ClinVar Genomic variation as it relates to human health
NM_001110792.2(MECP2):c.455C>T (p.Ala152Val)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001110792.2(MECP2):c.455C>T (p.Ala152Val)
Variation ID: 11823 Accession: VCV000011823.60
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: Xq28 X: 154031409 (GRCh38) [ NCBI UCSC ] X: 153296860 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Oct 20, 2024 Mar 8, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001110792.2:c.455C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001104262.1:p.Ala152Val missense NM_004992.4:c.419C>T MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_004983.1:p.Ala140Val missense NM_001316337.2:c.140C>T NP_001303266.1:p.Ala47Val missense NM_001369391.2:c.140C>T NP_001356320.1:p.Ala47Val missense NM_001369392.2:c.140C>T NP_001356321.1:p.Ala47Val missense NM_001369393.2:c.140C>T NP_001356322.1:p.Ala47Val missense NM_001369394.2:c.140C>T NP_001356323.1:p.Ala47Val missense NM_001386137.1:c.-142C>T 5 prime UTR NM_001386138.1:c.-142C>T 5 prime UTR NM_001386139.1:c.-142C>T 5 prime UTR NC_000023.11:g.154031409G>A NC_000023.10:g.153296860G>A NG_007107.3:g.110695C>T LRG_764:g.110695C>T LRG_764t1:c.455C>T LRG_764p1:p.Ala152Val LRG_764t2:c.419C>T LRG_764p2:p.Ala140Val P51608:p.Ala140Val AJ132917.1:c.419C>T - Protein change
- A140V, A152V, A47V
- Other names
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NM_001110792.2(MECP2):c.455C>T
p.Ala152Val
- Canonical SPDI
- NC_000023.11:154031408:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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Trans-Omics for Precision Medicine (TOPMed) 0.00000
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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MECP2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
1896 | 2224 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
|
- | RCV000020628.20 | |
Pathogenic (5) |
criteria provided, multiple submitters, no conflicts
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Mar 8, 2024 | RCV000012596.47 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Sep 10, 2015 | RCV000414791.10 | |
Pathogenic (1) |
criteria provided, single submitter
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Oct 13, 2023 | RCV000544176.16 | |
Pathogenic (1) |
criteria provided, single submitter
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Apr 3, 2020 | RCV001374894.9 | |
Pathogenic (1) |
criteria provided, single submitter
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Jul 3, 2018 | RCV001249626.12 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Jan 1, 2016 | RCV001197458.10 | |
Pathogenic/Likely pathogenic (10) |
criteria provided, multiple submitters, no conflicts
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Oct 1, 2021 | RCV000224266.40 | |
Pathogenic (1) |
criteria provided, single submitter
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Sep 29, 2022 | RCV002326676.10 | |
Pathogenic (1) |
no assertion criteria provided
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Jun 15, 2024 | RCV004734513.1 | |
Likely pathogenic (1) |
no assertion criteria provided
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- | RCV001004016.9 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Apr 20, 2020 | RCV001257756.9 | |
Pathogenic (1) |
criteria provided, single submitter
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May 23, 2022 | RCV002466399.9 | |
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Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Aug 26, 2014)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: not provided
Allele origin:
germline
|
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Accession: SCV000281580.1
First in ClinVar: Jun 08, 2016 Last updated: Jun 08, 2016 |
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Likely pathogenic
(Sep 10, 2015)
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criteria provided, single submitter
Method: clinical testing
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Downslanted palpebral fissures
Hearing impairment Intellectual disability Microcephaly Micrognathia Motor delay Postnatal growth retardation Stenosis of the external auditory canal
Affected status: yes
Allele origin:
unknown
|
Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV000492695.1
First in ClinVar: Jan 13, 2017 Last updated: Jan 13, 2017 |
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Pathogenic
(Apr 10, 2014)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
|
Eurofins Ntd Llc (ga)
Accession: SCV000202987.7
First in ClinVar: Jan 29, 2015 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 1
Sex: mixed
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Pathogenic
(Jul 03, 2018)
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criteria provided, single submitter
Method: clinical testing
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X-linked intellectual disability-psychosis-macroorchidism syndrome
Severe neonatal-onset encephalopathy with microcephaly Syndromic X-linked intellectual disability Lubs type Rett syndrome Autism, susceptibility to, X-linked 3
