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NM_001110792.2(MECP2):c.418C>T (p.Gln140Ter) AND Rett syndrome

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Mar 14, 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:
RCV000133086.3

Allele description [Variation Report for NM_001110792.2(MECP2):c.418C>T (p.Gln140Ter)]

NM_001110792.2(MECP2):c.418C>T (p.Gln140Ter)

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.418C>T (p.Gln140Ter)
Other names:
NM_001110792.2(MECP2):c.418C>T; p.Gln140Ter
HGVS:
  • NC_000023.11:g.154031446G>A
  • NG_007107.3:g.110658C>T
  • NM_001110792.2:c.418C>TMANE SELECT
  • NM_001316337.2:c.103C>T
  • NM_001369391.2:c.103C>T
  • NM_001369392.2:c.103C>T
  • NM_001369393.2:c.103C>T
  • NM_001369394.2:c.103C>T
  • NM_001386137.1:c.-179C>T
  • NM_001386138.1:c.-179C>T
  • NM_001386139.1:c.-179C>T
  • NM_004992.4:c.382C>T
  • NP_001104262.1:p.Gln140Ter
  • NP_001303266.1:p.Gln35Ter
  • NP_001356320.1:p.Gln35Ter
  • NP_001356321.1:p.Gln35Ter
  • NP_001356322.1:p.Gln35Ter
  • NP_001356323.1:p.Gln35Ter
  • NP_004983.1:p.Gln128Ter
  • NP_004983.1:p.Gln128Ter
  • LRG_764t1:c.418C>T
  • LRG_764t2:c.382C>T
  • AJ132917.1:c.382C>T
  • LRG_764:g.110658C>T
  • LRG_764p1:p.Gln140Ter
  • LRG_764p2:p.Gln128Ter
  • NC_000023.10:g.153296897G>A
  • NG_007107.2:g.110682C>T
  • NM_004992.3:c.382C>T
Protein change:
Q128*
Links:
dbSNP: rs267608469
NCBI 1000 Genomes Browser:
rs267608469
Molecular consequence:
  • NM_001386137.1:c.-179C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386138.1:c.-179C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386139.1:c.-179C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001110792.2:c.418C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001316337.2:c.103C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001369391.2:c.103C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001369392.2:c.103C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001369393.2:c.103C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001369394.2:c.103C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_004992.4:c.382C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV000188075RettBASE
no assertion criteria provided
Pathogenic
(Sep 27, 2012) 		unknowncuration

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

SCV004809014Centre for Population Genomics, CPG
criteria provided, single submitter

(McKnight et al. (Hum Mutat. 2022))		Pathogenic
(Mar 14, 2024) 		germlinecuration

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

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration
not providedunknownyes2not providednot provided2Nocuration

Citations

PubMed

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

Genetic and epileptic features in Rett syndrome.

Kim HJ, Kim SH, Kim HD, Lee JS, Lee YM, Koo KY, Lee JS, Kang HC.

Yonsei Med J. 2012 May;53(3):495-500. doi: 10.3349/ymj.2012.53.3.495.

PubMed [citation]
PMID:
22476991
PMCID:
PMC3343433
See all PubMed Citations (3)

Details of each submission

From RettBASE, SCV000188075.2

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

Description

"Rett syndrome - not certain"

PubMed [ID: 16473305]

"Rett syndrome - not certain"

PubMed [ID: 22476991]

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

From Centre for Population Genomics, CPG, SCV004809014.1

#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 pathogenic. At least the following criteria are met: Predicted to result in loss of function, and LOF is a known mechanism of disease (PVS1). 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). PMID: 16473305, PMID: 22476991

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

Last Updated: Sep 29, 2024