NM_001110792.2(MECP2):c.1195_1494del (p.Pro399_Ser498del) AND Rett syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jan 16, 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:: RCV000170147.3

Allele description [Variation Report for NM_001110792.2(MECP2):c.1195_1494del (p.Pro399_Ser498del)]

NM_001110792.2(MECP2):c.1195_1494del (p.Pro399_Ser498del)

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.1195_1494del (p.Pro399_Ser498del)

Other names:

NM_001110792.2(MECP2):c.1195_1494del; p.Pro399_Ser498del

HGVS:

NC_000023.11:g.154030370_154030669del
NG_007107.3:g.111435_111734del
NM_001110792.2:c.1195_1494delMANE SELECT
NM_001316337.2:c.880_1179del
NM_001369391.2:c.880_1179del
NM_001369392.2:c.880_1179del
NM_001369393.2:c.880_1179del
NM_001369394.2:c.880_1179del
NM_001386137.1:c.490_789del
NM_001386138.1:c.490_789del
NM_001386139.1:c.490_789del
NM_004992.4:c.1159_1458del
NP_001104262.1:p.Pro399_Ser498del
NP_001303266.1:p.Pro294_Ser393del
NP_001356320.1:p.Pro294_Ser393del
NP_001356321.1:p.Pro294_Ser393del
NP_001356322.1:p.Pro294_Ser393del
NP_001356323.1:p.Pro294_Ser393del
NP_001373066.1:p.Pro164_Ser263del
NP_001373067.1:p.Pro164_Ser263del
NP_001373068.1:p.Pro164_Ser263del
NP_004983.1:p.Pro387_Ser486del
LRG_764t1:c.1195_1494del
LRG_764t2:c.1159_1458del
LRG_764:g.111435_111734del
LRG_764p1:p.Pro399_Ser498del
LRG_764p2:p.Pro387_Ser486del
NC_000023.10:g.153295821_153296120del
NG_007107.2:g.111459_111758del
NM_004992.3:c.1159_1458del300

Links:

dbVar: nssv7487077; dbVar: nsv1197469; dbSNP: rs1557134858

NCBI 1000 Genomes Browser:

rs1557134858

Molecular consequence:

NM_001110792.2:c.1195_1494del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001316337.2:c.880_1179del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001369391.2:c.880_1179del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001369392.2:c.880_1179del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001369393.2:c.880_1179del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001369394.2:c.880_1179del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001386137.1:c.490_789del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001386138.1:c.490_789del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001386139.1:c.490_789del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004992.4:c.1159_1458del - inframe_deletion - [Sequence Ontology: SO:0001822]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000222475	RettBASE	no assertion criteria provided	Pathogenic (Jan 21, 2008)	unknown	curation	PubMed (1) [See all records that cite this PMID]
SCV004232233	Centre for Population Genomics, CPG	criteria provided, single submitter (McKnight et al. (Hum Mutat. 2022))	Uncertain significance (Jan 16, 2024)	germline	curation	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000222475

RettBASE

no assertion criteria provided

Pathogenic
(Jan 21, 2008)

unknown

curation

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

SCV004232233

Centre for Population Genomics, CPG

criteria provided, single submitter

(McKnight et al. (Hum Mutat. 2022))

Uncertain significance
(Jan 16, 2024)

germline

curation

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

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	1	not provided	not provided	1	not provided	curation
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation

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

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, SCV000222475.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	curation	PubMed (1)

Description

"Rett syndrome - not certain"

PubMed [ID: 16473305]

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	1	blood	not provided		1	not provided	not provided	not provided

From Centre for Population Genomics, CPG, SCV004232233.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	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 a variant of uncertain significance. At least the following criteria are met: Protein length changes due to in-frame deletions/insertions (PM4). This variant is absent from gnomAD (PM2_Supporting).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

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