The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000162.5(GCK):c.1339del (p.Arg447fs)

CA16618465

421604 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 57099451-f505-43a6-a591-6aff6abf1335

HGVS expressions

NM_000162.5:c.1339del
NM_000162.5(GCK):c.1339del (p.Arg447fs)
NC_000007.14:g.44145196del
CM000669.2:g.44145196del
NC_000007.13:g.44184795del
CM000669.1:g.44184795del
NC_000007.12:g.44151320del
NG_008847.1:g.49229del
NG_008847.2:g.57976del
ENST00000395796.8:c.*1337del
ENST00000616242.5:c.*459del
ENST00000683378.1:n.565del
ENST00000336642.9:c.373del
ENST00000345378.7:c.1342del
ENST00000403799.8:c.1339del
ENST00000671824.1:c.1402del
ENST00000672743.1:n.351del
ENST00000673284.1:c.1339del
ENST00000336642.8:n.391del
ENST00000345378.6:c.1342del
ENST00000395796.7:c.1336del
ENST00000403799.7:c.1339del
ENST00000437084.1:c.1288del
ENST00000459642.1:n.719del
ENST00000616242.4:n.1336del
NM_000162.3:c.1339del
NM_033507.1:c.1342del
NM_033508.1:c.1336del
NM_000162.4:c.1339del
NM_001354800.1:c.1339del
NM_001354801.1:c.328del
NM_001354802.1:c.199del
NM_001354803.1:c.373del
NM_033507.2:c.1342del
NM_033508.2:c.1336del
NM_033507.3:c.1342del
NM_033508.3:c.1336del
NM_001354803.2:c.373del

Pathogenic

Met criteria codes 3
PVS1 PS4_Moderate PM2_Supporting
Not Met criteria codes 2
PP1 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 GCK Version 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1339del variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 447 (NM_000162.5), adding 167 novel amino acids before encountering a stop codon (p.(Arg447GlyfsTer167)). 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 from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in 6 unrelated individuals with non-autoimmune/insulin-deficient diabetes (PMID 22761713; ClinVar ID 421604.2; internal lab contributors) (PS4_Moderate). This variant was identified in individuals with diabetes consistent with a GCK-MODY phenotype; however, PP4 is unable to be evaluated due to insufficient clinical information (PMID: 22761713, internal lab contributors). This variant segregated with disease with 2 informative meioses in a family with MODY, however this does not meet the thresholds for PP1 set by Jarvik and Browning (PMID: 27236918) (internal lab contributors). In summary, c.1339del meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PVS1, PM2_Supporting, PS4_Moderate.
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).
PS4_Moderate
Identified in 6 cases
PM2_Supporting
Absent in gnomAD
Not Met criteria codes
PP1
2 meiosis in one family from an internal contributor
PP4
This variant was identified in individuals with diabetes consistent with a GCK-MODY phenotype; however, PP4 is unable to be evaluated due to insufficient clinical information (PMID: 22761713, internal lab contributors).
Approved on: 2023-09-01
Published on: 2023-09-01
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.