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.392_*127delinsT

CA2496602227

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 8c77ed6d-252c-4d0d-b3e5-98331731629a

HGVS expressions

NM_001354803.2:c.392_*127delinsT
NC_000007.14:g.44145009_44145176delinsA
CM000669.2:g.44145009_44145176delinsA
NC_000007.13:g.44184608_44184775delinsA
CM000669.1:g.44184608_44184775delinsA
NC_000007.12:g.44151133_44151300delinsA
NG_008847.1:g.49248_49415delinsT
NG_008847.2:g.57995_58162delinsT
ENST00000395796.8:c.*1356_*1523delinsT
ENST00000616242.5:c.*478_*645delinsT
ENST00000683378.1:n.584_751delinsT
ENST00000336642.9:c.392_*127delinsT
ENST00000345378.7:c.1361_*127delinsT
ENST00000403799.8:c.1358_*127delinsT
ENST00000671824.1:c.1421_*127delinsT
ENST00000672743.1:n.370_381+156delinsT
ENST00000673284.1:c.1358_1369+156delinsT
ENST00000336642.8:n.410_577delinsT
ENST00000345378.6:c.1361_*127delinsT
ENST00000395796.7:c.1355_*127delinsT
ENST00000403799.7:c.1358_*127delinsT
ENST00000459642.1:n.738_905delinsT
ENST00000616242.4:n.1355_1522delinsT
NM_000162.3:c.1358_*127delinsT
NM_033507.1:c.1361_*127delinsT
NM_033508.1:c.1355_*127delinsT
NM_000162.4:c.1358_*127delinsT
NM_001354800.1:c.1358_1369+156delinsT
NM_001354801.1:c.347_*127delinsT
NM_001354802.1:c.218_229+156delinsT
NM_001354803.1:c.392_*127delinsT
NM_033507.2:c.1361_*127delinsT
NM_033508.2:c.1355_*127delinsT
NM_000162.5:c.1358_*127delinsT
NM_033507.3:c.1361_*127delinsT
NM_033508.3:c.1355_*127delinsT

Likely Pathogenic

Met criteria codes 2
PM2_Supporting PVS1
Not Met criteria codes 2
PS4 PP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for HNF1A Version 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1358_*127del168insT variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 453 (NM_000162.5), adding 25 novel amino acids before encountering a stop codon (p.(S453LfsX25)). This variant, located in exon 10 of 10, is predicted to cause loss of a stop codon and result in an elongated protein. The additional residues are expected to cause improper folding, resulting in loss of function in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID 19790256). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). This variant was identified in an individual with diabetes; however, PP4 could not be evaluated due to lack of clinical information (internal lab contributor). PS4_Moderate also cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributor). In summary, c.1358_*127del168insT 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
PM2_Supporting
Absent in gnomAD v2.1.1 (PM2_Supporting).
PVS1
This variant, located in exon 10 of 10, is predicted to cause loss of a stop codon and result in an elongated protein. The additional residues are expected to cause improper folding, resulting in loss of function in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID 19790256).
Not Met criteria codes
PS4
This variant was identified in one individual with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributor).
PP4
This variant was identified in an individual with diabetes; however, there was insufficient information to evaluate for PP4 (internal lab contributors).
Approved on: 2023-06-20
Published on: 2023-06-20
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.