NM_000162.5(GCK):c.188G>A (p.Arg63His) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 8, 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:: RCV003665331.2

Allele description [Variation Report for NM_000162.5(GCK):c.188G>A (p.Arg63His)]

NM_000162.5(GCK):c.188G>A (p.Arg63His)

Gene:

GCK:glucokinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p13

Genomic location:

Preferred name:

NM_000162.5(GCK):c.188G>A (p.Arg63His)

HGVS:

NC_000007.14:g.44153321C>T
NG_008847.2:g.49850G>A
NM_000162.5:c.188G>AMANE SELECT
NM_001354800.1:c.188G>A
NM_033507.3:c.191G>A
NM_033508.3:c.185G>A
NP_000153.1:p.Arg63His
NP_001341729.1:p.Arg63His
NP_277042.1:p.Arg64His
NP_277043.1:p.Arg62His
LRG_1074t1:c.188G>A
LRG_1074t2:c.191G>A
LRG_1074:g.49850G>A
LRG_1074p1:p.Arg63His
LRG_1074p2:p.Arg64His
NC_000007.13:g.44192920C>T

Protein change:

R62H

Molecular consequence:

NM_000162.5:c.188G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354800.1:c.188G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_033507.3:c.191G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_033508.3:c.185G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004375660	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 8, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30590153, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004375660

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 8, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Citations

PubMed

First evidence of changes in enzyme kinetics and stability of glucokinase affected by somatic cancer-associated variations.

Těšínský M, Šimčíková D, Heneberg P.

Biochim Biophys Acta Proteins Proteom. 2019 Mar;1867(3):213-218. doi: 10.1016/j.bbapap.2018.12.008. Epub 2018 Dec 24.

PubMed [citation]

PMID:: 30590153

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004375660.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on GCK function (PMID: 30590153). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt GCK protein function. This variant has not been reported in the literature in individuals affected with GCK-related conditions. This variant is present in population databases (rs746444094, gnomAD 0.004%). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 63 of the GCK protein (p.Arg63His).

#	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

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine