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.365dup

CA2017997770

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 1c703f03-c39d-4661-b412-ec75dd83011c

HGVS expressions

NM_001354803.2:c.365dup
NC_000007.14:g.44145205dup
CM000669.2:g.44145205dup
NC_000007.13:g.44184804dup
CM000669.1:g.44184804dup
NC_000007.12:g.44151329dup
NG_008847.1:g.49221dup
NG_008847.2:g.57968dup
ENST00000395796.8:c.*1329dup
ENST00000616242.5:c.*451dup
ENST00000683378.1:n.557dup
ENST00000336642.9:c.365dup
ENST00000345378.7:c.1334dup
ENST00000403799.8:c.1331dup
ENST00000671824.1:c.1394dup
ENST00000672743.1:n.343dup
ENST00000673284.1:c.1331dup
ENST00000336642.8:n.383dup
ENST00000345378.6:c.1334dup
ENST00000395796.7:c.1328dup
ENST00000403799.7:c.1331dup
ENST00000437084.1:c.1280dup
ENST00000459642.1:n.711dup
ENST00000616242.4:n.1328dup
NM_000162.3:c.1331dup
NM_033507.1:c.1334dup
NM_033508.1:c.1328dup
NM_000162.4:c.1331dup
NM_001354800.1:c.1331dup
NM_001354801.1:c.320dup
NM_001354802.1:c.191dup
NM_001354803.1:c.365dup
NM_033507.2:c.1334dup
NM_033508.2:c.1328dup
NM_000162.5:c.1331dup
NM_033507.3:c.1334dup
NM_033508.3:c.1328dup

Likely Pathogenic

Met criteria codes 2
PVS1 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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1331dup variant in the GCK gene causes a frameshift in the protein at codon 445 (NM_000162.5), adding 14 novel amino acids before encountering a stop codon (p.(Ser445GlnfsTer14)). While this variant, located in exon 10/10, is predicted to result in a premature stop codon that is predicted to escape nonsense mediated decay, it is a functionally important region in a gene where loss-of-function is an established disease mechanism (PVS1; PMID: 19790256). Additionally, this variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in one individual with a clinical picture consistent with monogenic diabetes; however PS4_Moderate cannot be applied because this number is below the MDEP threshold (internal lab contributor). This variant was identified in an individual with a phenotype suggestive of GCK-hyperglycemia; however, PP4 is unable to be evaluated due to insufficient clinical information (internal lab contributors). This variant segregated with disease with one informative meiosis in a family with MODY; however, this does not meet the thresholds for PP1 set by Jarvik and Browning (PMID: 27236918) (internal lab contributor). In summary, c.1331dup meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.2.0 approved 6/7/2023): PVS1, PM2_Supporting.
Met criteria codes
PVS1
While this variant, located in exon 10/10, may cause a premature stop codon that is predicted to escape nonsense mediated decay, it is a functionally important region in a gene where loss-of-function is an established disease mechanism (PVS1)
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PS4
This variant was identified in one individual with a clinical picture consistent with monogenic diabetes, however PS4_Moderate cannot be applied because this number is below the MDEP threshold (internal lab contributor)
PP4
This variant was identified in an individual with a phenotype suggestive of GCK-hyperglycemia; however, PP4 is unable to be evaluated due to insufficient clinical information (internal lab contributors).
PP1
NOT MET: This variant segregated with disease with one informative meiosis in a family with MODY, however this does not meet the thresholds for PP1 set by Jarvik and Browning (PMID: 27236918) (internal lab contributor).
Approved on: 2023-07-30
Published on: 2023-07-30
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