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NM_001110792.2(MECP2):c.1482C>T (p.Thr494=) AND Rett syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Aug 14, 2023
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:
RCV003380471.1

Allele description [Variation Report for NM_001110792.2(MECP2):c.1482C>T (p.Thr494=)]

NM_001110792.2(MECP2):c.1482C>T (p.Thr494=)

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.1482C>T (p.Thr494=)
Other names:
NM_001110792.2(MECP2):c.1482C>T; p.Thr494=
HGVS:
  • NC_000023.11:g.154030382G>A
  • NG_007107.3:g.111722C>T
  • NM_001110792.2:c.1482C>TMANE SELECT
  • NM_001316337.2:c.1167C>T
  • NM_001369391.2:c.1167C>T
  • NM_001369392.2:c.1167C>T
  • NM_001369393.2:c.1167C>T
  • NM_001369394.2:c.1167C>T
  • NM_001386137.1:c.777C>T
  • NM_001386138.1:c.777C>T
  • NM_001386139.1:c.777C>T
  • NM_004992.4:c.1446C>T
  • NP_001104262.1:p.Thr494=
  • NP_001303266.1:p.Thr389=
  • NP_001356320.1:p.Thr389=
  • NP_001356321.1:p.Thr389=
  • NP_001356322.1:p.Thr389=
  • NP_001356323.1:p.Thr389=
  • NP_001373066.1:p.Thr259=
  • NP_001373067.1:p.Thr259=
  • NP_001373068.1:p.Thr259=
  • NP_004983.1:p.Thr482=
  • NP_004983.1:p.Thr482=
  • LRG_764t1:c.1482C>T
  • LRG_764t2:c.1446C>T
  • AJ132917.1:c.1446C>T
  • LRG_764:g.111722C>T
  • LRG_764p1:p.Thr494=
  • LRG_764p2:p.Thr482=
  • NC_000023.10:g.153295833G>A
  • NG_007107.2:g.111746C>T
  • NM_004992.3:c.1446C>T
Links:
dbSNP: rs76895094
NCBI 1000 Genomes Browser:
rs76895094
Molecular consequence:
  • NM_001110792.2:c.1482C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001316337.2:c.1167C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369391.2:c.1167C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369392.2:c.1167C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369393.2:c.1167C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001369394.2:c.1167C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001386137.1:c.777C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001386138.1:c.777C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001386139.1:c.777C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004992.4:c.1446C>T - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV004098743Centre for Population Genomics, CPG
criteria provided, single submitter

(McKnight et al. (Hum Mutat. 2022))		Likely benign
(Aug 14, 2023) 		germlinecuration

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

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Recommendations by the ClinGen Rett/Angelman-like expert panel for gene-specific variant interpretation methods.

McKnight D, Bean L, Karbassi I, Beattie K, Bienvenu T, Bonin H, Fang P, Chrisodoulou J, Friez M, Helgeson M, Krishnaraj R, Meng L, Mighion L, Neul J, Percy A, Ramsden S, Zoghbi H, Das S.

Hum Mutat. 2022 Aug;43(8):1097-1113. doi: 10.1002/humu.24302. Epub 2021 Dec 2.

PubMed [citation]
PMID:
34837432
PMCID:
PMC9135956

Details of each submission

From Centre for Population Genomics, CPG, SCV004098743.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

This variant has been collected from RettBASE and curated to current modified ACMG/AMP criteria.Based on the classification scheme defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders Specifications to the ACMG/AMP Variant Interpretation Guidelines VCEP 2.0, this variant is classified as Likely benign. At least the following criteria are met: Synonymous or intronic variant outside donor and acceptor splice regions where splicing prediction algorithms do not support significant splicing alteration (spliceAI score <=0.1) (BP4, BP7).

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

Last Updated: Nov 3, 2024