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NM_000162.5(GCK):c.680-2A>G AND Maturity onset diabetes mellitus in young

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Feb 12, 2016
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002360845.3

Allele description [Variation Report for NM_000162.5(GCK):c.680-2A>G]

NM_000162.5(GCK):c.680-2A>G

Gene:
GCK:glucokinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p13
Genomic location:
Preferred name:
NM_000162.5(GCK):c.680-2A>G
HGVS:
  • NC_000007.14:g.44147835T>C
  • NG_008847.2:g.55336A>G
  • NM_000162.5:c.680-2A>GMANE SELECT
  • NM_001354800.1:c.680-2A>G
  • NM_033507.3:c.683-2A>G
  • NM_033508.3:c.677-2A>G
  • LRG_1074t1:c.680-2A>G
  • LRG_1074t2:c.683-2A>G
  • LRG_1074:g.55336A>G
  • NC_000007.13:g.44187434T>C
  • NM_000162.3:c.680-2A>G
Links:
dbSNP: rs1562715657
NCBI 1000 Genomes Browser:
rs1562715657
Molecular consequence:
  • NM_000162.5:c.680-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354800.1:c.680-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_033507.3:c.683-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_033508.3:c.677-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Maturity onset diabetes mellitus in young (MODY)
Synonyms:
Mason type diabetes
Identifiers:
MONDO: MONDO:0018911; MedGen: C0342276; Orphanet: 552; OMIM: 606391; Human Phenotype Ontology: HP:0004904

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002605137Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic
criteria provided, single submitter

(K & H Uppaluri Personalized Medicine Clinic Variant Classification & Assertion Criteria_Updated V.1)		Likely pathogenicunknownresearch

PubMed (6)
[See all records that cite these PMIDs]

Citation Link,

SCV002665064Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Feb 12, 2016) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedresearch

Citations

PubMed

Clinical implications of the glucokinase impaired function - GCK MODY today.

Hulín J, Škopková M, Valkovičová T, Mikulajová S, Rosoľanková M, Papcun P, Gašperíková D, Staník J.

Physiol Res. 2020 Dec 22;69(6):995-1011. Epub 2020 Nov 2. Review.

PubMed [citation]
PMID:
33129248
PMCID:
PMC8549873

GCK mutations in Chinese MODY2 patients: a family pedigree report and review of Chinese literature.

Ping Xiao Y, Hua Xu X, Lan Fang Y, Jiang L, Chen C, Liang L, Lin Wang C.

J Pediatr Endocrinol Metab. 2016 Aug 1;29(8):959-64. doi: 10.1515/jpem-2015-0354. Review.

PubMed [citation]
PMID:
27269892
See all PubMed Citations (6)

Details of each submission

From Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic, SCV002605137.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedresearch PubMed (6)

Description

Potent mutations in GCK gene is associated with poor secretion of insulin. Its associated with milder forms of diabetes, which can be controlled by diet . However, there is no sufficient evidence to ascertain the significance of rs1562715657 in MODY, yet.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Ambry Genetics, SCV002665064.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.680-2A>G intronic variant results from an A to G substitution two nucleotides upstream from coding exon 7 in the GCK gene. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6503 samples (13006 alleles) with coverage at this position. This nucleotide position is highly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to abolish the native splice acceptor site; however, direct evidence is unavailable. Alterations that disrupt the canonical splice acceptor site are typically deleterious in nature (ACMG Recommendations for Standards for Interpretation and Reporting of Sequence Variations. Revision 2007. Genet Med. 2008;10:294). As such, the c.680-2A>G variant is classified as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2024