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NM_001110792.2(MECP2):c.518G>A (p.Gly173Glu) AND Rett syndrome

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Mar 18, 2024
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:
RCV000133136.3

Allele description [Variation Report for NM_001110792.2(MECP2):c.518G>A (p.Gly173Glu)]

NM_001110792.2(MECP2):c.518G>A (p.Gly173Glu)

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.518G>A (p.Gly173Glu)
Other names:
NM_001110792.2(MECP2):c.518G>A; p.Gly173Glu
HGVS:
  • NC_000023.11:g.154031346C>T
  • NG_007107.3:g.110758G>A
  • NM_001110792.2:c.518G>AMANE SELECT
  • NM_001316337.2:c.203G>A
  • NM_001369391.2:c.203G>A
  • NM_001369392.2:c.203G>A
  • NM_001369393.2:c.203G>A
  • NM_001369394.2:c.203G>A
  • NM_001386137.1:c.-129+50G>A
  • NM_001386138.1:c.-129+50G>A
  • NM_001386139.1:c.-129+50G>A
  • NM_004992.4:c.482G>A
  • NP_001104262.1:p.Gly173Glu
  • NP_001303266.1:p.Gly68Glu
  • NP_001356320.1:p.Gly68Glu
  • NP_001356321.1:p.Gly68Glu
  • NP_001356322.1:p.Gly68Glu
  • NP_001356323.1:p.Gly68Glu
  • NP_004983.1:p.Gly161Glu
  • NP_004983.1:p.Gly161Glu
  • LRG_764t1:c.518G>A
  • LRG_764t2:c.482G>A
  • AJ132917.1:c.482G>A
  • LRG_764:g.110758G>A
  • LRG_764p1:p.Gly173Glu
  • LRG_764p2:p.Gly161Glu
  • NC_000023.10:g.153296797C>T
  • NG_007107.2:g.110782G>A
  • NM_004992.3:c.482G>A
Protein change:
G161E
Links:
dbSNP: rs61748417
NCBI 1000 Genomes Browser:
rs61748417
Molecular consequence:
  • NM_001386137.1:c.-129+50G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001386138.1:c.-129+50G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001386139.1:c.-129+50G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001110792.2:c.518G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001316337.2:c.203G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369391.2:c.203G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369392.2:c.203G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369393.2:c.203G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369394.2:c.203G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004992.4:c.482G>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
SCV000188128RettBASE
no assertion criteria provided
Uncertain significance
(Nov 1, 2007) 		unknowncuration

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

SCV004808831Centre for Population Genomics, CPG
criteria provided, single submitter

(McKnight et al. (Hum Mutat. 2022))		Likely pathogenic
(Mar 18, 2024) 		germlinecuration

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

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot provided1not providedcuration
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Diagnostic mutational analysis of MECP2 in Korean patients with Rett syndrome.

Kim IJ, Kim YJ, Son BH, Nam SO, Kang HC, Kim HD, Yoo MA, Choi OH, Kim CM.

Exp Mol Med. 2006 Apr 30;38(2):119-25.

PubMed [citation]
PMID:
16672765

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 RettBASE, SCV000188128.2

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

Description

"Rett syndrome - classical"

PubMed [ID: 16672765]

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

From Centre for Population Genomics, CPG, SCV004808831.1

#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 3.0, this variant is classified as likely pathogenic. At least the following criteria are met: Occurs in the well-characterized Methyl-DNA binding (MDB) functional domain of MECP2 (PM1). Another missense variant in the same codon has been classified as pathogenic (PM5) Computational prediction analysis tools suggests a deleterious impact (REVEL score>= 0.75) (PP3). At least one individual with this variant has been reported with a clinical phenotype consistent with Rett syndrome (PP4). (16672765, 35606502) This variant is absent from gnomAD (PM2_Supporting).

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

Last Updated: Apr 15, 2024