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.142G>A (p.Glu48Lys)

CA4239714

1299600 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 72f30e42-3961-4251-a4d6-50ef16077603

HGVS expressions

NM_000162.5:c.142G>A
NM_000162.5(GCK):c.142G>A (p.Glu48Lys)
NC_000007.14:g.44153367C>T
CM000669.2:g.44153367C>T
NC_000007.13:g.44192966C>T
CM000669.1:g.44192966C>T
NC_000007.12:g.44159491C>T
NG_008847.1:g.41057G>A
NG_008847.2:g.49804G>A
ENST00000395796.8:c.*140G>A
ENST00000616242.5:c.142G>A
ENST00000682635.1:n.628G>A
ENST00000345378.7:c.145G>A
ENST00000403799.8:c.142G>A
ENST00000671824.1:c.142G>A
ENST00000673284.1:c.142G>A
ENST00000345378.6:c.145G>A
ENST00000395796.7:c.139G>A
ENST00000403799.7:c.142G>A
ENST00000437084.1:c.142G>A
ENST00000616242.4:c.139G>A
NM_000162.3:c.142G>A
NM_033507.1:c.145G>A
NM_033508.1:c.139G>A
NM_000162.4:c.142G>A
NM_001354800.1:c.142G>A
NM_033507.2:c.145G>A
NM_033508.2:c.139G>A
NM_033507.3:c.145G>A
NM_033508.3:c.139G>A

Likely Benign

Met criteria codes 4
BS2 BP2 PP2 PP4_Moderate
Not Met criteria codes 6
BS1 BP4 PP1 PP3 PM1 PM2

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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.142G>A variant in the glucokinase gene, GCK, causes an amino acid change of glutamic acid to lysine at codon 48 (p.(Glu48Lys)) 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). The Popmax filtering allele frequency of the c.142G>A variant in gnomAD v2.1.1 is 0.00001685, which falls between ClinGen MDEP-established cutoffs for PM2_Supporting (0.000003) and BS1 (0.00004); thus, neither criterion will be applied. 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 negative antibodies) (PP4_Moderate; internal lab contributors). This variant was observed in unknown phase in that individual with the variant c.461T>G p.Val154Gly (internal lab contributors), which is classified as likely pathogenic by the ClinGen MDEP (BP2). This variant segregated with hyperglycemia with two 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). This variant was identified in an individual with normal fasting glucose (BS2; PMID: 23799006, internal lab contributor). This variant has a REVEL score of 0.6959, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on GCK function. In summary, c.142G>A meets the criteria to be classified as likely benign for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): BS2, PP4_Moderate, BP2, PP2.
Met criteria codes
BS2
This variant was identified in two individuals with normal fasting glucose (BS2; PMID: 23799006, internal lab contributors).
BP2
This variant has been observed in unknown phase with the variant c.461T>G p.Val154Gly (internal lab contributors), which is classified as likely pathogenic by the ClinGen MDEP (BP2).
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 negative antibodies) (PP4_Moderate; internal lab contributors).
Not Met criteria codes
BS1
The Popmax filtering allele frequency of the c.142G>A variant in gnomAD v2.1.1 is 0.00001685, which falls between ClinGen MDEP-established cutoffs for PM2_Supporting (0.000003) and BS1 (0.00004); thus, neither criterion will be applied.
BP4
This variant has a REVEL score of 0.6959, which is between the ClinGen MDEP thresholds, predicting neither a damaging nor benign impact on GCK function.
PP1
This variant segregated with hyperglycemia with two 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).
PP3
This variant has a REVEL score of 0.6959, which is between the ClinGen MDEP thresholds, predicting neither a damaging nor benign impact on GCK function.
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
The Popmax filtering allele frequency of the c.142G>A variant in gnomAD v2.1.1 is 0.00001685, which falls between ClinGen MDEP-established cutoffs for PM2_Supporting (0.000003) and BS1 (0.00004); thus, neither criterion will be applied.
Approved on: 2023-11-22
Published on: 2023-11-22
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