U.S. flag

An official website of the United States government

NM_000162.5(GCK):c.483+26C>A AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 10, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002468267.3

Allele description [Variation Report for NM_000162.5(GCK):c.483+26C>A]

NM_000162.5(GCK):c.483+26C>A

Gene:
GCK:glucokinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p13
Genomic location:
Preferred name:
NM_000162.5(GCK):c.483+26C>A
HGVS:
  • NC_000007.14:g.44150930G>T
  • NG_008847.2:g.52241C>A
  • NM_000162.5:c.483+26C>AMANE SELECT
  • NM_001354800.1:c.483+26C>A
  • NM_033507.3:c.486+26C>A
  • NM_033508.3:c.480+26C>A
  • LRG_1074t1:c.483+26C>A
  • LRG_1074t2:c.486+26C>A
  • LRG_1074:g.52241C>A
  • NC_000007.13:g.44190529G>T
  • NM_000162.3:c.483+26C>A
Links:
dbSNP: rs142668032
NCBI 1000 Genomes Browser:
rs142668032
Molecular consequence:
  • NM_000162.5:c.483+26C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354800.1:c.483+26C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_033507.3:c.486+26C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_033508.3:c.480+26C>A - intron variant - [Sequence Ontology: SO:0001627]
Observations:
1

Condition(s)

Name:
Type 2 diabetes mellitus
Synonyms:
DIABETES MELLITUS, TYPE 2, PROTECTION AGAINST; Type II diabetes mellitus; Diabetes mellitus, noninsulin-dependent, late onset
Identifiers:
MONDO: MONDO:0005148; MeSH: D003924; MedGen: C0011860; OMIM: 125853; Human Phenotype Ontology: HP:0005978
Name:
Hyperinsulinism due to glucokinase deficiency (HHF3)
Synonyms:
Hyperinsulinemic hypoglycemia familial 3
Identifiers:
MONDO: MONDO:0011236; MedGen: C1865290; OMIM: 602485
Name:
Maturity-onset diabetes of the young type 2
Synonyms:
MODY type 2; Diabetes mellitus MODY type 2; MODY glucokinase-related; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007453; MedGen: C0342277; Orphanet: 552; OMIM: 125851

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002764326New York Genome Center
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Sep 10, 2021) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center, SCV002764326.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The heterozygous c.483+26C>A intronic variant identified in intron 4 (of 9) of the GCK gene has been reported in three family members affected with familial impaired glucose fasting phenotype [PMID: 31529753]. The variant has 0.0005519 allele frequency in the gnomAD(v3) database (84 out of 152200 heterozygous alleles, 1 homozygote) and has 0.0004491 allele frequency in gnomAD(v2) database (127 out of 282778 heterozygous alleles, 1 homozygote). In vitro functional studies using the minigene expression assay showed the skipping of exon 5 of GCK [PMID: 31529753]. This variant has been reported in the ClinVar database as a Variant of Uncertain Significance [Variation ID:1188508]. The variant affects a weakly conserved nucleotide in intron 4 of the GCK gene and is predicted by in silico tools to have no significant effect on canonical mRNA splicing [Splice AI = 0.00, TRAP = 0.012]. Based on the available evidence, the heterozygousc.483+26C>A variant identified in the GCK gene is reported as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

Last Updated: Oct 13, 2024