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


Variant: NM_001354803.2:c.332_343del

CA2580617739

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 34c3946e-9335-439a-a200-56d398511703

HGVS expressions

NM_001354803.2:c.332_343del
NC_000007.14:g.44145227_44145238del
CM000669.2:g.44145227_44145238del
NC_000007.13:g.44184826_44184837del
CM000669.1:g.44184826_44184837del
NC_000007.12:g.44151351_44151362del
NG_008847.1:g.49188_49199del
NG_008847.2:g.57935_57946del
ENST00000395796.8:c.*1296_*1307del
ENST00000616242.5:c.*418_*429del
ENST00000683378.1:n.524_535del
ENST00000336642.9:c.332_343del
ENST00000345378.7:c.1301_1312del
ENST00000403799.8:c.1298_1309del
ENST00000671824.1:c.1361_1372del
ENST00000672743.1:n.310_321del
ENST00000673284.1:c.1298_1309del
ENST00000336642.8:c.350_361del
ENST00000345378.6:c.1301_1312del
ENST00000395796.7:c.1295_1306del
ENST00000403799.7:c.1298_1309del
ENST00000437084.1:c.1247_1258del
ENST00000459642.1:n.678_689del
ENST00000616242.4:c.1295_1306del
NM_000162.3:c.1298_1309del
NM_033507.1:c.1301_1312del
NM_033508.1:c.1295_1306del
NM_000162.4:c.1298_1309del
NM_001354800.1:c.1298_1309del
NM_001354801.1:c.287_298del
NM_001354802.1:c.158_169del
NM_001354803.1:c.332_343del
NM_033507.2:c.1301_1312del
NM_033508.2:c.1295_1306del
NM_000162.5:c.1298_1309del
NM_033507.3:c.1301_1312del
NM_033508.3:c.1295_1306del

Likely Pathogenic

Met criteria codes 4
PP1 PM4 PM2_Supporting PP4_Moderate
Not Met criteria codes 2
PS4 PM1

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.1298_1309del variant in the glucokinase gene, GCK, is a 12 base pair deletion resulting in the in-frame deletion of 4 amino acid(s) at codon 433 (p.(Ser433_Ile436del)) within exon 10 of NM_000162.5. The c.1298_1309del variant is predicted to change the length of the protein due an in-frame deletion of 4 amino acids in a nonrepeat region (PM4). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). 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 (PMID: 12955723, internal lab contributors). One of these individuals had a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative antibodies) (PP4_Moderate; internal lab contributors). This variant segregated with hyperglycemia, with 2 informative meioses in 2 families (PP1; internal lab contributors). In summary, c.1298_1309del 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, approved 8/11/2023): PP4_Moderate, PM4, PP1, PM2_Supporting.
Met criteria codes
PP1
This variant segregated with hyperglycemia, with 2 informative meioses in 2 families (PP1; internal lab contributors).
PM4
The c.1298_1309del variant is predicted to change the length of the protein due an in-frame deletion of 4 amino acids in a nonrepeat region (PM4).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
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 negative antibodies) (PP4_Moderate; internal lab contributors).
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 (PMID: 12955723, internal lab contributors).
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-11-24
Published on: 2023-11-24
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.