Affected status: yes
Allele origin:
germline
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Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital
Accession: SCV001423701.1
First in ClinVar: Jul 27, 2020 Last updated: Jul 27, 2020 |
Comment:
[ACMG/AMP: PS3, PM1, PM2, PS4_Moderate, PP1, PP3, PP5] This alteration is supported by well-established in vitro or in vivo functional studies to have a damaging … (more)
[ACMG/AMP: PS3, PM1, PM2, PS4_Moderate, PP1, PP3, PP5] This alteration is supported by well-established in vitro or in vivo functional studies to have a damaging effect on protein function or splicing [PS3], is located in a mutational hotspot and/or critical and well-established functional domain [PM1], is absent from or rarely observed in large-scale population databases [PM2], has previously been observed in multiple unrelated patients with the same phenotype [PS4_Moderate], has been shown to cosegregate with disease in multiple affected family members [PP1], is predicted to be damaging by multiple functional prediction tools [PP3], was reported as a pathogenic/likely pathogenic alteration by a reputable source (ClinVar or other correspondence from a clinical testing laboratory) [PP5]. (less)
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Pathogenic
(Oct 23, 2020)
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criteria provided, single submitter
Method: clinical testing
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not provided
(X-linked inheritance)
Affected status: yes
Allele origin:
germline
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Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001447675.1
First in ClinVar: Nov 28, 2020 Last updated: Nov 28, 2020 |
Clinical Features:
Intellectual disability (present) , Global developmental delay (present) , Obesity (present)
Sex: female
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Likely pathogenic
(Jan 01, 2016)
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criteria provided, single submitter
Method: clinical testing
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Autism, susceptibility to, X-linked 3
Affected status: yes
Allele origin:
unknown
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Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV001368203.2
First in ClinVar: Jul 06, 2020 Last updated: Jul 06, 2020 |
Comment:
This variant was classified as: Likely pathogenic.
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Pathogenic
(Apr 03, 2020)
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criteria provided, single submitter
Method: clinical testing
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Neurodevelopmental disorder
Affected status: yes
Allele origin:
germline
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Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes
Accession: SCV001572181.1
First in ClinVar: May 01, 2021 Last updated: May 01, 2021 |
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Likely pathogenic
(Dec 07, 2018)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
maternal
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Laboratoire Génétique Moléculaire, CHRU TOURS
Accession: SCV001760753.1
First in ClinVar: Jul 24, 2021 Last updated: Jul 24, 2021 |
Clinical Features:
Intellectual disability (present) , Reading disability (present) , Autistic behavior (present) , Sleep disturbance (present) , Feeding difficulties (present)
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Pathogenic
(May 23, 2022)
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criteria provided, single submitter
Method: clinical testing
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Syndromic X-linked intellectual disability Lubs type
(X-linked recessive inheritance)
Affected status: yes
Allele origin:
germline
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Genetics and Molecular Pathology, SA Pathology
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002761554.1
First in ClinVar: Dec 17, 2022 Last updated: Dec 17, 2022 |
Comment:
The MECP2 c.455C>T variant is classified as PATHOGENIC (PS4, PP1_strong, PM2, PP3) The MECP2 c.455C>T variant is a single nucleotide change in exon 3/3 of … (more)
The MECP2 c.455C>T variant is classified as PATHOGENIC (PS4, PP1_strong, PM2, PP3) The MECP2 c.455C>T variant is a single nucleotide change in exon 3/3 of the MECP2 gene, which is predicted to change the amino acid alanine at position 152 in the protein to valine. This recurrent variant has been reported in multiple individuals with a clinical presentation of X-linked syndromic Intellectual disability or non-classic Rett phenotype (PS4). This variant has been reported in dbSNP (rs28934908) but is absent from population databases (PM2). This variant has been reported to co-segregate with disease in a large number of individuals in multiple families (PMID:11007980, PMID:26350204, PMID:25473036, PMID:27465203, PMID:12325019) (PP1_strong). Computational predictions support a deleterious effect on the gene or gene product (PP3). This variant has been reported in ClinVar as Pathogenic / Likely Pathogenic by other diagnostic laboratories (ClinVar Variation ID: 11823) and is classified as damaging in the HGMD disease database (CM003325). (less)
