The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document


Variant: NM_001354803.2:c.155T>A

CA367398869

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 69e32040-c6a1-42ad-a581-319eed5ecfac

HGVS expressions

NM_001354803.2:c.155T>A
NC_000007.14:g.44145629A>T
CM000669.2:g.44145629A>T
NC_000007.13:g.44185228A>T
CM000669.1:g.44185228A>T
NC_000007.12:g.44151753A>T
NG_008847.1:g.48795T>A
NG_008847.2:g.57542T>A
ENST00000395796.8:c.*1119T>A
ENST00000616242.5:c.*241T>A
ENST00000683378.1:n.347T>A
ENST00000336642.9:c.155T>A
ENST00000345378.7:c.1124T>A
ENST00000403799.8:c.1121T>A
ENST00000671824.1:c.1184T>A
ENST00000672743.1:n.133T>A
ENST00000673284.1:c.1121T>A
ENST00000336642.8:n.173T>A
ENST00000345378.6:c.1124T>A
ENST00000395796.7:c.1118T>A
ENST00000403799.7:c.1121T>A
ENST00000437084.1:c.1070T>A
ENST00000459642.1:n.501T>A
ENST00000616242.4:n.1118T>A
NM_000162.3:c.1121T>A
NM_033507.1:c.1124T>A
NM_033508.1:c.1118T>A
NM_000162.4:c.1121T>A
NM_001354800.1:c.1121T>A
NM_001354801.1:c.110T>A
NM_001354802.1:c.-20T>A
NM_001354803.1:c.155T>A
NM_033507.2:c.1124T>A
NM_033508.2:c.1118T>A
NM_000162.5:c.1121T>A
NM_033507.3:c.1124T>A
NM_033508.3:c.1118T>A

Likely Pathogenic

Met criteria codes 5
PP3 PP2 PP4_Moderate PM5_Supporting PM2_Supporting
Not Met criteria codes 1
PS4

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.1121T>A variant in the glucokinase gene, GCK, causes an amino acid change of valine to glutamic acid at codon 374 (p.(Val374Glu)) of NM_000162.5. GCK is defined by the ClinGen MDEP VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.968, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). 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). Another missense variant, c.1120G>A p.(Val374Met), has been classified as likely pathogenic by the ClinGen MDEP VCEP (PM5_Supporting). This variant was identified in two unrelated individuals with hypglycemia; however, this number does not meet the MDEP cutoff for PS4_Moderate (Solano et al. 2019. Rev Esp Endocrinol Pediatr 10(2):69-73, internal lab contributors). In summary, this variant meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.2.0, approved 6/7/2023): PP2, PP3, PM2_Supporting, PP4_Moderate, PM5_Supporting .
Met criteria codes
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.968, 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).
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).
PM5_Supporting
Another missense variant, c.1120G>A p.(Val374Met), has been classified as likely pathogenic by the ClinGen MDEP VCEP (PM5_Supporting).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PS4
This variant was identified in two unrelated individuals with hyperglycemia; however, this number does not meet the MDEP cutoff for PS4_Moderate (Solano et al. 2019. Rev Esp Endocrinol Pediatr 10(2):69-73, internal lab contributors).
Approved on: 2023-08-09
Published on: 2023-08-10
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