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
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_001354803.2:c.166_167del

CA2580612101

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: e48e2a42-8d22-41bb-94c0-c92f02b352c6

HGVS expressions

NM_001354803.2:c.166_167del
NC_000007.14:g.44145622_44145623del
CM000669.2:g.44145622_44145623del
NC_000007.13:g.44185221_44185222del
CM000669.1:g.44185221_44185222del
NC_000007.12:g.44151746_44151747del
NG_008847.1:g.48806_48807del
NG_008847.2:g.57553_57554del
ENST00000395796.8:c.*1130_*1131del
ENST00000616242.5:c.*252_*253del
ENST00000683378.1:n.358_359del
ENST00000336642.9:c.166_167del
ENST00000345378.7:c.1135_1136del
ENST00000403799.8:c.1132_1133del
ENST00000671824.1:c.1195_1196del
ENST00000672743.1:n.144_145del
ENST00000673284.1:c.1132_1133del
ENST00000336642.8:c.184_185del
ENST00000345378.6:c.1135_1136del
ENST00000395796.7:c.1129_1130del
ENST00000403799.7:c.1132_1133del
ENST00000437084.1:c.1081_1082del
ENST00000459642.1:n.512_513del
ENST00000616242.4:c.1129_1130del
NM_000162.3:c.1132_1133del
NM_033507.1:c.1135_1136del
NM_033508.1:c.1129_1130del
NM_000162.4:c.1132_1133del
NM_001354800.1:c.1132_1133del
NM_001354801.1:c.121_122del
NM_001354802.1:c.-9_-8del
NM_001354803.1:c.166_167del
NM_033507.2:c.1135_1136del
NM_033508.2:c.1129_1130del
NM_000162.5:c.1132_1133del
NM_033507.3:c.1135_1136del
NM_033508.3:c.1129_1130del

Likely Pathogenic

Met criteria codes 2
PVS1 PM2_Supporting
Not Met criteria codes 2
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 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1132_1133del variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 378 in NM_000162.5, adding 80 novel amino acids before encountering a stop codon (p.(Ala378CysfsTer80)). While this variant, located in exon 9 of 10, is predicted to cause a premature stop codon and to escape nonsense mediated decay, it is in a functionally important region of a gene where loss-of-function is an established disease mechanism (PVS1; PMID: 19790256). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant segregated with diabetes with two informative meioses in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMID: 27236918, internal lab contributors). 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.1132_1133del meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PVS1, PM2_supporting.
Met criteria codes
PVS1
While this variant, located in exon 9 of 10, is predicted to cause a premature stop codon and to escape nonsense mediated decay, it is in a functionally important region of a gene where loss-of-function is an established disease mechanism (PVS1; PMID: 19790256). 
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting). gnomAD v4.0.0: absent
Not Met criteria codes
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
This variant segregated with diabetes with two informative meioses in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMID: 27236918, internal lab contributors).
Approved on: 2024-04-28
Published on: 2024-04-28
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.