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NM_000162.5(GCK):c.1174C>T (p.Arg392Cys) AND GCK-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 7, 2023
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:
RCV003420270.4

Allele description [Variation Report for NM_000162.5(GCK):c.1174C>T (p.Arg392Cys)]

NM_000162.5(GCK):c.1174C>T (p.Arg392Cys)

Gene:
GCK:glucokinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p13
Genomic location:
Preferred name:
NM_000162.5(GCK):c.1174C>T (p.Arg392Cys)
Other names:
NM_000162.5(GCK):c.1174C>T; p.Arg392Cys
HGVS:
  • NC_000007.14:g.44145576G>A
  • NG_008847.2:g.57595C>T
  • NM_000162.5:c.1174C>TMANE SELECT
  • NM_001354800.1:c.1174C>T
  • NM_001354801.1:c.163C>T
  • NM_001354802.1:c.34C>T
  • NM_001354803.2:c.208C>T
  • NM_033507.3:c.1177C>T
  • NM_033508.3:c.1171C>T
  • NP_000153.1:p.Arg392Cys
  • NP_001341729.1:p.Arg392Cys
  • NP_001341730.1:p.Arg55Cys
  • NP_001341731.1:p.Arg12Cys
  • NP_001341732.1:p.Arg70Cys
  • NP_277042.1:p.Arg393Cys
  • NP_277043.1:p.Arg391Cys
  • LRG_1074t1:c.1174C>T
  • LRG_1074t2:c.1177C>T
  • LRG_1074:g.57595C>T
  • LRG_1074p1:p.Arg392Cys
  • LRG_1074p2:p.Arg393Cys
  • NC_000007.13:g.44185175G>A
  • NM_000162.3:c.1174C>T
  • NM_000162.4:c.1174C>T
Protein change:
R12C
Links:
dbSNP: rs1167124132
NCBI 1000 Genomes Browser:
rs1167124132
Molecular consequence:
  • NM_000162.5:c.1174C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354800.1:c.1174C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354801.1:c.163C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354802.1:c.34C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354803.2:c.208C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033507.3:c.1177C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033508.3:c.1171C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
GCK-related disorder
Synonyms:
GCK-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004107580PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jul 7, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004107580.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The GCK c.1174C>T variant is predicted to result in the amino acid substitution p.Arg392Cys. This variant was reported in a family in a low birth weight study (Hattersley et al. 1998. PubMed ID: 9662401). This variant has been reported in multiple individuals with maturity-onset diabetes of the young (Thomson et al. 2003. PubMed ID: 14517956; Katashima et al. 2021. PubMed ID: 34746319; Table S1, Mirshahi et al. 2022. PubMed ID: 36257325; Table S4, Colclough et al. 2022. PubMed ID: 34789499). This variant was also observed in three carriers, one carrier with diabetes and two carriers in the non-diabetes group (Table S1, Billings et al. 2022. PubMed ID: 36208030).This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. In ClinVar, this variant is interpreted as uncertain/likely pathogenic/pathogenic (https://preview.ncbi.nlm.nih.gov/clinvar/variation/585909/). In summary, this variant is interpreted as likely pathogenic.

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

Last Updated: May 19, 2024