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.10G>A (p.Asp4Asn)

CA4239800

911766 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: a5c6e8a9-39a1-438e-a5b8-805772c41d1b
Approved on: 2023-12-08
Published on: 2023-12-08

HGVS expressions

NM_000162.5:c.10G>A
NM_000162.5(GCK):c.10G>A (p.Asp4Asn)
NC_000007.14:g.44188944C>T
CM000669.2:g.44188944C>T
NC_000007.13:g.44228543C>T
CM000669.1:g.44228543C>T
NC_000007.12:g.44195068C>T
NG_008847.1:g.5480G>A
NG_008847.2:g.14227G>A
ENST00000616242.5:c.10G>A
ENST00000682635.1:n.496G>A
ENST00000403799.8:c.10G>A
ENST00000671824.1:c.10G>A
ENST00000673284.1:c.10G>A
ENST00000403799.7:c.10G>A
ENST00000437084.1:c.10G>A
ENST00000476008.1:n.480+8747G>A
NM_000162.3:c.10G>A
NM_000162.4:c.10G>A
NM_001354800.1:c.10G>A
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Likely Benign

Met criteria codes 3
PP2 BS2 BP2
Not Met criteria codes 4
PP3 PM2 BS1 BP4

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.10G>A variant in the glucokinase gene, GCK, causes an amino acid change of aspartic acid to asparagine at codon 4 (p.(Asp4Asn)) of NM_000162.5. GCK is defined by the ClinGen MDEP as a gene that has a low rate of benign missense variation and has pathogenic missense variants as a common mechanism of disease (PP2). This variant has a REVEL score of 0.312, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on GCK function.The Popmax filtering allele frequency of the c.10G>A variant in gnomAD v2.1.1 is 0.00001687, which falls between ClinGen MDEP-established cutoffs for PM2_Supporting (0.000003) and BS1 (0.00004); thus, neither criterion will be applied. This variant was identified in an individual with a normal fasting glucose and HbA1c less than or equal to 5.5% (BS2; internal lab contributors). This variant has been observed in unknown phase with the variant c.835G>T p.Glu279* (PMID: 8433729), which meets the criteria for as pathogenic by the ClinGen MDEP (BP2). In summary, c.10G>A meets the criteria to be classified as likely benign for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): BS2, BP2, PP2.
Met criteria codes
PP2
GCK is defined by the ClinGen MDEP as a gene that has a low rate of benign missense variation and has pathogenic missense variants as a common mechanism of disease (PP2).
BS2
This variant was identified in an individual with a normal fasting glucose and HbA1c less than or equal to 5.5% (BS2; internal lab contributors).
BP2
This variant has been observed in unknown phase with the variant c.835G>T p.Glu279* (PMID: 8433729), which meets the criteria for as pathogenic by the ClinGen MDEP (BP2).
Not Met criteria codes
PP3
This variant has a REVEL score of 0.312, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on GCK function
PM2
The Popmax filtering allele frequency of the c.10G>A variant in gnomAD v2.1.1 is 0.00001687, which falls between ClinGen MDEP-established cutoffs for PM2_Supporting (0.000003) and BS1 (0.00004); thus, neither criterion will be applied.
BS1
The Popmax filtering allele frequency of the c.10G>A variant in gnomAD v2.1.1 is 0.00001687, which falls between ClinGen MDEP-established cutoffs for PM2_Supporting (0.000003) and BS1 (0.00004); thus, neither criterion will be applied.
BP4
This variant has a REVEL score of 0.312, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on GCK function.
Curation History
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