NM_000162.5(GCK):c.1019G>A (p.Ser340Asn) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 2, 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:
RCV001903778.6

Allele description [Variation Report for NM_000162.5(GCK):c.1019G>A (p.Ser340Asn)]

NM_000162.5(GCK):c.1019G>A (p.Ser340Asn)

Gene:
GCK:glucokinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p13
Genomic location:
Preferred name:
NM_000162.5(GCK):c.1019G>A (p.Ser340Asn)
HGVS:
  • NC_000007.14:g.44146463C>T
  • NG_008847.2:g.56708G>A
  • NM_000162.5:c.1019G>AMANE SELECT
  • NM_001354800.1:c.1019G>A
  • NM_001354801.1:c.8+156G>A
  • NM_033507.3:c.1022G>A
  • NM_033508.3:c.1016G>A
  • NP_000153.1:p.Ser340Asn
  • NP_001341729.1:p.Ser340Asn
  • NP_277042.1:p.Ser341Asn
  • NP_277043.1:p.Ser339Asn
  • LRG_1074t1:c.1019G>A
  • LRG_1074t2:c.1022G>A
  • LRG_1074:g.56708G>A
  • LRG_1074p1:p.Ser340Asn
  • LRG_1074p2:p.Ser341Asn
  • NC_000007.13:g.44186062C>T
Protein change:
S339N
Links:
dbSNP: rs1376631949
NCBI 1000 Genomes Browser:
rs1376631949
Molecular consequence:
  • NM_001354801.1:c.8+156G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000162.5:c.1019G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354800.1:c.1019G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033507.3:c.1022G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033508.3:c.1016G>A - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
effect on RNA splicing function [Variation Ontology: 0397]

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
SCV002173610Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 2, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]
PMID:
9536098
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002173610.3

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

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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant  is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1405403). This missense change has been observed in individual(s) with autosomal dominant maturity onset diabetes of the young (PMID: 28323911, 33852230). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 340 of the GCK protein (p.Ser340Asn). This variant also falls at the last nucleotide of exon 8, which is part of the consensus splice site for this exon.

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

Last Updated: Sep 29, 2024