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NM_001110792.2(MECP2):c.789C>T (p.Pro263=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 27, 2021)
Last evaluated:
Sep 3, 2020
Accession:
VCV000143686.9
Variation ID:
143686
Description:
single nucleotide variant
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NM_001110792.2(MECP2):c.789C>T (p.Pro263=)

Allele ID
153418
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 154031075 (GRCh38) GRCh38 UCSC
X: 153296526 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_764:g.111029C>T
LRG_764t1:c.789C>T LRG_764p1:p.Pro263=
LRG_764t2:c.753C>T LRG_764p2:p.Pro251=
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000023.11:154031074:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00026 (A)

Allele frequency
1000 Genomes Project 0.00026
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00009
The Genome Aggregation Database (gnomAD) 0.00013
Exome Aggregation Consortium (ExAC) 0.00018
The Genome Aggregation Database (gnomAD) 0.00005
Trans-Omics for Precision Medicine (TOPMed) 0.00014
The Genome Aggregation Database (gnomAD), exomes 0.00017
Trans-Omics for Precision Medicine (TOPMed) 0.00011
Links
ClinGen: CA170377
dbSNP: rs63582063
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Feb 15, 2019 RCV000133227.7
Benign 2 criteria provided, multiple submitters, no conflicts Dec 20, 2017 RCV000712284.4
Likely benign 1 criteria provided, single submitter Feb 8, 2016 RCV000719501.1
Benign 1 criteria provided, single submitter Sep 3, 2020 RCV001085738.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MECP2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1341 1603

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Apr 10, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000193640.2
Submitted: (Sep 15, 2015)
Evidence details
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000310762.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Dec 20, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000842735.1
Submitted: (Aug 31, 2018)
Evidence details
Publications
PubMed (4)
Benign
(Feb 15, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001362254.1
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (4)
Comment:
Variant summary: The variant, MECP2 c.753C>T results in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have … (more)
Likely benign
(Feb 08, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000850368.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, … (more)
Benign
(Sep 03, 2020)
criteria provided, single submitter
Method: clinical testing
Severe neonatal-onset encephalopathy with microcephaly
Allele origin: germline
Invitae
Accession: SCV000645676.4
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001941763.1
Submitted: (Sep 27, 2021)
Evidence details
Benign
(Nov 01, 2011)
no assertion criteria provided
Method: curation
Not specified
Allele origin: unknown
RettBASE
Accession: SCV000188227.2
Submitted: (Nov 21, 2014)
Evidence details

Functional evidence

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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 this variant

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Title Author Journal Year Link
Analysis of Hungarian patients with Rett syndrome phenotype for MECP2, CDKL5 and FOXG1 gene mutations. Hadzsiev K Journal of human genetics 2011 PMID: 21160487
Evaluation of CSF neurotransmitters and folate in 25 patients with Rett disorder and effects of treatment. Temudo T Brain & development 2009 PMID: 18572337
Comprehensive diagnosis of Rett's syndrome relying on genetic, epigenetic and expression evidence of deficiency of the methyl-CpG-binding protein 2 gene: study of a cohort of Israeli patients. Petel-Galil Y Journal of medical genetics 2006 PMID: 17142618
Influence of MECP2 gene mutation and X-chromosome inactivation on the Rett syndrome phenotype. Chae JH Journal of child neurology 2004 PMID: 15526954

Text-mined citations for rs63582063...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Dec 04, 2021