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NM_001110792.2(MECP2):c.327C>A (p.Asp109Glu) AND Rett syndrome

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Oct 12, 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:
RCV000133051.3

Allele description [Variation Report for NM_001110792.2(MECP2):c.327C>A (p.Asp109Glu)]

NM_001110792.2(MECP2):c.327C>A (p.Asp109Glu)

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.327C>A (p.Asp109Glu)
Other names:
NM_001110792.2(MECP2):c.327C>A; p.Asp109Glu
HGVS:
  • NC_000023.11:g.154032293G>T
  • NG_007107.3:g.109811C>A
  • NM_001110792.2:c.327C>AMANE SELECT
  • NM_001316337.2:c.12C>A
  • NM_001369391.2:c.12C>A
  • NM_001369392.2:c.12C>A
  • NM_001369393.2:c.12C>A
  • NM_001369394.2:c.12C>A
  • NM_001386137.1:c.-270C>A
  • NM_001386138.1:c.-270C>A
  • NM_001386139.1:c.-270C>A
  • NM_004992.4:c.291C>A
  • NP_001104262.1:p.Asp109Glu
  • NP_001303266.1:p.Asp4Glu
  • NP_001356320.1:p.Asp4Glu
  • NP_001356321.1:p.Asp4Glu
  • NP_001356322.1:p.Asp4Glu
  • NP_001356323.1:p.Asp4Glu
  • NP_004983.1:p.Asp97Glu
  • NP_004983.1:p.Asp97Glu
  • LRG_764t1:c.327C>A
  • LRG_764t2:c.291C>A
  • AJ132917.1:c.291C>A
  • LRG_764:g.109811C>A
  • LRG_764p1:p.Asp109Glu
  • LRG_764p2:p.Asp97Glu
  • NC_000023.10:g.153297744G>T
  • NG_007107.2:g.109835C>A
  • NM_004992.3:c.291C>A
  • P51608:p.Asp97Glu
Protein change:
D109E
Links:
UniProtKB: P51608#VAR_023552; dbSNP: rs61754449
NCBI 1000 Genomes Browser:
rs61754449
Molecular consequence:
  • NM_001386137.1:c.-270C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386138.1:c.-270C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386139.1:c.-270C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001110792.2:c.327C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001316337.2:c.12C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369391.2:c.12C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369392.2:c.12C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369393.2:c.12C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369394.2:c.12C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004992.4:c.291C>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000188039RettBASE
no assertion criteria provided
Uncertain significance
(Jan 21, 2008) 		unknowncuration

PubMed (2)
[See all records that cite these PMIDs]

SCV004101600Centre for Population Genomics, CPG
criteria provided, single submitter

(McKnight et al. (Hum Mutat. 2022))		Uncertain significance
(Oct 12, 2023) 		germlinecuration

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

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes2not providednot provided2not providedcuration
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Mutation screening in Rett syndrome patients.

Xiang F, Buervenich S, Nicolao P, Bailey ME, Zhang Z, Anvret M.

J Med Genet. 2000 Apr;37(4):250-5.

PubMed [citation]
PMID:
10745042
PMCID:
PMC1734556

Spectrum and distribution of MECP2 mutations in 424 Rett syndrome patients: a molecular update.

Philippe C, Villard L, De Roux N, Raynaud M, Bonnefond JP, Pasquier L, Lesca G, Mancini J, Jonveaux P, Moncla A, Chelly J, Bienvenu T.

Eur J Med Genet. 2006 Jan-Feb;49(1):9-18.

PubMed [citation]
PMID:
16473305
See all PubMed Citations (3)

Details of each submission

From RettBASE, SCV000188039.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedcuration PubMed (2)
2not provided1not providednot providedcuration PubMed (2)

Description

"Rett syndrome - not certain"

PubMed [ID: 10745042]

"Rett syndrome - Not certain"

PubMed [ID: 16473305]

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyes1bloodnot provided1not providednot providednot provided
2unknownyes1bloodnot provided1not providednot providednot provided

From Centre for Population Genomics, CPG, SCV004101600.1

#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 a variant of uncertain significance. At least the following criteria are met: Occurs in the well-characterized Methyl-DNA binding (MDB) functional domain of MECP2 (PM1). Computational prediction analysis tools suggests a deleterious impact (REVEL score >=0.75) (PP3). This variant is absent from gnomAD (PM2_Supporting). Has been observed in at least 2 individuals with phenotypes consistent with MECP2-related disease (PS4_Supporting, PMIDs: 10745042, 16473305).

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

Last Updated: Nov 20, 2023