: 17573900, 23433541, 33477506). In summary, c.106C>T meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PP2, PP3, PP4, PS2_Moderate, PP1_Strong,
Met criteria codes
PP4
Vits2006 (PMID:16965331) reported one individual from Luxembourg dx with DM at age 11, fasting glucose 6.4 mmol/L, HbA1c 6.6%, BMI 23.2 kg/m2, treated with diet.
PP3
REVEL=0.911>0.7
PP2
gnomAD missense constraint score for GCK is 4.39, which is significant.
PP1_Strong
Five meioses from three families (PMIDs: 17573900, 23433541, 33477506).
PS2_Moderate
This variant was identified as a de novo occurrence with confirmed parental relationships in an individual with diabetes, but whose clinical picture is not highly specific for GCK-MODY (PMID:8168652).
Not Met criteria codes
PS3
Miller 1999 (PMID:10426385) reported Arg36Trp GCK had similar kinetic property as wildtype (Vmax and S0.5), and normal thermal stability, but proposed possible damage to interaction with GLUT2. GKRP/GKA binding studies not done.
PS4
No PS4 at any level if not met PM2_Supporting
PM2
gnomAD v2.1.1 Popmax Filtering AF 0.000002920 <0.000003 (ENF) but 2 alleles in African/African American subpopulation in gnomAD v2.1.1.
BA1
gnomAD v2.1.1 Popmax Filtering AF 0.000002920 <0.0001
BS3
Miller 1999 (PMID:10426385) reported Arg36Trp GCK had similar kinetic property as wildtype (Vmax and S0.5), and normal thermal stability, but proposed possible damage to interaction with GLUT2. GKRP/GKA binding studies not done.
BS1
gnomAD v2.1.1 Popmax Filtering AF 0.000002920 <0.00004
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-10-10
Published on: 2023-10-10
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