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.340A>T

CA367397094

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: b9fdf1be-e713-4663-99b7-34a1f581d8a7

HGVS expressions

NM_001354803.2:c.340A>T
NC_000007.14:g.44145228T>A
CM000669.2:g.44145228T>A
NC_000007.13:g.44184827T>A
CM000669.1:g.44184827T>A
NC_000007.12:g.44151352T>A
NG_008847.1:g.49196A>T
NG_008847.2:g.57943A>T
ENST00000395796.8:c.*1304A>T
ENST00000616242.5:c.*426A>T
ENST00000683378.1:n.532A>T
ENST00000336642.9:c.340A>T
ENST00000345378.7:c.1309A>T
ENST00000403799.8:c.1306A>T
ENST00000671824.1:c.1369A>T
ENST00000672743.1:n.318A>T
ENST00000673284.1:c.1306A>T
ENST00000336642.8:c.358A>T
ENST00000345378.6:c.1309A>T
ENST00000395796.7:c.1303A>T
ENST00000403799.7:c.1306A>T
ENST00000437084.1:c.1255A>T
ENST00000459642.1:n.686A>T
ENST00000616242.4:c.1303A>T
NM_000162.3:c.1306A>T
NM_033507.1:c.1309A>T
NM_033508.1:c.1303A>T
NM_000162.4:c.1306A>T
NM_001354800.1:c.1306A>T
NM_001354801.1:c.295A>T
NM_001354802.1:c.166A>T
NM_001354803.1:c.340A>T
NM_033507.2:c.1309A>T
NM_033508.2:c.1303A>T
NM_000162.5:c.1306A>T
NM_033507.3:c.1309A>T
NM_033508.3:c.1303A>T

Likely Pathogenic

Met criteria codes 7
PM5_Supporting PP3 PP2 PP1 PP4_Moderate PM2_Supporting PS4_Moderate
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.1306A>T variant in the glucokinase gene, GCK, causes an amino acid change of isoleucine to phenylalanine at codon 436 (p.(Ile436Phe)) 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). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.8259, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent in gnomAD v2.1.1 (PM2_Supporting), and was identified in 6 unrelated individuals with hyperglycemia (PS4_Moderate; internal lab contributors). Three 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) (PP4_Moderate; internal lab contributor). This variant segregated with diabetes/hyperglycemia, with 2 informative meioses in 2 families (PP1; internal lab contributor). Additionally, another missense variant, c.1307T>A (p.Ile436Asn), has been classified as likely pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Ile436Phe (PM5_Supporting). Taken together, this evidence supports the classification of c.1306A>T 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): PP4_Moderate, PS4_Moderate, PP1, PP2, PP3, PM2_Supporting, PM5_Supporting.
Met criteria codes
PM5_Supporting
Another missense variant, c.1307T>A (p.Ile436Asn), has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Ile436Phe (PM5_Supporting).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.8259, 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).
PP1
This variant segregated with diabetes/hyperglycemia, with 2 informative meioses in 2 families (PP1; internal lab contributor).
PP4_Moderate
This variant was identified in 3 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) (PP4_Moderate; internal lab contributors).
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
PS4_Moderate
This variant was identified in 6 unrelated individuals with hyperglycemia (PS4_Moderate; 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: 2024-01-22
Published on: 2024-01-22
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.