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NM_001110792.2(MECP2):c.413+6_413+9del AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jul 14, 2021
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:
RCV000144106.16

Allele description [Variation Report for NM_001110792.2(MECP2):c.413+6_413+9del]

NM_001110792.2(MECP2):c.413+6_413+9del

Gene:
MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_001110792.2(MECP2):c.413+6_413+9del
HGVS:
  • NC_000023.11:g.154032201ACTT[1]
  • NG_007107.3:g.109899TAAG[1]
  • NM_001110792.2:c.413+6_413+9delMANE SELECT
  • NM_001316337.2:c.98+6_98+9del
  • NM_001369391.2:c.98+6_98+9del
  • NM_001369392.2:c.98+6_98+9del
  • NM_001369393.2:c.98+6_98+9del
  • NM_001369394.2:c.98+6_98+9del
  • NM_001386137.1:c.-184+6_-184+9del
  • NM_001386138.1:c.-184+6_-184+9del
  • NM_001386139.1:c.-184+6_-184+9del
  • NM_004992.4:c.377+6_377+9del
  • LRG_764t1:c.413+6_413+9del
  • LRG_764t2:c.377+6_377+9del
  • AJ132917.1:c.377+6_377+9del
  • LRG_764:g.109899TAAG[1]
  • NC_000023.10:g.153297649_153297652del
  • NC_000023.10:g.153297652ACTT[1]
  • NC_000023.10:g.153297656_153297659delACTT
  • NC_000023.11:g.154032205_154032208del
  • NG_007107.2:g.109923TAAG[1]
  • NM_004992.3:c.377+6_377+9del
  • NM_004992.3:c.377+6_377+9delTAAG
  • NM_004992.4:c.377+6_377+9delTAAG
Links:
dbSNP: rs267608459
NCBI 1000 Genomes Browser:
rs267608459
Molecular consequence:
  • NM_001110792.2:c.413+6_413+9del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001316337.2:c.98+6_98+9del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001369391.2:c.98+6_98+9del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001369392.2:c.98+6_98+9del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001369393.2:c.98+6_98+9del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001369394.2:c.98+6_98+9del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001386137.1:c.-184+6_-184+9del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001386138.1:c.-184+6_-184+9del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001386139.1:c.-184+6_-184+9del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_004992.4:c.377+6_377+9del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002048054ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)		Uncertain significance
(Jul 14, 2021) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providednot providednot providednot providednot providednot provided1not providedliterature only

Details of each submission

From RettBASE, SCV000189182.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot providednot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providednot provided1not providednot providednot providednot providednot providednot provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002048054.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The MECP2 c.377+6_377+9delTAAG variant (rs267608459), also known as IVS2+2delTAAG, has not been reported in individuals with Rett syndrome but has been observed in an individual with infantile autism (Lam 2000). This variant is also reported in ClinVar (Variation ID: 156059). This variant is found in the East Asian population with an allele frequency of 0.01% (2/13,856 alleles) in the Genome Aggregation Database. This is an intronic variant, and computational analyses (Alamut v.2.11) predict that this variant may impact splicing by weaking the nearby canonical donor splice site. However, given the lack of clinical and functional data, the significance of the c.377+6_377+9delTAAG variant is uncertain at this time. References: Lam CW et al. Spectrum of mutations in the MECP2 gene in patients with infantile autism and Rett syndrome. J Med Genet. 2000 Dec;37(12):E41. PMID: 11106359.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Flagged submissions

Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000189182RettBASE
flagged submission
Reason: This record appears to be redundant with a more recent record from the same submitter.
Notes: SCV000189182 appears to be redundant with SCV000222602.
not providednot providednot provided

Last Updated: Nov 3, 2024