Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_000162.5(GCK):c.645C>T (p.Tyr215=)

Help
Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Feb 20, 2020)
Last evaluated:
Dec 31, 2019
Accession:
VCV000255401.4
Variation ID:
255401
Description:
single nucleotide variant
Help

NM_000162.5(GCK):c.645C>T (p.Tyr215=)

Allele ID
252884
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7p13
Genomic location
7: 44149794 (GRCh38) GRCh38 UCSC
7: 44189393 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.44189393G>A
NC_000007.14:g.44149794G>A
NM_000162.5:c.645C>T MANE Select NP_000153.1:p.Tyr215= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000007.14:44149793:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00439 (A)

Allele frequency
1000 Genomes Project 0.00439
Trans-Omics for Precision Medicine (TOPMed) 0.00566
The Genome Aggregation Database (gnomAD), exomes 0.00945
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00554
Exome Aggregation Consortium (ExAC) 0.00905
The Genome Aggregation Database (gnomAD) 0.00883
Links
ClinGen: CA4239566
dbSNP: rs144723656
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Apr 24, 2015 RCV000246889.2
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Dec 31, 2019 RCV000419746.3
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000280005.2
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000337358.2
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000342725.2
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000394978.2
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GCK - - GRCh38
GRCh37
509 532

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000302769.1
Submitted: (Apr 28, 2016)
Evidence details
Likely Benign
(Sep 28, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000511173.1
Submitted: (Feb 17, 2017)
Evidence details
Comment:
Converted during submission to Likely benign.
Benign
(Apr 24, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000513126.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Sep 11, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000842177.1
Submitted: (Aug 31, 2018)
Evidence details
Publications
PubMed (10)
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001120872.2
Submitted: (Jan 29, 2020)
Evidence details
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Maturity-onset diabetes of the young, type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000469418.3
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (6)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Transient Neonatal Diabetes, Recessive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000469419.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Permanent neonatal diabetes mellitus 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000469416.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Hyperinsulinism due to glucokinase deficiency
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000469417.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)

Functional evidence

Help
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

Help
Title Author Journal Year Link
Common genetic variation in the glucokinase gene (GCK) is associated with type 2 diabetes and rates of carbohydrate oxidation and energy expenditure. Muller YL Diabetologia 2014 PMID: 24728127
Three novel mutations in MODY and its phenotype in three different Czech families. Bazalová Z Diabetes research and clinical practice 2010 PMID: 20132997
Screening of mutations and polymorphisms in the glucokinase gene in Czech diabetic and healthy control populations. Lukášová P Physiological research 2008 PMID: 18271687
Mutations in GCK and HNF-1alpha explain the majority of cases with clinical diagnosis of MODY in Spain. Estalella I Clinical endocrinology 2007 PMID: 17573900
Half of clinically defined maturity-onset diabetes of the young patients in Denmark do not have mutations in HNF4A, GCK, and TCF1. Johansen A The Journal of clinical endocrinology and metabolism 2005 PMID: 15928245
Identification of novel polymorphisms in the glucokinase and glucose-6-phosphatase genes in infants who died suddenly and unexpectedly. Forsyth L Journal of molecular medicine (Berlin, Germany) 2005 PMID: 15918042
Identification of 21 novel glucokinase (GCK) mutations in UK and European Caucasians with maturity-onset diabetes of the young (MODY). Thomson KL Human mutation 2003 PMID: 14517956
Genetic epidemiology of MODY in the Czech republic: new mutations in the MODY genes HNF-4alpha, GCK and HNF-1alpha. Pruhova S Diabetologia 2003 PMID: 12627330
High frequency of mutations in MODY and mitochondrial genes in Scandinavian patients with familial early-onset diabetes. Lehto M Diabetologia 1999 PMID: 10447526
Glucokinase gene variants in subjects with late-onset NIDDM and impaired glucose tolerance. Laakso M Diabetes care 1995 PMID: 7555485
Linkage analysis and molecular scanning of glucokinase gene in NIDDM families. Zouali H Diabetes 1993 PMID: 8349034

Text-mined citations for rs144723656...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 23, 2021