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NM_000162.5(GCK):c.580-1G>A AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 18, 2018
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:
RCV000519932.2

Allele description [Variation Report for NM_000162.5(GCK):c.580-1G>A]

NM_000162.5(GCK):c.580-1G>A

Gene:
GCK:glucokinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p13
Genomic location:
Preferred name:
NM_000162.5(GCK):c.580-1G>A
HGVS:
  • NC_000007.14:g.44149860C>T
  • NG_008847.2:g.53311G>A
  • NM_000162.5:c.580-1G>AMANE SELECT
  • NM_001354800.1:c.580-1G>A
  • NM_033507.3:c.583-1G>A
  • NM_033508.3:c.577-1G>A
  • LRG_1074t1:c.580-1G>A
  • LRG_1074t2:c.583-1G>A
  • LRG_1074:g.53311G>A
  • NC_000007.13:g.44189459C>T
  • NM_000162.3:c.580-1G>A
Links:
dbSNP: rs1554335421
NCBI 1000 Genomes Browser:
rs1554335421
Molecular consequence:
  • NM_000162.5:c.580-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354800.1:c.580-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_033507.3:c.583-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_033508.3:c.577-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000617557GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(May 18, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000617557.2

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

Description

The c.580-1 G>A splice site variant in the GCK gene has been previously reported in association with MODY (Toaima et al., 2005; Gozlan et al., 2012). This variant destroys the canonical splice acceptor site in intron 5, and is expected to cause abnormal gene splicing (Toaima et al., 2005). The variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). In summary, we consider this variant to be pathogenic.

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

Last Updated: Jul 29, 2023