The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_001354803.2:c.203_205del

CA2580612099

1303094 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 5a7465b5-f319-4221-8be9-f313a38d3339

HGVS expressions

NM_001354803.2:c.203_205del
NC_000007.14:g.44145582_44145584del
CM000669.2:g.44145582_44145584del
NC_000007.13:g.44185181_44185183del
CM000669.1:g.44185181_44185183del
NC_000007.12:g.44151706_44151708del
NG_008847.1:g.48843_48845del
NG_008847.2:g.57590_57592del
ENST00000395796.8:c.*1167_*1169del
ENST00000616242.5:c.*289_*291del
ENST00000683378.1:n.395_397del
ENST00000336642.9:c.203_205del
ENST00000345378.7:c.1172_1174del
ENST00000403799.8:c.1169_1171del
ENST00000671824.1:c.1232_1234del
ENST00000672743.1:n.181_183del
ENST00000673284.1:c.1169_1171del
ENST00000336642.8:c.221_223del
ENST00000345378.6:c.1172_1174del
ENST00000395796.7:c.1166_1168del
ENST00000403799.7:c.1169_1171del
ENST00000437084.1:c.1118_1120del
ENST00000459642.1:n.549_551del
ENST00000616242.4:c.1166_1168del
NM_000162.3:c.1169_1171del
NM_033507.1:c.1172_1174del
NM_033508.1:c.1166_1168del
NM_000162.4:c.1169_1171del
NM_001354800.1:c.1169_1171del
NM_001354801.1:c.158_160del
NM_001354802.1:c.29_31del
NM_001354803.1:c.203_205del
NM_033507.2:c.1172_1174del
NM_033508.2:c.1166_1168del
NM_000162.5:c.1169_1171del
NM_033507.3:c.1172_1174del
NM_033508.3:c.1166_1168del

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PM4_Supporting PP1_Moderate PP4_Moderate
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.1169_1171del variant in the glucokinase gene, GCK, is a three-base pair deletion resulting in the in-frame deletion of isoleucine at codon 390 (p.(Ile390del)) within exon 9 of NM_000162.5. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The c.1169_1171del variant is predicted to change the length of the protein due to an in-frame deletion of a single amino acid in a non-repeat region (PM4_Supporting). This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and OGTT with 2H OGTT increment <3 mmol/l) (PP4_Moderate; internal lab contributors). This variant segregated with hyperglycemia, with four informative meioses in one family (PP1_Moderate; internal lab contributors). This variant was identified in three unrelated individuals with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors). In summary, c.1169_1171del 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): PM2_supporting, PM4_supporting, PP4_moderate, PP1_moderate.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting). gnomAD v4.0.0: absent
PM4_Supporting
The c.1169_1171del variant is predicted to change the length of the protein due to an in-frame deletion of a single amino acid in a non-repeat region (PM4_Supporting).
PP1_Moderate
This variant segregated with hyperglycemia, with four informative meioses in one family (PP1_Moderate; internal lab contributors).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and OGTT with 2H OGTT increment <3 mmol/l) (PP4_Moderate; internal lab contributors).
Not Met criteria codes
PS4
This variant was identified in three 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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