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Rett syndrome
(X-linked dominant inheritance)
Affected status: yes
Allele origin:
germline
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Lifecell International Pvt. Ltd
Accession: SCV003923342.1
First in ClinVar: May 13, 2023 Last updated: May 13, 2023 |
Comment:
A Hemizygote Missense variant c.419C>T in Exon 4 of the MECP2 gene that results in the amino acid substitution p.Ala140Val was identified. The observed variant … (more)
A Hemizygote Missense variant c.419C>T in Exon 4 of the MECP2 gene that results in the amino acid substitution p.Ala140Val was identified. The observed variant has a minor allele frequency of 0.0 % in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is medium, based on the effect of the protein and REVEL score. Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as PathogenicLikelyPathogenic(Variation ID: 11823). The variant has been previously reported by Winnepenninckx B, et al., 2002. Experimental study by Agarwal N, et al., 2011 showed MECP2 mutants affected in heterochromatin accumulation further exhibited the shortest residence time on heterochromatin, and their dysfunction lead to Rett syndrome. Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines. (less)
Ethnicity/Population group: Asian
Geographic origin: India
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Pathogenic
(Mar 08, 2024)
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criteria provided, single submitter
Method: curation
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X-linked intellectual disability-psychosis-macroorchidism syndrome
(X-linked inheritance)
Affected status: unknown
Allele origin:
germline
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Centre for Population Genomics, CPG
Accession: SCV004808968.1
First in ClinVar: Apr 06, 2024 Last updated: Apr 06, 2024 |
Comment:
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 … (more)
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: Has been observed in at least 5 individuals with phenotypes consistent with MECP2-related disease (PS4). (PMID: 11309367, 30536762, 11007980, 11885030, ClinVar Variation ID: 11823) Co-segregation with disease in multiple affected family members (3-4 informative meiosis) informative meiosis (PP1_Moderate). (PMID: 11007980, 11885030) Occurs in the well-characterized Methyl-DNA binding (MDB) functional domain of MECP2 (PM1). Computational prediction analysis tools suggests a deleterious impact (REVEL score>= 0.75) (PP3). This variant is absent from gnomAD (PM2_Supporting). (less)
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Pathogenic
(Sep 29, 2022)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002629906.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The c.419C>T (p.A140V) alteration is located in exon 4 (coding exon 3) of the MECP2 gene. This alteration results from a C to T substitution … (more)
The c.419C>T (p.A140V) alteration is located in exon 4 (coding exon 3) of the MECP2 gene. This alteration results from a C to T substitution at nucleotide position 419, causing the alanine (A) at amino acid position 140 to be replaced by a valine (V)._x000D_ _x000D_ Based on the available evidence, the MECP2 c.419C>T (p.A140V) alteration is classified as pathogenic for X-linked recessive MECP2-related neurodevelopmental disorder; however, this variant is unlikely to be causative of X-linked dominant typical RTT, atypical RTT, or neonatal severe encephalopathy. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been detected in numerous individuals and families with affected males demonstrating moderate to severe intellectual disability and movement disorders, and carrier females showing mild intellectual disability or who appear to be unaffected (Orrico, 2000; Couvert, 2001; Lambert, 2016). In addition, co-segregation with clinical findings has been described across multiple families (Orrico, 2000; Winnepenninckx, 2002; Lambert, 2016). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. (less)
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Pathogenic
(-)
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criteria provided, single submitter
Method: research
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Rett syndrome
(X-linked inheritance)
Affected status: yes
Allele origin:
unknown
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TIDEX, University of British Columbia
Accession: SCV000586832.1
First in ClinVar: May 03, 2018 Last updated: May 03, 2018 |
Sex: male
|
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Pathogenic
(Sep 22, 2017)
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criteria provided, single submitter
Method: clinical testing
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X-linked intellectual disability-psychosis-macroorchidism syndrome
Affected status: unknown
