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
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_001354803.2:c.191T>G

CA367398699

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 2992b28b-4b89-44a2-9d65-21816c260221

HGVS expressions

NM_001354803.2:c.191T>G
NC_000007.14:g.44145593A>C
CM000669.2:g.44145593A>C
NC_000007.13:g.44185192A>C
CM000669.1:g.44185192A>C
NC_000007.12:g.44151717A>C
NG_008847.1:g.48831T>G
NG_008847.2:g.57578T>G
ENST00000395796.8:c.*1155T>G
ENST00000616242.5:c.*277T>G
ENST00000683378.1:n.383T>G
ENST00000336642.9:c.191T>G
ENST00000345378.7:c.1160T>G
ENST00000403799.8:c.1157T>G
ENST00000671824.1:c.1220T>G
ENST00000672743.1:n.169T>G
ENST00000673284.1:c.1157T>G
ENST00000336642.8:c.209T>G
ENST00000345378.6:c.1160T>G
ENST00000395796.7:c.1154T>G
ENST00000403799.7:c.1157T>G
ENST00000437084.1:c.1106T>G
ENST00000459642.1:n.537T>G
ENST00000616242.4:c.1154T>G
NM_000162.3:c.1157T>G
NM_033507.1:c.1160T>G
NM_033508.1:c.1154T>G
NM_000162.4:c.1157T>G
NM_001354800.1:c.1157T>G
NM_001354801.1:c.146T>G
NM_001354802.1:c.17T>G
NM_001354803.1:c.191T>G
NM_033507.2:c.1160T>G
NM_033508.2:c.1154T>G
NM_000162.5:c.1157T>G
NM_033507.3:c.1160T>G
NM_033508.3:c.1154T>G

Likely Pathogenic

Met criteria codes 4
PP3 PP2 PM5_Strong 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 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c. variant in the glucokinase gene, GCK, causes an amino acid change of leucine to arginine at codon 386 (p.(Leu386Arg)) 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 0.979, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant was identified in 3 unrelated individuals with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors). Two other missense variants, c.1156C>G p.Leu386Val and c.1157T>C p.Leu386Pro, have been interpreted as pathogenic by the ClinGen MDEP, and p.Leu386Arg has a greater Grantham distance than p.Leu386Val and p.Leu386Pro (PM5_Strong). In summary, c.1157T>G 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): PM5_Strong, PP2, PP3, PM2_Supporting.
Met criteria codes
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.979, 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).
PM5_Strong
Two other missense variants, c.1156C>G p.Leu386Val and c.1157T>C p.Leu386Pro, have been interpreted as pathogenic by the ClinGen MDEP, and p.Leu386Arg has a greater Grantham distance than p.Leu386Val and p.Leu386Pro (PM5_Strong). Leu-Val 32 Leu-Arg 102 Leu-Pro 98
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PS4
This variant was identified in 3 unrelated individuals with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors).
Approved on: 2024-04-28
Published on: 2024-04-28
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