NM_001110792.2(MECP2):c.551C>T (p.Pro184Leu) AND Rett syndrome

Germline classification:: Benign (1 submission)
Last evaluated:: Mar 14, 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:: RCV003990988.1

Allele description [Variation Report for NM_001110792.2(MECP2):c.551C>T (p.Pro184Leu)]

NM_001110792.2(MECP2):c.551C>T (p.Pro184Leu)

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.551C>T (p.Pro184Leu)

Other names:

NM_001110792.2(MECP2):c.551C>T; p.Pro184Leu

HGVS:

NC_000023.11:g.154031313G>A
NG_007107.3:g.110791C>T
NM_001110792.2:c.551C>TMANE SELECT
NM_001316337.2:c.236C>T
NM_001369391.2:c.236C>T
NM_001369392.2:c.236C>T
NM_001369393.2:c.236C>T
NM_001369394.2:c.236C>T
NM_001386137.1:c.-128-27C>T
NM_001386138.1:c.-128-27C>T
NM_001386139.1:c.-128-27C>T
NM_004992.4:c.515C>T
NP_001104262.1:p.Pro184Leu
NP_001303266.1:p.Pro79Leu
NP_001356320.1:p.Pro79Leu
NP_001356321.1:p.Pro79Leu
NP_001356322.1:p.Pro79Leu
NP_001356323.1:p.Pro79Leu
NP_004983.1:p.Pro172Leu
NP_004983.1:p.Pro172Leu
LRG_764t1:c.551C>T
LRG_764t2:c.515C>T
AJ132917.1:c.515C>T
LRG_764:g.110791C>T
LRG_764p1:p.Pro184Leu
LRG_764p2:p.Pro172Leu
NC_000023.10:g.153296764G>A
NG_007107.2:g.110815C>T
NM_004992.3:c.515C>T

Protein change:

P172L

Links:

dbSNP: rs267608491

NCBI 1000 Genomes Browser:

rs267608491

Molecular consequence:

NM_001386137.1:c.-128-27C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001386138.1:c.-128-27C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001386139.1:c.-128-27C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001110792.2:c.551C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001316337.2:c.236C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369391.2:c.236C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369392.2:c.236C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369393.2:c.236C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369394.2:c.236C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_004992.4:c.515C>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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SGPP2 [Geospiza fortis]
SGPP2 [Geospiza fortis]
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004809021	Centre for Population Genomics, CPG	criteria provided, single submitter (McKnight et al. (Hum Mutat. 2022))	Benign (Mar 14, 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

SCV004809021

Centre for Population Genomics, CPG

criteria provided, single submitter

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

Benign
(Mar 14, 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	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation

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 Centre for Population Genomics, CPG, SCV004809021.1

#	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 benign. At least the following criteria are met: The variant is observed in at least 1 individual with no features of Rett Syndrome (BS2_Supporting). (RettBASE ID 4180) The allele frequency of this variant in at least one population in gnomAD is between 0.008% and 0.03% (BS1).

#	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: Nov 3, 2024

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