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NM_001110792.2(MECP2):c.414-3C>T AND Rett syndrome

Germline classification:
Benign (2 submissions)
Last evaluated:
Feb 18, 2022
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV000625805.9

Allele description [Variation Report for NM_001110792.2(MECP2):c.414-3C>T]

NM_001110792.2(MECP2):c.414-3C>T

Gene:
MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_001110792.2(MECP2):c.414-3C>T
HGVS:
  • NC_000023.11:g.154031453G>A
  • NG_007107.3:g.110651C>T
  • NM_001110792.2:c.414-3C>TMANE SELECT
  • NM_001316337.2:c.99-3C>T
  • NM_001369391.2:c.99-3C>T
  • NM_001369392.2:c.99-3C>T
  • NM_001369393.2:c.99-3C>T
  • NM_001369394.2:c.99-3C>T
  • NM_001386137.1:c.-183-3C>T
  • NM_001386138.1:c.-183-3C>T
  • NM_001386139.1:c.-183-3C>T
  • NM_004992.4:c.378-3C>T
  • LRG_764t1:c.414-3C>T
  • LRG_764t2:c.378-3C>T
  • LRG_764:g.110651C>T
  • NC_000023.10:g.153296904G>A
  • NG_007107.2:g.110675C>T
  • NM_001110792.1:c.414-3C>T
  • NM_004992.3:c.378-3C>T
Links:
dbSNP: rs267608465
NCBI 1000 Genomes Browser:
rs267608465
Molecular consequence:
  • NM_001110792.2:c.414-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001316337.2:c.99-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001369391.2:c.99-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001369392.2:c.99-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001369393.2:c.99-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001369394.2:c.99-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001386137.1:c.-183-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001386138.1:c.-183-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001386139.1:c.-183-3C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_004992.4:c.378-3C>T - intron variant - [Sequence Ontology: SO:0001627]
Observations:
2

Condition(s)

Name:
Rett syndrome (RTT)
Synonyms:
Autism, dementia, ataxia, and loss of purposeful hand use; Rett's disorder
Identifiers:
MONDO: MONDO:0010726; MedGen: C0035372; Orphanet: 3095; Orphanet: 778; OMIM: 312750

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000746360Genomic Research Center, Shahid Beheshti University of Medical Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Benign
(Apr 27, 2021) 		inheritedclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002047367ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel
reviewed by expert panel

(ClinGen RettAS ACMG Specifications V2)		Benign
(Feb 18, 2022) 		germlinecuration

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedyes2not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

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 Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000746360.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot provided2not providednot providednot provided

From ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel, SCV002047367.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.378-3C>T variant in MECP2 (NM_004992.3) has an allele frequency of 0.038% in "Other" sub population in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). The c.378-3C>T variant is observed in at least 2 unaffected individuals (Invitae internal database) (BS2). The c.378-3C>T variant is found in a patient with an alternate molecular basis of disease (Invitae internal database) (BP5). In summary, the c.378-3C>T variant in MECP2 is classified as benign for Rett Syndrome based on the ACMG/AMP criteria (BA1, BS2, BP5).

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

Last Updated: Aug 4, 2024