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NM_001110792.2(MECP2):c.516_517del (p.Gly173fs) AND Rett syndrome

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Jan 23, 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:
RCV000133133.3

Allele description [Variation Report for NM_001110792.2(MECP2):c.516_517del (p.Gly173fs)]

NM_001110792.2(MECP2):c.516_517del (p.Gly173fs)

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.516_517del (p.Gly173fs)
Other names:
NM_001110792.2(MECP2):c.516_517del; p.Gly173fs
HGVS:
  • NC_000023.11:g.154031347_154031348del
  • NG_007107.3:g.110756_110757del
  • NM_001110792.2:c.516_517delMANE SELECT
  • NM_001316337.2:c.201_202del
  • NM_001369391.2:c.201_202del
  • NM_001369392.2:c.201_202del
  • NM_001369393.2:c.201_202del
  • NM_001369394.2:c.201_202del
  • NM_001386137.1:c.-129+48_-129+49del
  • NM_001386138.1:c.-129+48_-129+49del
  • NM_001386139.1:c.-129+48_-129+49del
  • NM_004992.4:c.480_481del
  • NP_001104262.1:p.Gly173fs
  • NP_001303266.1:p.Gly68fs
  • NP_001356320.1:p.Gly68fs
  • NP_001356321.1:p.Gly68fs
  • NP_001356322.1:p.Gly68fs
  • NP_001356323.1:p.Gly68fs
  • NP_004983.1:p.Gly161fs
  • LRG_764t1:c.516_517del
  • LRG_764t2:c.480_481del
  • AJ132917.1:c.480_481delTG
  • LRG_764:g.110756_110757del
  • LRG_764p1:p.Gly173fs
  • LRG_764p2:p.Gly161fs
  • NC_000023.10:g.153296798_153296799del
  • NG_007107.2:g.110780_110781del
  • NM_004992.3:c.480_481delTG
Protein change:
G161fs
Links:
dbSNP: rs267608486
NCBI 1000 Genomes Browser:
rs267608486
Molecular consequence:
  • NM_001110792.2:c.516_517del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001316337.2:c.201_202del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369391.2:c.201_202del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369392.2:c.201_202del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369393.2:c.201_202del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369394.2:c.201_202del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004992.4:c.480_481del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001386137.1:c.-129+48_-129+49del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001386138.1:c.-129+48_-129+49del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001386139.1:c.-129+48_-129+49del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV000188125RettBASE
no assertion criteria provided
Pathogenic
(Apr 5, 2002) 		unknowncuration

SCV005040713Centre for Population Genomics, CPG
criteria provided, single submitter

(McKnight et al. (Hum Mutat. 2022))		Likely pathogenic
(Jan 23, 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 providedunknownyes1not providednot provided1Nocuration

Citations

PubMed

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, SCV000188125.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providedNocurationnot provided

Description

Rett syndrome - Atypical

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

From Centre for Population Genomics, CPG, SCV005040713.1

#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: May 7, 2024