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.1284_1362del (p.Arg429fs)

CA1139660051

995104 (ClinVar)

Gene: GCK
Condition: maturity-onset diabetes of the young type 2
Inheritance Mode: Semidominant inheritance
UUID: 09297ac8-0832-4b6a-974b-c524adc36aed

HGVS expressions

NM_000162.5:c.1284_1362del
NM_000162.5(GCK):c.1284_1362del (p.Arg429fs)
NC_000007.14:g.44145175_44145253del
CM000669.2:g.44145175_44145253del
NC_000007.13:g.44184774_44184852del
CM000669.1:g.44184774_44184852del
NC_000007.12:g.44151299_44151377del
NG_008847.1:g.49174_49252del
NG_008847.2:g.57921_57999del
ENST00000395796.8:c.*1282_*1360del
ENST00000616242.5:c.*404_*482del
ENST00000683378.1:n.510_588del
ENST00000336642.9:c.318_396del
ENST00000345378.7:c.1287_1365del
ENST00000403799.8:c.1284_1362del
ENST00000671824.1:c.1347_1425del
ENST00000672743.1:n.296_374del
ENST00000673284.1:c.1284_1362del
ENST00000336642.8:c.336_414del
ENST00000345378.6:c.1287_1365del
ENST00000395796.7:c.1281_1359del
ENST00000403799.7:c.1284_1362del
ENST00000437084.1:c.1233_1311del
ENST00000459642.1:n.664_742del
ENST00000616242.4:c.1281_1359del
NM_000162.3:c.1284_1362del
NM_033507.1:c.1287_1365del
NM_033508.1:c.1281_1359del
NM_000162.4:c.1284_1362del
NM_001354800.1:c.1284_1362del
NM_001354801.1:c.273_351del
NM_001354802.1:c.144_222del
NM_001354803.1:c.318_396del
NM_033507.2:c.1287_1365del
NM_033508.2:c.1281_1359del
NM_033507.3:c.1287_1365del
NM_033508.3:c.1281_1359del
NM_001354803.2:c.318_396del

Likely Pathogenic

Met criteria codes 2
PM2_Supporting PVS1
Not Met criteria codes 3
PS4 PP1 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.1284_1362del variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 429 (NM_000162.5), adding 159 novel amino acids before encountering a stop codon (p.(Arg429fsX159)). This variant, located in exon 10 of 10, is predicted to cause loss of a stop codon and result in an elongated protein. The additional residues are expected to cause improper folding, resulting in loss of function in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID 19790256). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). This variant was identified in two individuals with diabetes/hyperglycemia consistent with GCK-MODY; however, PP4 is unable to be evaluated due to insufficient clinical information (internal lab contributors). PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors). In summary, c.1284_1362del 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): PVS1, PM2_supporting.
Met criteria codes
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
PVS1
This variant, located in exon 10 of 10, is predicted to cause loss of a stop codon and result in an elongated protein. The additional residues are expected to cause improper folding, resulting in loss of function in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID 19790256).
Not Met criteria codes
PS4
2 cases
PP1
Single meiosis in one family
PP4
This variant was identified in two individuals with diabetes/hyperglycemia consistent with GCK-MODY; however, PP4 is unable to be evaluated due to insufficient clinical information (internal lab contributors).
Approved on: 2023-11-03
Published on: 2023-11-03
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