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NM_001110792.2(MECP2):c.732del (p.Lys245fs) AND Rett syndrome

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Jan 9, 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:
RCV000133205.5

Allele description [Variation Report for NM_001110792.2(MECP2):c.732del (p.Lys245fs)]

NM_001110792.2(MECP2):c.732del (p.Lys245fs)

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.732del (p.Lys245fs)
Other names:
NM_001110792.2(MECP2):c.732del; p.Lys245fs
HGVS:
  • NC_000023.11:g.154031132del
  • NG_007107.3:g.110972del
  • NM_001110792.2:c.732delMANE SELECT
  • NM_001316337.2:c.417del
  • NM_001369391.2:c.417del
  • NM_001369392.2:c.417del
  • NM_001369393.2:c.417del
  • NM_001369394.2:c.417del
  • NM_001386137.1:c.27del
  • NM_001386138.1:c.27del
  • NM_001386139.1:c.27del
  • NM_004992.4:c.696del
  • NP_001104262.1:p.Lys245fs
  • NP_001303266.1:p.Lys140fs
  • NP_001356320.1:p.Lys140fs
  • NP_001356321.1:p.Lys140fs
  • NP_001356322.1:p.Lys140fs
  • NP_001356323.1:p.Lys140fs
  • NP_001373066.1:p.Lys10fs
  • NP_001373067.1:p.Lys10fs
  • NP_001373068.1:p.Lys10fs
  • NP_004983.1:p.Lys233fs
  • NP_004983.1:p.Lys233fs
  • LRG_764t1:c.732del
  • LRG_764t2:c.696del
  • AJ132917.1:c.696delC
  • LRG_764:g.110972del
  • LRG_764p1:p.Lys245fs
  • LRG_764p2:p.Lys233fs
  • NC_000023.10:g.153296583del
  • NG_007107.2:g.110996del
  • NM_004992.3:c.696del
  • NM_004992.3:c.696delC
Protein change:
K10fs
Links:
dbSNP: rs61749741
NCBI 1000 Genomes Browser:
rs61749741
Molecular consequence:
  • NM_001110792.2:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001316337.2:c.417del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369391.2:c.417del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369392.2:c.417del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369393.2:c.417del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369394.2:c.417del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001386137.1:c.27del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001386138.1:c.27del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001386139.1:c.27del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004992.4:c.696del - 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
SCV000188203RettBASE
no assertion criteria provided
Pathogenic
(Dec 3, 2010) 		de novo, unknowncuration

PubMed (5)
[See all records that cite these PMIDs]

SCV004232232Centre for Population Genomics, CPG
criteria provided, single submitter

(McKnight et al. (Hum Mutat. 2022))		Pathogenic
(Jan 9, 2024) 		germlinecuration

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

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes2not providednot provided2not providedcuration
not providedde novoyes3not providednot provided3Nocuration
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Mutation analysis of the methyl-CpG binding protein 2 gene (MECP2) in patients with Rett syndrome.

Obata K, Matsuishi T, Yamashita Y, Fukuda T, Kuwajima K, Horiuchi I, Nagamitsu S, Iwanaga R, Kimura A, Omori I, Endo S, Mori K, Kondo I.

J Med Genet. 2000 Aug;37(8):608-10. No abstract available.

PubMed [citation]
PMID:
10991688
PMCID:
PMC1734655

DHPLC analysis of the MECP2 gene in Italian Rett patients.

Nicolao P, Carella M, Giometto B, Tavolato B, Cattin R, Giovannucci-Uzielli ML, Vacca M, Della Regione F, Piva S, Bortoluzzi S, Gasparini P.

Hum Mutat. 2001 Aug;18(2):132-40.

PubMed [citation]
PMID:
11462237
See all PubMed Citations (6)

Details of each submission

From RettBASE, SCV000188203.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedcuration PubMed (5)
2not provided1not providedNocuration PubMed (5)
3not provided1not providedNocuration PubMed (5)
4not provided1not providednot providedcuration PubMed (5)
5not provided1not providednot providedcuration PubMed (5)

Description

"Rett syndrome - not certain"

PubMed [ID: 10991688]

"Rett syndrome - classical"

PubMed [ID: 11462237]

"Rett syndrome - Classical"

PubMed [ID: 15737703]

"Rett syndrome - Classical"

PubMed [ID: 16473305]

"Rett syndrome - Classical"

PubMed [ID: 20031356]

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyes1bloodnot provided1not providednot providednot provided
2de novoyes1bloodnot provided1not providednot providednot provided
3de novoyes1not providednot provided1not providednot providednot provided
4de novoyes1Bloodnot provided1not providednot providednot provided
5unknownyes1bloodnot provided1not providednot providednot provided

From Centre for Population Genomics, CPG, SCV004232232.1

#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). Has been observed in at least 5 individuals with phenotypes consistent with MECP2-related disease (PS4). (PMID: 10991688‚ 15737703‚ 16473305‚11462237, 16225173, 20031356, 31327966, 19652677) This variant has been identified as a de novo occurrence in at least one individual with Rett syndrome without confirmation of paternity and maternity (PM6). PMID: 16225173, PMID: 11462237 This variant is absent from gnomAD (PM2_Supporting).

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

Last Updated: Oct 26, 2024