NM_001110792.2(MECP2):c.413+2dup AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 30, 2016
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:: RCV000413817.1

Allele description [Variation Report for NM_001110792.2(MECP2):c.413+2dup]

NM_001110792.2(MECP2):c.413+2dup

Gene:

MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_001110792.2(MECP2):c.413+2dup

HGVS:

NC_000023.11:g.154032205dup
NG_007107.2:g.109923dup
NG_007107.3:g.109899dup
NM_001110792.2:c.413+2dupMANE SELECT
NM_001316337.2:c.98+2dup
NM_001369391.2:c.98+2dup
NM_001369392.2:c.98+2dup
NM_001369393.2:c.98+2dup
NM_001369394.2:c.98+2dup
NM_001386137.1:c.-184+2dup
NM_001386138.1:c.-184+2dup
NM_001386139.1:c.-184+2dup
NM_004992.4:c.377+2dup
LRG_764t1:c.413+2dup
LRG_764t2:c.377+2dup
LRG_764:g.109899dup
NC_000023.10:g.153297656dup
NM_004992.3:c.377+2dupT

Links:

dbSNP: rs1057518521

NCBI 1000 Genomes Browser:

rs1057518521

Molecular consequence:

NM_001110792.2:c.413+2dup - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001316337.2:c.98+2dup - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001369391.2:c.98+2dup - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001369392.2:c.98+2dup - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001369393.2:c.98+2dup - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001369394.2:c.98+2dup - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001386137.1:c.-184+2dup - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001386138.1:c.-184+2dup - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001386139.1:c.-184+2dup - splice donor variant - [Sequence Ontology: SO:0001575]
NM_004992.4:c.377+2dup - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000492251	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Nov 30, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000492251

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Nov 30, 2016)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000492251.1

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

Description

A variant of uncertain significance has been identified in the MECP2 gene. The c.377+2dupT variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The c.377+2dupT results in an intronic duplication. Several in-silico splice prediction models predict that c.377+2dupT destroys the donor site for intron 3 which may lead to abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

#	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 17, 2022

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