NM_000162.5(GCK):c.1019G>A (p.Ser340Asn) AND Maturity onset diabetes mellitus in young

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 1, 2022
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:: RCV003329421.2

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)

Name:: Maturity onset diabetes mellitus in young (MODY)
Synonyms:: Mason type diabetes
Identifiers:: MONDO: MONDO:0018911; MedGen: C0342276; Orphanet: 552; OMIM: 606391; Human Phenotype Ontology: HP:0004904

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004037058	Dept of Medical Genetics, AP-HP Sorbonne University, Pitié-Salpêtrière hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 1, 2022)	germline	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

SCV004037058

Dept of Medical Genetics, AP-HP Sorbonne University, Pitié-Salpêtrière hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Nov 1, 2022)

germline

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
not provided	germline	yes	not provided	not provided	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 Dept of Medical Genetics, AP-HP Sorbonne University, Pitié-Salpêtrière hospital, SCV004037058.1

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

Description

minigene showed effect on RNA splicing: complex alteration with 3 transcripts. 1/ deletion of the last 8 pb of exon 8 (r.1012_1019del, p.Val338Argfs*118); 2/ retention of the first 17 pb of intron 8 (r.1019_1020delins18, p.Ser340Lysfs*19); 3/ skipping of exon 8 (r.864_1019del, p.Tyr289_Ser340del). PS3 PM2 PP4

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

Last Updated: Sep 29, 2024

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