Allele origin:
maternal
|
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000782728.1
First in ClinVar: Feb 03, 2017 Last updated: Feb 03, 2017 |
|
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Likely pathogenic
(Apr 20, 2020)
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criteria provided, single submitter
Method: clinical testing
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Intellectual disability
(X-linked inheritance)
Affected status: yes
Allele origin:
maternal
|
Diagnostic Laboratory, Strasbourg University Hospital
Accession: SCV001434568.1
First in ClinVar: Oct 03, 2020 Last updated: Oct 03, 2020 |
Clinical Features:
Dysmorphic features (present) , slight intellectual disability (present) , hypotonia (present) , cerebellar ataxia (present) , autistic disturbances (present) , normal MRI (present) , Slight … (more)
Dysmorphic features (present) , slight intellectual disability (present) , hypotonia (present) , cerebellar ataxia (present) , autistic disturbances (present) , normal MRI (present) , Slight synophris (present) , distal ligamentous laxity (present) , delayed sitting (14 months old) (present) , delayed walking (18 months old) (present) , normal language (present) , Drugs-induced sleep disorders (present) , attention deficit (present) , Tourette's syndrome (present) , obsessive-compulsive disorder (present) (less)
Family history: no
Age: 10-19 years
Sex: male
Tissue: blood
Method: targeted capture
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Pathogenic
(Jul 17, 2020)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV001823566.1
First in ClinVar: Sep 08, 2021 Last updated: Sep 08, 2021 |
Comment:
Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does … (more)
Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 30542205, 33144682, 32581362, 32371413, 12325019, 27465203, 24328834, 25473036, 29431277, 30536762, 31273722, 11885030, 11007980, 26418480, 26350204, 11805248, 27929079, 12843318, 21831886) (less)
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Pathogenic
(Nov 04, 2022)
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criteria provided, single submitter
Method: clinical testing
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X-linked intellectual disability-psychosis-macroorchidism syndrome
Affected status: yes
Allele origin:
maternal
|
Eurofins-Biomnis
Accession: SCV003935107.1
First in ClinVar: Jun 24, 2023 Last updated: Jun 24, 2023 |
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Pathogenic
(Jul 05, 2023)
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criteria provided, single submitter
Method: clinical testing
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X-linked intellectual disability-psychosis-macroorchidism syndrome
(X-linked recessive inheritance)
Affected status: yes
Allele origin:
maternal
|
Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV004027691.1
First in ClinVar: Aug 26, 2023 Last updated: Aug 26, 2023 |
Comment:
Criteria applied: PS4,PM5_STR,PS2_MOD,PM2_SUP,PP2,PP3
Clinical Features:
Tall stature (present) , Obesity (present) , Global developmental delay (present) , Gynecomastia (present) , Long face (present) , Long philtrum (present)
Sex: male
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Pathogenic
(Oct 13, 2023)
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criteria provided, single submitter
Method: clinical testing
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Severe neonatal-onset encephalopathy with microcephaly
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000645665.7
First in ClinVar: Dec 26, 2017 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 140 of the MECP2 protein (p.Ala140Val). … (more)
This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 140 of the MECP2 protein (p.Ala140Val). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with neurodevelopmental disorders (PMID: 11007980, 12325019, 25473036, 26350204, 27465203). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 11823). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt MECP2 protein function. Experimental studies have shown that this missense change does not substantially affect MECP2 function (PMID: 12843318, 21831886, 26418480). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Oct 01, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV002063369.20
First in ClinVar: Jan 29, 2022 Last updated: Oct 20, 2024 |
Number of individuals with the variant: 1
|
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Likely pathogenic
(-)
|
no assertion criteria provided
Method: research
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Atypical behavior
Affected status: yes
Allele origin:
unknown
|
NIHR Bioresource Rare Diseases, University of Cambridge
Accession: SCV001162077.1
First in ClinVar: Feb 27, 2020 Last updated: Feb 27, 2020 |
Number of individuals with the variant: 1
Sex: female
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Pathogenic
(Oct 01, 2002)
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no assertion criteria provided
Method: literature only
