NM_002397.5(MEF2C):c.401_402+2del AND Inborn genetic diseases

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 12, 2017
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:: RCV002317557.9

Allele description [Variation Report for NM_002397.5(MEF2C):c.401_402+2del]

NM_002397.5(MEF2C):c.401_402+2del

Gene:

MEF2C:myocyte enhancer factor 2C [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

5q14.3

Genomic location:

Preferred name:

NM_002397.5(MEF2C):c.401_402+2del

HGVS:

NC_000005.10:g.88761184CA[1]
NG_023427.1:g.147918GT[1]
NM_001131005.2:c.259-61_259-58del
NM_001193347.1:c.319-61_319-58del
NM_001193348.1:c.259-9143_259-9140del
NM_001193349.3:c.259-9143_259-9140del
NM_001193350.2:c.401_402+2del
NM_001308002.3:c.401_402+2del
NM_001363581.2:c.401_402+2del
NM_001364329.2:c.401_402+2del
NM_001364330.2:c.401_402+2del
NM_001364331.2:c.401_402+2del
NM_001364332.2:c.259-9143_259-9140del
NM_001364333.2:c.401_402+2del
NM_001364334.2:c.401_402+2del
NM_001364335.2:c.401_402+2del
NM_001364336.2:c.401_402+2del
NM_001364337.2:c.401_402+2del
NM_001364338.2:c.319-61_319-58del
NM_001364339.2:c.401_402+2del
NM_001364340.2:c.401_402+2del
NM_001364341.2:c.401_402+2del
NM_001364342.2:c.401_402+2del
NM_001364343.2:c.259-61_259-58del
NM_001364344.2:c.259-9143_259-9140del
NM_001364345.2:c.401_402+2del
NM_001364346.2:c.401_402+2del
NM_001364347.2:c.401_402+2del
NM_001364348.2:c.401_402+2del
NM_001364349.2:c.401_402+2del
NM_001364350.2:c.401_402+2del
NM_001364352.2:c.259-61_259-58del
NM_001364353.2:c.23_24+2del
NM_001364354.2:c.259-9143_259-9140del
NM_001364355.2:c.259-9143_259-9140del
NM_001364356.2:c.23_24+2del
NM_001364357.2:c.-24-9143_-24-9140del
NM_002397.5:c.401_402+2delMANE SELECT
NC_000005.9:g.88057000_88057003del
NC_000005.9:g.88057001CA[1]
NM_002397.4:c.401_402+2delGTGT

Links:

dbSNP: rs1561875779

NCBI 1000 Genomes Browser:

rs1561875779

Molecular consequence:

NM_001131005.2:c.259-61_259-58del - intron variant - [Sequence Ontology: SO:0001627]
NM_001193347.1:c.319-61_319-58del - intron variant - [Sequence Ontology: SO:0001627]
NM_001193348.1:c.259-9143_259-9140del - intron variant - [Sequence Ontology: SO:0001627]
NM_001193349.3:c.259-9143_259-9140del - intron variant - [Sequence Ontology: SO:0001627]
NM_001364332.2:c.259-9143_259-9140del - intron variant - [Sequence Ontology: SO:0001627]
NM_001364338.2:c.319-61_319-58del - intron variant - [Sequence Ontology: SO:0001627]
NM_001364343.2:c.259-61_259-58del - intron variant - [Sequence Ontology: SO:0001627]
NM_001364344.2:c.259-9143_259-9140del - intron variant - [Sequence Ontology: SO:0001627]
NM_001364352.2:c.259-61_259-58del - intron variant - [Sequence Ontology: SO:0001627]
NM_001364354.2:c.259-9143_259-9140del - intron variant - [Sequence Ontology: SO:0001627]
NM_001364355.2:c.259-9143_259-9140del - intron variant - [Sequence Ontology: SO:0001627]
NM_001364357.2:c.-24-9143_-24-9140del - intron variant - [Sequence Ontology: SO:0001627]
NM_001193350.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001308002.3:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001363581.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364329.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364330.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364331.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364333.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364334.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364335.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364336.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364337.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364339.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364340.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364341.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364342.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364345.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364346.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364347.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364348.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364349.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364350.2:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364353.2:c.23_24+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001364356.2:c.23_24+2del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_002397.5:c.401_402+2del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000851043	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely pathogenic (Jun 12, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000851043

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely pathogenic
(Jun 12, 2017)

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 Ambry Genetics, SCV000851043.5

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

Description

The c.401_402+2delGTGT variant results from a deletion of 4 nucleotides located at positions 401 to 402 as well as the first 2 intronic nucleotides after coding exon 3 of the MEF2C gene, deleting the canonical donor splice site. These nucleotide positions are highly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to abolish the native donor splice site; however, direct evidence is unavailable. Alterations that disrupt the canonical splice donor site are typically deleterious in nature (ACMG Recommendations for Standards for Interpretation and Reporting of Sequence Variations. Revision 2007. Genet Med. 2008;10:294). As such, this variant is classified as likely pathogenic.

#	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 1, 2024

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