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.430T>C

CA367396721

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 694e6804-6d69-4bb3-a596-68f4a7a9a7e6

HGVS expressions

NM_001354803.2:c.430T>C
NC_000007.14:g.44145138A>G
CM000669.2:g.44145138A>G
NC_000007.13:g.44184737A>G
CM000669.1:g.44184737A>G
NC_000007.12:g.44151262A>G
NG_008847.1:g.49286T>C
NG_008847.2:g.58033T>C
ENST00000395796.8:c.*1394T>C
ENST00000616242.5:c.*516T>C
ENST00000683378.1:n.622T>C
ENST00000336642.9:c.430T>C
ENST00000345378.7:c.1399T>C
ENST00000403799.8:c.1396T>C
ENST00000671824.1:c.1459T>C
ENST00000672743.1:n.381+27T>C
ENST00000673284.1:c.1369+27T>C
ENST00000336642.8:n.448T>C
ENST00000345378.6:c.1399T>C
ENST00000395796.7:c.1393T>C
ENST00000403799.7:c.1396T>C
ENST00000437084.1:c.1345T>C
ENST00000459642.1:n.776T>C
ENST00000616242.4:n.1393T>C
NM_000162.3:c.1396T>C
NM_033507.1:c.1399T>C
NM_033508.1:c.1393T>C
NM_000162.4:c.1396T>C
NM_001354800.1:c.1369+27T>C
NM_001354801.1:c.385T>C
NM_001354802.1:c.229+27T>C
NM_001354803.1:c.430T>C
NM_033507.2:c.1399T>C
NM_033508.2:c.1393T>C
NM_000162.5:c.1396T>C
NM_033507.3:c.1399T>C
NM_033508.3:c.1393T>C

Likely Pathogenic

Met criteria codes 2
PVS1 PM2_Supporting
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.1396T>C variant in the glucokinase gene, GCK, is causes an animo acid change at the stop codon of the final exon (10/10), resulting in the addition of 144 amino acids at the end of the protein (p.(Ter466ArgextTer144)). 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 a clinical picture consistent with non-autoimmune/insulin-dependent 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). In summary, c.1396T>C 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
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).
PM2_Supporting
Absent in gnomAD
Not Met criteria codes
PS4
One case in internal database
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).
Approved on: 2023-08-10
Published on: 2023-08-10
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