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INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED, SYNDROMIC 13
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000032831.4
First in ClinVar: Apr 04, 2013 Last updated: Aug 21, 2021 |
Comment on evidence:
In an adult mother and daughter with mildly impaired intellectual development, speech difficulties, and gait disturbances, Orrico et al. (2000) identified a 493C-T transition in … (more)
In an adult mother and daughter with mildly impaired intellectual development, speech difficulties, and gait disturbances, Orrico et al. (2000) identified a 493C-T transition in the MECP2 gene, resulting in an ala140-to-val (A140V) substitution in a highly conserved region in the alpha helix of the methyl-CpG binding domain. Four of the mother's adult sons who inherited the mutation had severe mental retardation, impaired language development, and movement disorders with tremor and bradykinesia (MRXS13; 300055). The mutation was not present in the normal father or in 300 X chromosomes from normal individuals. The pattern of X-chromosome inactivation in the mother and daughter were close to random. The authors suggested that missense mutations such as A140V may correlate with milder disease than those resulting from truncating mutations, possibly through the presence of residual protein function. Dotti et al. (2002) reviewed the clinical findings of the family reported by Orrico et al. (2000) and noted that although the mental retardation and neurologic signs were more pronounced in the men than in the women, the women did demonstrate abnormalities. Features present in all 6 family members included slowly progressive spastic paraparesis/pyramidal signs, distal atrophy of the legs, and mild dysmorphic features. In 2 males with nonspecific sporadic mental retardation, Couvert et al. (2001) identified the A140V mutation. No other clinical details were provided. Winnepenninckx et al. (2002) identified the A140V mutation in 5 affected males from a large kindred with X-linked mental retardation, which the authors designated MRX79 (300055). Variable clinical features included delayed psychomotor development, tremor, mood instability, and hyperkinetic behavior. Four carrier females in the family appeared to be unaffected. Winnepenninckx et al. (2002) referred to several other reports of the A140V mutation and estimated that this mutation occurs in approximately 1% of all X-linked mental retardation families. Klauck et al. (2002) identified the A140V mutation in affected members of a pedigree with mental retardation associated with psychosis, pyramidal signs, and macroorchidism, designated PPMX, and consistent with MRXS13. They pointed out that there had been independent reports of 2 patients with familial mental retardation and 2 patients with sporadic mental retardation caused by this mutation in the MECP2 gene. They suggested that A140V is a hotspot for mutation, resulting in moderate to severe mental retardation in males. They designed a simple and reliable PCR approach for detection of the A140V mutation as a prescreen in unexplained cases of mental retardation before further extensive mutation analyses. Cohen et al. (2002) identified the A140V mutation in a boy with a developmental language disorder and onset of psychosis and childhood schizophrenia (see 300055) at age 12 years. His unaffected mother also carried the mutation. The report expanded the phenotypic spectrum of males with the A140V mutation. Villard (2007) stated that the A140V mutation had never been reported in a girl with classic Rett syndrome (312750), suggesting that it results in serious disorders only when present in male patients. (less)
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001808146.1 First in ClinVar: Aug 27, 2021 Last updated: Aug 27, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001742501.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001969847.1 First in ClinVar: Oct 08, 2021 Last updated: Oct 08, 2021 |
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Likely pathogenic
(Apr 26, 2016)
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no assertion criteria provided
Method: research
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Rett syndrome
Affected status: unknown
Allele origin:
germline
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RettBASE
Accession: SCV000188092.3
First in ClinVar: Aug 15, 2014 Last updated: Jan 30, 2017 |
Number of individuals with the variant: 28
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Pathogenic
(Apr 17, 2023)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
unknown
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Genetics and Genomic Medicine Centre, NeuroGen Healthcare, NeuroGen Healthcare
Accession: SCV004175157.1
First in ClinVar: Jun 17, 2024 Last updated: Jun 17, 2024 |
Clinical Features:
delayed speech and language development (present) , autism (present) , behavioral abnormality (present) , abnormal facial shape (present)
Age: 0-9 years
Sex: female
Ethnicity/Population group: South East Asian
