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NM_000162.5(GCK):c.1335T>A (p.Ser445Arg) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 14, 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:
RCV002004046.6

Allele description [Variation Report for NM_000162.5(GCK):c.1335T>A (p.Ser445Arg)]

NM_000162.5(GCK):c.1335T>A (p.Ser445Arg)

Gene:
GCK:glucokinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p13
Genomic location:
Preferred name:
NM_000162.5(GCK):c.1335T>A (p.Ser445Arg)
HGVS:
  • NC_000007.14:g.44145199A>T
  • NG_008847.2:g.57972T>A
  • NM_000162.5:c.1335T>AMANE SELECT
  • NM_001354800.1:c.1335T>A
  • NM_001354801.1:c.324T>A
  • NM_001354802.1:c.195T>A
  • NM_001354803.2:c.369T>A
  • NM_033507.3:c.1338T>A
  • NM_033508.3:c.1332T>A
  • NP_000153.1:p.Ser445Arg
  • NP_001341729.1:p.Ser445Arg
  • NP_001341730.1:p.Ser108Arg
  • NP_001341731.1:p.Ser65Arg
  • NP_001341732.1:p.Ser123Arg
  • NP_277042.1:p.Ser446Arg
  • NP_277043.1:p.Ser444Arg
  • LRG_1074t1:c.1335T>A
  • LRG_1074t2:c.1338T>A
  • LRG_1074:g.57972T>A
  • LRG_1074p1:p.Ser445Arg
  • LRG_1074p2:p.Ser446Arg
  • NC_000007.13:g.44184798A>T
Protein change:
S108R
Links:
dbSNP: rs2128818794
NCBI 1000 Genomes Browser:
rs2128818794
Molecular consequence:
  • NM_000162.5:c.1335T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354800.1:c.1335T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354801.1:c.324T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354802.1:c.195T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354803.2:c.369T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033507.3:c.1338T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033508.3:c.1332T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002291544Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jul 14, 2021)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Lower Circulating miR-122 Level in Patients with HNF1A Variant-Induced Diabetes Compared with Type 2 Diabetes.

Huang X, Gong S, Ma Y, Cai X, Zhou L, Luo Y, Li M, Liu W, Zhang S, Zhang X, Ren Q, Zhu Y, Zhou X, Zhang R, Chen L, Gao X, Zhang F, Wang Y, Han X, Ji L.

J Diabetes Res. 2018;2018:7842064. doi: 10.1155/2018/7842064.

PubMed [citation]
PMID:
30155490
PMCID:
PMC6093029

A new clinical screening strategy and prevalence estimation for glucokinase variant-induced diabetes in an adult Chinese population.

Ma Y, Han X, Zhou X, Li Y, Gong S, Zhang S, Cai X, Zhou L, Luo Y, Li M, Liu W, Zhang X, Ren Q, Ji L.

Genet Med. 2019 Apr;21(4):939-947. doi: 10.1038/s41436-018-0282-3. Epub 2018 Sep 24.

PubMed [citation]
PMID:
30245511
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002291544.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. This variant has been observed in individual(s) with GCK-related conditions (PMID: 30155490, 30245511). This variant is not present in population databases (ExAC no frequency). This sequence change replaces serine with arginine at codon 445 of the GCK protein (p.Ser445Arg). The serine residue is highly conserved and there is a moderate physicochemical difference between serine and arginine.

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

Last Updated: Sep 29, 2024