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.630G>T (p.Met210Ile)

CA213814

36236 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: d17187f9-d65a-4117-af07-cfcb9e907236
Approved on: 2024-01-22
Published on: 2024-01-22

HGVS expressions

NM_000162.5:c.630G>T
NM_000162.5(GCK):c.630G>T (p.Met210Ile)
NC_000007.14:g.44149809C>A
CM000669.2:g.44149809C>A
NC_000007.13:g.44189408C>A
CM000669.1:g.44189408C>A
NC_000007.12:g.44155933C>A
NG_008847.1:g.44615G>T
NG_008847.2:g.53362G>T
ENST00000395796.8:c.*628G>T
ENST00000616242.5:c.630G>T
ENST00000682635.1:n.1116G>T
ENST00000345378.7:c.633G>T
ENST00000403799.8:c.630G>T
ENST00000671824.1:c.630G>T
ENST00000673284.1:c.630G>T
ENST00000345378.6:c.633G>T
ENST00000395796.7:c.627G>T
ENST00000403799.7:c.630G>T
ENST00000437084.1:c.579G>T
ENST00000616242.4:c.627G>T
NM_000162.3:c.630G>T
NM_033507.1:c.633G>T
NM_033508.1:c.627G>T
NM_000162.4:c.630G>T
NM_001354800.1:c.630G>T
NM_033507.2:c.633G>T
NM_033508.2:c.627G>T
NM_033507.3:c.633G>T
NM_033508.3:c.627G>T
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Pathogenic

Met criteria codes 5
PM2_Supporting PM5_Strong PS1 PP3 PP2
Not Met criteria codes 2
PS4 PP4

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.630G>T variant in the glucokinase gene, GCK, causes an amino acid change of methionine to isoleucine at codon 210 (p.(Met210Ile)) 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 0.9399, 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 an individual with diabetes; however, PP4 is unable to be evaluated due to lack of clinical information (ClinVar ID 36236). Two other missense variants, c.629T>A (p.Met210Lys) and c.629T>C (p.Met210Thr), have been classified as pathogenic by the ClinGen MDEP (PM5_Strong). The nucleotide change c.630G>A, which causes the same amino acid change, has been classified as pathogenic for monogenic diabetes by the ClinGen MDEP (PS1). Taken together, the c.630G>T meets the criteria to be classified as 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, PS1, PP2, PP3, PM2_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
PM5_Strong
Two other missense variants, c.629T>A (p.Met210Lys) and c.629T>C (p.Met210Thr), have been classified as pathogenic by the ClinGen MDEP (PM5_Strong).
PS1
The nucleotide change c.630G>A, which causes the same amino acid change, has been classified as pathogenic for monogenic diabetes by the ClinGen MDEP (PS1).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.9399, 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).
Not Met criteria codes
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
This variant was identified in an individual with diabetes; however, PP4 is unable to be evaluated due to lack of clinical information (ClinVar ID 36236).
Curation History
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