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  • No ClinVar Id was directly found from the curated document


Variant: NM_001354803.2:c.299_307delinsTGCGAGCCACCTTCAT

CA1139771342

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 468bd8d0-6a0c-4f35-97ff-54fa4f64ca67

HGVS expressions

NM_001354803.2:c.299_307delinsTGCGAGCCACCTTCAT
NC_000007.14:g.44145261_44145269delinsATGAAGGTGGCTCGCA
CM000669.2:g.44145261_44145269delinsATGAAGGTGGCTCGCA
NC_000007.13:g.44184860_44184868delinsATGAAGGTGGCTCGCA
CM000669.1:g.44184860_44184868delinsATGAAGGTGGCTCGCA
NC_000007.12:g.44151385_44151393delinsATGAAGGTGGCTCGCA
NG_008847.1:g.49155_49163delinsTGCGAGCCACCTTCAT
NG_008847.2:g.57902_57910delinsTGCGAGCCACCTTCAT
ENST00000395796.8:c.*1263_*1271delinsTGCGAGCCACCTTCAT
ENST00000616242.5:c.*385_*393delinsTGCGAGCCACCTTCAT
ENST00000683378.1:n.491_499delinsTGCGAGCCACCTTCAT
ENST00000336642.9:c.299_307delinsTGCGAGCCACCTTCAT
ENST00000345378.7:c.1268_1276delinsTGCGAGCCACCTTCAT
ENST00000403799.8:c.1265_1273delinsTGCGAGCCACCTTCAT
ENST00000671824.1:c.1328_1336delinsTGCGAGCCACCTTCAT
ENST00000672743.1:n.277_285delinsTGCGAGCCACCTTCAT
ENST00000673284.1:c.1265_1273delinsTGCGAGCCACCTTCAT
ENST00000336642.8:n.317_325delinsTGCGAGCCACCTTCAT
ENST00000345378.6:c.1268_1276delinsTGCGAGCCACCTTCAT
ENST00000395796.7:c.1262_1270delinsTGCGAGCCACCTTCAT
ENST00000403799.7:c.1265_1273delinsTGCGAGCCACCTTCAT
ENST00000437084.1:c.1214_1222delinsTGCGAGCCACCTTCAT
ENST00000459642.1:n.645_653delinsTGCGAGCCACCTTCAT
ENST00000616242.4:n.1262_1270delinsTGCGAGCCACCTTCAT
NM_000162.3:c.1265_1273delinsTGCGAGCCACCTTCAT
NM_033507.1:c.1268_1276delinsTGCGAGCCACCTTCAT
NM_033508.1:c.1262_1270delinsTGCGAGCCACCTTCAT
NM_000162.4:c.1265_1273delinsTGCGAGCCACCTTCAT
NM_001354800.1:c.1265_1273delinsTGCGAGCCACCTTCAT
NM_001354801.1:c.254_262delinsTGCGAGCCACCTTCAT
NM_001354802.1:c.125_133delinsTGCGAGCCACCTTCAT
NM_001354803.1:c.299_307delinsTGCGAGCCACCTTCAT
NM_033507.2:c.1268_1276delinsTGCGAGCCACCTTCAT
NM_033508.2:c.1262_1270delinsTGCGAGCCACCTTCAT
NM_000162.5:c.1265_1273delinsTGCGAGCCACCTTCAT
NM_033507.3:c.1268_1276delinsTGCGAGCCACCTTCAT
NM_033508.3:c.1262_1270delinsTGCGAGCCACCTTCAT

Likely Pathogenic

Met criteria codes 2
PM2_Supporting PVS1
Not Met criteria codes 3
PS4 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.1265_1273delinsTGCGAGCCACCTTCAT variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 422 (NM_000162.5), adding 39 novel amino acids before encountering a stop codon (p.(Arg422LeufsTer39)). While this variant, located in exon 10 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). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). This variant was identified in an individual with diabetes; however, PP4 is unable to be evaluated due to insufficient clinical information (internal lab contributors). In summary, c.1265_1273delinsTGCGAGCCACCTTCAT 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
This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
PVS1
While this variant, located in exon 10 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).
Not Met criteria codes
PS4
One case from internal lab collaborators (4 cases needed to meet PS4_Moderate)
PP1
Segregation in 2 family members in case from internal lab collaborator, but no information about whether relatives are affected.
PP4
This variant was identified in an individual with diabetes; however, PP4 is unable to be evaluated due to insufficient clinical information (internal lab contributors).
Approved on: 2023-06-20
Published on: 2023-06-20
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