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NM_000162.5(GCK):c.1136C>T (p.Ala379Val) AND not provided

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Apr 28, 2022
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:
RCV000992036.4

Allele description [Variation Report for NM_000162.5(GCK):c.1136C>T (p.Ala379Val)]

NM_000162.5(GCK):c.1136C>T (p.Ala379Val)

Gene:
GCK:glucokinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p13
Genomic location:
Preferred name:
NM_000162.5(GCK):c.1136C>T (p.Ala379Val)
Other names:
NM_000162.5(GCK):c.1136C>T; p.Ala379Val
HGVS:
  • NC_000007.14:g.44145614G>A
  • NG_008847.2:g.57557C>T
  • NM_000162.5:c.1136C>TMANE SELECT
  • NM_001354800.1:c.1136C>T
  • NM_001354801.1:c.125C>T
  • NM_001354802.1:c.-5C>T
  • NM_001354803.2:c.170C>T
  • NM_033507.3:c.1139C>T
  • NM_033508.3:c.1133C>T
  • NP_000153.1:p.Ala379Val
  • NP_001341729.1:p.Ala379Val
  • NP_001341730.1:p.Ala42Val
  • NP_001341732.1:p.Ala57Val
  • NP_277042.1:p.Ala380Val
  • NP_277043.1:p.Ala378Val
  • LRG_1074t1:c.1136C>T
  • LRG_1074t2:c.1139C>T
  • LRG_1074:g.57557C>T
  • LRG_1074p1:p.Ala379Val
  • LRG_1074p2:p.Ala380Val
  • NC_000007.13:g.44185213G>A
  • NM_000162.3:c.1136C>T
Protein change:
A378V
Links:
dbSNP: rs193922265
NCBI 1000 Genomes Browser:
rs193922265
Molecular consequence:
  • NM_001354802.1:c.-5C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000162.5:c.1136C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354800.1:c.1136C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354801.1:c.125C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354803.2:c.170C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033507.3:c.1139C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033508.3:c.1133C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001144000Athena Diagnostics
criteria provided, single submitter

(Athena Diagnostics Criteria)		Likely pathogenic
(Dec 10, 2018) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV002512860GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(Apr 28, 2022) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Mutations in GCK and HNF-1alpha explain the majority of cases with clinical diagnosis of MODY in Spain.

Estalella I, Rica I, Perez de Nanclares G, Bilbao JR, Vazquez JA, San Pedro JI, Busturia MA, Castaño L; Spanish MODY Group..

Clin Endocrinol (Oxf). 2007 Oct;67(4):538-46. Epub 2007 Jun 15.

PubMed [citation]
PMID:
17573900

Biochemical characterization of novel glucokinase mutations isolated from Spanish maturity-onset diabetes of the young (MODY2) patients.

Estalella I, Garcia-Gimeno MA, Marina A, Castaño L, Sanz P.

J Hum Genet. 2008;53(5):460-466. doi: 10.1007/s10038-008-0271-5. Epub 2008 Mar 6.

PubMed [citation]
PMID:
18322640
See all PubMed Citations (5)

Details of each submission

From Athena Diagnostics, SCV001144000.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

Not found in the total gnomAD dataset, and the data is high quality (0/265258 chr). Found in at least one symptomatic patient. Predicted to have a damaging effect on the protein. Damaging to protein function(s) relevant to disease mechanism.

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

From GeneDx, SCV002512860.2

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

Description

Observed in patients with MODY in published literature (Estalella I et al., 2007; Weinert LS et al., 2014); Published functional studies demonstrate a damaging effect on enzyme activity (Estalella I et al., 2008); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Missense variants in this gene are often considered pathogenic (HGMD); This variant is associated with the following publications: (PMID: 28012402, 22389783, 22332836, 32375122, 25174781, 17573900, 18322640)

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

Last Updated: May 7, 2024