NM_000162.5(GCK):c.483+2_483+16del AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Nov 1, 2023
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:: RCV000992052.3

Allele description [Variation Report for NM_000162.5(GCK):c.483+2_483+16del]

NM_000162.5(GCK):c.483+2_483+16del

Gene:

GCK:glucokinase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

7p13

Genomic location:

Preferred name:

NM_000162.5(GCK):c.483+2_483+16del

HGVS:

NC_000007.14:g.44150940_44150954del
NC_000007.14:g.44150943_44150957del
NG_008847.2:g.52217_52231del
NM_000162.5:c.483+2_483+16delMANE SELECT
NM_001354800.1:c.483+2_483+16del
NM_033507.3:c.486+2_486+16del
NM_033508.3:c.480+2_480+16del
LRG_1074t1:c.483+2_483+16del
LRG_1074t2:c.486+2_486+16del
LRG_1074:g.52217_52231del
NC_000007.13:g.44190542_44190556del
NC_000007.14:g.44150943_44150957del
NM_000162.3:c.483+2_483+16del

Links:

OMIM: 138079.0006; dbSNP: rs1583601110

NCBI 1000 Genomes Browser:

rs1583601110

Molecular consequence:

NM_000162.5:c.483+2_483+16del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354800.1:c.483+2_483+16del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_033507.3:c.486+2_486+16del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_033508.3:c.480+2_480+16del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001144018	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Dec 17, 2018)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 24430320, 8376578, 26467025
SCV005202003	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Nov 1, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001144018

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Pathogenic
(Dec 17, 2018)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV005202003

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Nov 1, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Prevalence of vascular complications among patients with glucokinase mutations and prolonged, mild hyperglycemia.

Steele AM, Shields BM, Wensley KJ, Colclough K, Ellard S, Hattersley AT.

JAMA. 2014 Jan 15;311(3):279-86. doi: 10.1001/jama.2013.283980.

PubMed [citation]

PMID:: 24430320

Deletion of the donor splice site of intron 4 in the glucokinase gene causes maturity-onset diabetes of the young.

Sun F, Knebelmann B, Pueyo ME, Zouali H, Lesage S, Vaxillaire M, Passa P, Cohen D, Velho G, Antignac C, et al.

J Clin Invest. 1993 Sep;92(3):1174-80.

PubMed [citation]

PMID:: 8376578
PMCID:: PMC288255

See all PubMed Citations (3)

Details of each submission

From Athena Diagnostics, SCV001144018.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

The variant disrupts a canonical splice site. Found in at least one symptomatic patient, and not found in general population data.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV005202003.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Canonical splice site variant predicted to result in an in-frame loss of the adjacent exon in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 8376578)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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