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NM_001110792.2(MECP2):c.940C>T (p.Pro314Ser) AND Rett syndrome

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Mar 25, 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:
RCV000133278.11

Allele description [Variation Report for NM_001110792.2(MECP2):c.940C>T (p.Pro314Ser)]

NM_001110792.2(MECP2):c.940C>T (p.Pro314Ser)

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.940C>T (p.Pro314Ser)
Other names:
NM_001110792.2(MECP2):c.940C>T; p.Pro314Ser
HGVS:
  • NC_000023.11:g.154030924G>A
  • NG_007107.3:g.111180C>T
  • NM_001110792.2:c.940C>TMANE SELECT
  • NM_001316337.2:c.625C>T
  • NM_001369391.2:c.625C>T
  • NM_001369392.2:c.625C>T
  • NM_001369393.2:c.625C>T
  • NM_001369394.2:c.625C>T
  • NM_001386137.1:c.235C>T
  • NM_001386138.1:c.235C>T
  • NM_001386139.1:c.235C>T
  • NM_004992.4:c.904C>T
  • NP_001104262.1:p.Pro314Ser
  • NP_001303266.1:p.Pro209Ser
  • NP_001356320.1:p.Pro209Ser
  • NP_001356321.1:p.Pro209Ser
  • NP_001356322.1:p.Pro209Ser
  • NP_001356323.1:p.Pro209Ser
  • NP_001373066.1:p.Pro79Ser
  • NP_001373067.1:p.Pro79Ser
  • NP_001373068.1:p.Pro79Ser
  • NP_004983.1:p.Pro302Ser
  • NP_004983.1:p.Pro302Ser
  • LRG_764t1:c.940C>T
  • LRG_764t2:c.904C>T
  • AJ132917.1:c.904C>T
  • LRG_764:g.111180C>T
  • LRG_764p1:p.Pro314Ser
  • LRG_764p2:p.Pro302Ser
  • NC_000023.10:g.153296375G>A
  • NG_007107.2:g.111204C>T
  • NM_004992.3:c.904C>T
Protein change:
P209S
Links:
dbSNP: rs61751373
NCBI 1000 Genomes Browser:
rs61751373
Molecular consequence:
  • NM_001110792.2:c.940C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001316337.2:c.625C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369391.2:c.625C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369392.2:c.625C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369393.2:c.625C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369394.2:c.625C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001386137.1:c.235C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001386138.1:c.235C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001386139.1:c.235C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004992.4:c.904C>T - 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
SCV000188286RettBASE
no assertion criteria provided
Uncertain significance
(Nov 1, 2007) 		unknowncuration

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

SCV004808900Centre for Population Genomics, CPG
criteria provided, single submitter

(McKnight et al. (Hum Mutat. 2022))		Likely pathogenic
(Mar 25, 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 provided1Nocuration
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Mutation analysis of the MECP2 gene in patients of Slavic origin with Rett syndrome: novel mutations and polymorphisms.

Zahorakova D, Rosipal R, Hadac J, Zumrova A, Bzduch V, Misovicova N, Baxova A, Zeman J, Martasek P.

J Hum Genet. 2007;52(4):342-348. doi: 10.1007/s10038-007-0121-x. Epub 2007 Feb 15.

PubMed [citation]
PMID:
17387578

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, SCV000188286.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providedNocuration PubMed (1)

Description

"Rett syndrome - Classical"

PubMed [ID: 17387578]

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

From Centre for Population Genomics, CPG, SCV004808900.1

#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 Transcriptional repression domain (TRD) 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). 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 17387578 ClinVar Variation ID: 143735) .

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

Last Updated: Nov 10, 2024