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Variant: NM_033508.3:c.506_514dup

CA2573050986

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 24b253f1-e1c8-4229-8a21-c29ee64f6165
Approved on: 2023-05-26
Published on: 2023-05-26

HGVS expressions

NM_033508.3:c.506_514dup
NC_000007.14:g.44150036_44150044dup
CM000669.2:g.44150036_44150044dup
NC_000007.13:g.44189635_44189643dup
CM000669.1:g.44189635_44189643dup
NC_000007.12:g.44156160_44156168dup
NG_008847.1:g.44385_44393dup
NG_008847.2:g.53132_53140dup
ENST00000395796.8:c.*507_*515dup
ENST00000616242.5:c.509_517dup
ENST00000682635.1:n.995_1003dup
ENST00000345378.7:c.512_520dup
ENST00000403799.8:c.509_517dup
ENST00000671824.1:c.509_517dup
ENST00000673284.1:c.509_517dup
ENST00000345378.6:c.512_520dup
ENST00000395796.7:c.506_514dup
ENST00000403799.7:c.509_517dup
ENST00000437084.1:c.458_466dup
ENST00000616242.4:n.506_514dup
NM_000162.3:c.509_517dup
NM_033507.1:c.512_520dup
NM_033508.1:c.506_514dup
NM_000162.4:c.509_517dup
NM_001354800.1:c.509_517dup
NM_033507.2:c.512_520dup
NM_033508.2:c.506_514dup
NM_000162.5:c.509_517dup
NM_033507.3:c.512_520dup

Likely Pathogenic

Met criteria codes 4
PM4 PP4_Moderate PM2_Supporting PS3_Moderate
Not Met criteria codes 2
PM1 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 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.509_517dup variant in the glucokinase gene, GCK, is a 9 base pair insertion resulting in the in-frame addition of 3 amino acid(s) at codon 173 (p.(Lys172_Ala173insGlyPheLys)) within exon 5 of NM_000162.5. The c.509_517dup variant is predicted to change the length of the protein due an in-frame insertion of 3 amino acids in a nonrepeat region (PM4). This variant is absent in gnomAD v2.1.1 (PM2_Supporting), was identified in two unrelated individuals with mildly elevated HbA1c; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (Internal contributors). One of these individuals has a phenotype specific for GCK-MODY (persistent FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%) (PP4_Moderate; Internal contributor). The Relative Activity Index (RAI) of this variant was found to be 0, which is below the MDEP cutoff (<0.5) (PS3_Moderate; Internal lab contributor). In summary, the c.509_517dup variant meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.1, approved 3/23/23): PM4, PM2_Supporting, PP4_Moderate, PS3_Moderate.
Met criteria codes
PM4
The c.509_517dup variant is predicted to change the length of the protein due an in-frame insertion of 3 amino acids in a nonrepeat region (PM4).
PP4_Moderate
Several fasting glucoses between 125-137 mg/dl and HbA1cs, 6.5-6.6% and none outside GCK ranges of fasting glucose 100-144 mg/dl and HbA1C 5.6 – 7.6%.
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
PS3_Moderate
RAI = 0 (Internal laboratory contributor)
Not Met criteria codes
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
This variant was identified in two unrelated individuals with mildly elevated HbA1c; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (Internal lab contributors).
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