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NM_001110792.2(MECP2):c.590del (p.Gly197fs) AND Rett syndrome

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Jan 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:
RCV000133159.3

Allele description [Variation Report for NM_001110792.2(MECP2):c.590del (p.Gly197fs)]

NM_001110792.2(MECP2):c.590del (p.Gly197fs)

Gene:
MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_001110792.2(MECP2):c.590del (p.Gly197fs)
Other names:
NM_001110792.2(MECP2):c.590del; p.Gly197fs
HGVS:
  • NC_000023.11:g.154031275del
  • NG_007107.3:g.110830del
  • NM_001110792.2:c.590delMANE SELECT
  • NM_001316337.2:c.275del
  • NM_001369391.2:c.275del
  • NM_001369392.2:c.275del
  • NM_001369393.2:c.275del
  • NM_001369394.2:c.275del
  • NM_001386137.1:c.-116del
  • NM_001386138.1:c.-116del
  • NM_001386139.1:c.-116del
  • NM_004992.4:c.554del
  • NP_001104262.1:p.Gly197fs
  • NP_001303266.1:p.Gly92fs
  • NP_001356320.1:p.Gly92fs
  • NP_001356321.1:p.Gly92fs
  • NP_001356322.1:p.Gly92fs
  • NP_001356323.1:p.Gly92fs
  • NP_004983.1:p.Gly185fs
  • LRG_764t1:c.590del
  • LRG_764t2:c.554del
  • AJ132917.1:c.554delG
  • LRG_764:g.110830del
  • LRG_764p1:p.Gly197fs
  • LRG_764p2:p.Gly185fs
  • NC_000023.10:g.153296726del
  • NG_007107.2:g.110854del
  • NM_004992.3:c.554delG
Protein change:
G185fs
Links:
dbSNP: rs61749707
NCBI 1000 Genomes Browser:
rs61749707
Molecular consequence:
  • NM_001386137.1:c.-116del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386138.1:c.-116del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386139.1:c.-116del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001110792.2:c.590del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001316337.2:c.275del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369391.2:c.275del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369392.2:c.275del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369393.2:c.275del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369394.2:c.275del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004992.4:c.554del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000188151RettBASE
no assertion criteria provided
Pathogenic
(Apr 10, 2002) 		unknowncuration

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

SCV004808993Centre for Population Genomics, CPG
criteria provided, single submitter

(McKnight et al. (Hum Mutat. 2022))		Likely pathogenic
(Jan 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 provided1not providedcuration
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Diagnostic testing for Rett syndrome by DHPLC and direct sequencing analysis of the MECP2 gene: identification of several novel mutations and polymorphisms.

Buyse IM, Fang P, Hoon KT, Amir RE, Zoghbi HY, Roa BB.

Am J Hum Genet. 2000 Dec;67(6):1428-36. Epub 2000 Oct 30.

PubMed [citation]
PMID:
11055898
PMCID:
PMC1287920

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, SCV000188151.2

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

Description

"Rett syndrome - Not certain"

PubMed [ID: 11055898]

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyes1not providednot provided1not providednot providednot provided

From Centre for Population Genomics, CPG, SCV004808993.1

#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: Predicted to result in loss of function, and LOF is a known mechanism of disease (PVS1). 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