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.1130_1138del (p.Arg377_Ala379del)

CA645369436

429640 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 4ed4eb55-54cb-4124-b293-d942e356bd7e

HGVS expressions

NM_000162.5:c.1130_1138del
NM_000162.5(GCK):c.1130_1138del (p.Arg377_Ala379del)
NC_000007.14:g.44145615_44145623del
CM000669.2:g.44145615_44145623del
NC_000007.13:g.44185214_44185222del
CM000669.1:g.44185214_44185222del
NC_000007.12:g.44151739_44151747del
NG_008847.1:g.48804_48812del
NG_008847.2:g.57551_57559del
ENST00000395796.8:c.*1128_*1136del
ENST00000616242.5:c.*250_*258del
ENST00000683378.1:n.356_364del
ENST00000336642.9:c.164_172del
ENST00000345378.7:c.1133_1141del
ENST00000403799.8:c.1130_1138del
ENST00000671824.1:c.1193_1201del
ENST00000672743.1:n.142_150del
ENST00000673284.1:c.1130_1138del
ENST00000336642.8:c.182_190del
ENST00000345378.6:c.1133_1141del
ENST00000395796.7:c.1127_1135del
ENST00000403799.7:c.1130_1138del
ENST00000437084.1:c.1079_1087del
ENST00000459642.1:n.510_518del
ENST00000616242.4:c.1127_1135del
NM_000162.3:c.1130_1138del
NM_033507.1:c.1133_1141del
NM_033508.1:c.1127_1135del
NM_000162.4:c.1130_1138del
NM_001354800.1:c.1130_1138del
NM_001354801.1:c.119_127del
NM_001354802.1:c.-11_-3del
NM_001354803.1:c.164_172del
NM_033507.2:c.1133_1141del
NM_033508.2:c.1127_1135del
NM_033507.3:c.1133_1141del
NM_033508.3:c.1127_1135del
NM_001354803.2:c.164_172del

Uncertain Significance

Met criteria codes 2
PM4 PM2_Supporting
Not Met criteria codes 3
PS4 PP4 PP1

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.1130_1138del variant in the glucokinase gene, GCK, is a 9 base pair deletion resulting in the in-frame deletion of 3 amino acids at codon 377 (p.(Arg377_Ala379del)) within exon 9 of NM_000162.5. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The c.1130_1138del variant is predicted to change the length of the protein due an in-frame deletion of three amino acids in a non-repeat region (PM4). This variant segregated with hyperglycemia with two informative meioses in one family with MODY, which is below the threshold for PP1 (PMID: 31063852). This variant was identified in two unrelated individuals with a clinical picture consistent with monogenic diabetes; however, PS4_Moderate cannot be applied because this number is below the MDEP threshold (PMID 31063852, internal lab contributors). This variant was identified in an individual with hyperglycemia, however, PP4 is unable to be evaluated due to insufficient clinical information. In summary, this variant meets the criteria to be classified as uncertain significance for monogenic diabetes, ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.3.0, approved 8/11/2023): PM4, PM2_Supporting.
Met criteria codes
PM4
The c.1130_1138del variant is predicted to change the length of the protein due an in-frame deletion of three amino acids in a non-repeat region (PM4).
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 a clinical picture consistent with monogenic diabetes, however PS4_Moderate cannot be applied because this number is below the MDEP threshold (PMID 31063852, internal lab contributors)
PP4
This variant was identified in an individual with hyperglycemia, however, there is insufficient clinical information to evaluate for PP4.
PP1
This variant segregated with disease diabetes with only two informative meioses in one family with MODY (PP1; PMID 31063852 ).
Approved on: 2024-02-02
Published on: 2024-02-02
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