NM_000162.5(GCK):c.1020-10C>A AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 25, 2019
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:: RCV000029832.3

Allele description [Variation Report for NM_000162.5(GCK):c.1020-10C>A]

NM_000162.5(GCK):c.1020-10C>A

Gene:

GCK:glucokinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p13

Genomic location:

Preferred name:

NM_000162.5(GCK):c.1020-10C>A

HGVS:

NC_000007.14:g.44145740G>T
NG_008847.2:g.57431C>A
NM_000162.5:c.1020-10C>AMANE SELECT
NM_001354800.1:c.1020-10C>A
NM_001354801.1:c.9-10C>A
NM_001354802.1:c.-121-10C>A
NM_001354803.2:c.54-10C>A
NM_033507.3:c.1023-10C>A
NM_033508.3:c.1017-10C>A
LRG_1074t1:c.1020-10C>A
LRG_1074t2:c.1023-10C>A
LRG_1074:g.57431C>A
NC_000007.13:g.44185339G>T
NM_000162.3:c.1020-10C>A

Links:

dbSNP: rs193922257

NCBI 1000 Genomes Browser:

rs193922257

Molecular consequence:

NM_000162.5:c.1020-10C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354800.1:c.1020-10C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354801.1:c.9-10C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354802.1:c.-121-10C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354803.2:c.54-10C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_033507.3:c.1023-10C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_033508.3:c.1017-10C>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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RecName: Full=High mobility group nucleosome-binding domain-containing protein 5...
RecName: Full=High mobility group nucleosome-binding domain-containing protein 5; AltName: Full=Nucleosome-binding protein 1
gi|23396771|sp|P82970.1|HMGN5_HUMAN

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000052487	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Jan 25, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000052487

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Jan 25, 2019)

germline

clinical testing

Citation Link

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000052487.3

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

Description

Variant summary: GCK c.1020-10C>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing (ACMG PP3): Two predict the variant abolishes the canonical 3' acceptor site. Three predict the variant weakens the canonical 3' acceptor site. Five predict the variant creates a novel 3' acceptor site in intron 8. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 187084 control chromosomes (gnomAD, ACMG PM2). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.1020-10C>A in individuals affected with Maturity Onset Diabetes of the Young 2/Neonatal Diabetes Mellitus and no experimental evidence demonstrating its impact on protein function have been reported. A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cites the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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: May 7, 2024

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