NM_000162.5(GCK):c.1312T>G (p.Phe438Val) AND Maturity-onset diabetes of the young type 2

Germline classification:: Likely pathogenic (1 submission)
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:: RCV002227427.2

Allele description [Variation Report for NM_000162.5(GCK):c.1312T>G (p.Phe438Val)]

NM_000162.5(GCK):c.1312T>G (p.Phe438Val)

Gene:

GCK:glucokinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p13

Genomic location:

Preferred name:

NM_000162.5(GCK):c.1312T>G (p.Phe438Val)

HGVS:

NC_000007.14:g.44145222A>C
NG_008847.2:g.57949T>G
NM_000162.5:c.1312T>GMANE SELECT
NM_001354800.1:c.1312T>G
NM_001354801.1:c.301T>G
NM_001354802.1:c.172T>G
NM_001354803.2:c.346T>G
NM_033507.3:c.1315T>G
NM_033508.3:c.1309T>G
NP_000153.1:p.Phe438Val
NP_001341729.1:p.Phe438Val
NP_001341730.1:p.Phe101Val
NP_001341731.1:p.Phe58Val
NP_001341732.1:p.Phe116Val
NP_277042.1:p.Phe439Val
NP_277043.1:p.Phe437Val
LRG_1074t1:c.1312T>G
LRG_1074t2:c.1315T>G
LRG_1074:g.57949T>G
LRG_1074p1:p.Phe438Val
LRG_1074p2:p.Phe439Val
NC_000007.13:g.44184821A>C

Protein change:

F101V

Links:

dbSNP: rs2128818820

NCBI 1000 Genomes Browser:

rs2128818820

Molecular consequence:

NM_000162.5:c.1312T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354800.1:c.1312T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354801.1:c.301T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354802.1:c.172T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354803.2:c.346T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_033507.3:c.1315T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_033508.3:c.1309T>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Maturity-onset diabetes of the young type 2
Synonyms:: MODY type 2; Diabetes mellitus MODY type 2; MODY glucokinase-related; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007453; MedGen: C0342277; Orphanet: 552; OMIM: 125851

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Slc25a48 solute carrier family 25, member 48 [Mus musculus]
Slc25a48 solute carrier family 25, member 48 [Mus musculus]
Gene ID:328258

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002506581	National Newborn Screening Laboratory, Hospital Nacional de Niños	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002506581

National Newborn Screening Laboratory, Hospital Nacional de Niños

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
Latin American	unknown	yes	18	10	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From National Newborn Screening Laboratory, Hospital Nacional de Niños, SCV002506581.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Latin American	18	not provided	not provided	clinical testing	PubMed (1)

Description

This is a missense variant located within exon 10 and generates a change from the aminoacid Phenylalanine to Valine in position 438. It is located in a mutational hot spot (PM1). It is not present in population databases (GnomAD exomes, GnomAD genomes) (PM2). Multiple lines of computational evidence support a deleterious effect on the gene (PP3). Missense variant in a gene that has a low rate of benign missense variation for which missense variants are a common mechanism of a disease (PP2).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	blood	not provided		18	not provided	10	not provided

Last Updated: Jun 23, 2024

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