Geographic origin: Bangladesh
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Pathogenic
(Jun 15, 2024)
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no assertion criteria provided
Method: clinical testing
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MECP2-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV005360864.1
First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024 |
Comment:
The MECP2 c.419C>T variant is predicted to result in the amino acid substitution p.Ala140Val. This variant has been reported in several patients to be causative … (more)
The MECP2 c.419C>T variant is predicted to result in the amino acid substitution p.Ala140Val. This variant has been reported in several patients to be causative for X-linked intellectual disability with variable neurobehavioral and dysmorphic features (see for example, Orrico et al. 2000. PubMed ID: 11007980; Sheik et al. 2016. PubMed ID: 27929079; Lambert et al. 2016. PubMed ID: 27465203; Venkateswaran et al. 2014. PubMed ID: 24328834). In vitro functional studies demonstrate this variant affects MECP2 function (Nan et al. 2007. PubMed ID: 17296936; Sheikh et al. 2016. PubMed ID: 27929079) and a mouse model demonstrates this variant disrupts neuronal signaling. This variant has not been reported in a large population database, indicating this variant is rare. Taken together, this variant is interpreted as pathogenic. (less)
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not provided
(-)
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no classification provided
Method: literature only
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Rett syndrome
Affected status: unknown
Allele origin:
germline
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GeneReviews
Accession: SCV000041141.3
First in ClinVar: Apr 04, 2013 Last updated: Oct 01, 2022 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Whole-genome sequencing of patients with rare diseases in a national health system. | Turro E | Nature | 2020 | PMID: 32581362 |
MECP2 Disorders. | Adam MP | - | 2019 | PMID: 20301670 |
From Function to Phenotype: Impaired DNA Binding and Clustering Correlates with Clinical Severity in Males with Missense Mutations in MECP2. | Sheikh TI | Scientific reports | 2016 | PMID: 27929079 |
Expanding phenotype of p.Ala140Val mutation in MECP2 in a 4 generation family with X-linked intellectual disability and spasticity. | Lambert S | European journal of medical genetics | 2016 | PMID: 27465203 |
Impact of Rett Syndrome Mutations on MeCP2 MBD Stability. | Kucukkal TG | Biochemistry | 2015 | PMID: 26418480 |
Targeted Next-Generation Sequencing Analysis of 1,000 Individuals with Intellectual Disability. | Grozeva D | Human mutation | 2015 | PMID: 26350204 |
Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders. | Soden SE | Science translational medicine | 2014 | PMID: 25473036 |
Adolescent onset cognitive regression and neuropsychiatric symptoms associated with the A140V MECP2 mutation. | Venkateswaran S | Developmental medicine and child neurology | 2014 | PMID: 24328834 |
MeCP2 Rett mutations affect large scale chromatin organization. | Agarwal N | Human molecular genetics | 2011 | PMID: 21831886 |
MECP2 mutations in males. | Villard L | Journal of medical genetics | 2007 | PMID: 17351020 |
MECP2 gene mutations in non-syndromic X-linked mental retardation: phenotype-genotype correlation. | Gomot M | American journal of medical genetics. Part A | 2003 | PMID: 14598336 |
Heterogeneity in residual function of MeCP2 carrying missense mutations in the methyl CpG binding domain. | Kudo S | Journal of medical genetics | 2003 | PMID: 12843318 |
Identification of a family with nonspecific mental retardation (MRX79) with the A140V mutation in the MECP2 gene: is there a need for routine screening? | Winnepenninckx B | Human mutation | 2002 | PMID: 12325019 |
A mutation hot spot for nonspecific X-linked mental retardation in the MECP2 gene causes the PPM-X syndrome. | Klauck SM | American journal of human genetics | 2002 | PMID: 11885030 |
A Rett syndrome MECP2 mutation that causes mental retardation in men. | Dotti MT | Neurology | 2002 | PMID: 11805248 |
MECP2 mutation in a boy with language disorder and schizophrenia. | Cohen D | The American journal of psychiatry | 2002 | PMID: 11772708 |
MECP2 is highly mutated in X-linked mental retardation. | Couvert P | Human molecular genetics | 2001 | PMID: 11309367 |
Two affected boys in a Rett syndrome family: clinical and molecular findings. | Villard L | Neurology | 2000 | PMID: 11071498 |
MECP2 mutation in male patients with non-specific X-linked mental retardation. | Orrico A | FEBS letters | 2000 | PMID: 11007980 |
http://mecp2.chw.edu.au/ | - | - | - | - |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=MECP2 | - | - | - | - |
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/a721e9a7-c375-4aba-8ac5-5c2562bba553 | - | - | - | - |
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Text-mined citations for rs28934908 ...
HelpRecord last updated Nov 03, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.