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NM_001110792.2(MECP2):c.978C>T (p.Ile326=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Sep 19, 2021)
Last evaluated:
Nov 21, 2020
Accession:
VCV000143750.8
Variation ID:
143750
Description:
single nucleotide variant
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NM_001110792.2(MECP2):c.978C>T (p.Ile326=)

Allele ID
153482
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 154030886 (GRCh38) GRCh38 UCSC
X: 153296337 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
AJ132917.1:c.942C>T
NC_000023.11:g.154030886G>A
NG_007107.2:g.111242C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000023.11:154030885:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00079 (A)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00028
Trans-Omics for Precision Medicine (TOPMed) 0.00037
1000 Genomes Project 0.00079
The Genome Aggregation Database (gnomAD), exomes 0.00040
Exome Aggregation Consortium (ExAC) 0.00044
The Genome Aggregation Database (gnomAD) 0.00023
Links
ClinGen: CA170412
dbSNP: rs61751446
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 3 criteria provided, multiple submitters, no conflicts Jun 22, 2017 RCV000133295.7
Benign 1 criteria provided, single submitter Nov 21, 2020 RCV000472062.6
Benign 1 criteria provided, single submitter Jan 3, 2017 RCV000717800.1
Benign 1 criteria provided, single submitter Jul 7, 2020 RCV001682841.1
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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
1338 1600

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jan 03, 2017)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000848659.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Benign
(Jul 07, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001898751.1
Submitted: (Sep 19, 2021)
Evidence details
Benign
(Nov 21, 2020)
criteria provided, single submitter
Method: clinical testing
Severe neonatal-onset encephalopathy with microcephaly
Allele origin: germline
Invitae
Accession: SCV000556750.6
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jun 22, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000248008.2
Submitted: (Oct 04, 2017)
Evidence details
Likely benign
(May 04, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000341193.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Mar 29, 2011)
no assertion criteria provided
Method: curation
Not specified
Allele origin: unknown
RettBASE
Accession: SCV000188304.2
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
Systematic resequencing of X-chromosome synaptic genes in autism spectrum disorder and schizophrenia. Piton A Molecular psychiatry 2011 PMID: 20479760
Low frequency of MECP2 mutations in mentally retarded males. Yntema HG European journal of human genetics : EJHG 2002 PMID: 12111644
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=MECP2 - - - -

Text-mined citations for rs61751446...

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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 Nov 06, 2021