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NM_001110792.2(MECP2):c.1241C>T (p.Pro414Leu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jul 4, 2021)
Last evaluated:
Dec 31, 2019
Accession:
VCV000138195.13
Variation ID:
138195
Description:
single nucleotide variant
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NM_001110792.2(MECP2):c.1241C>T (p.Pro414Leu)

Allele ID
141898
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 154030623 (GRCh38) GRCh38 UCSC
X: 153296074 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_004992.3:c.1205C>T NP_004983.1:p.Pro402Leu missense
P51608:p.Pro402Leu
AJ132917.1:c.1205C>T
... more HGVS
Protein change
P402L, P414L, P309L, P179L
Other names
p.P402L:CCC>CTC
Canonical SPDI
NC_000023.11:154030622:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00053 (A)

Allele frequency
1000 Genomes Project 0.00053
Trans-Omics for Precision Medicine (TOPMed) 0.00008
Links
ClinGen: CA199300
UniProtKB: P51608#VAR_018221
dbSNP: rs61753014
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Dec 21, 2016 RCV000169924.3
Uncertain significance 1 criteria provided, single submitter Jun 1, 2016 RCV000526298.6
Likely benign 1 criteria provided, single submitter Apr 12, 2018 RCV000719105.1
Benign 1 criteria provided, single submitter Dec 31, 2019 RCV001088771.1
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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
(Dec 21, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000604150.1
Submitted: (Jun 30, 2017)
Evidence details
Benign
(May 29, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000170234.10
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
Severe neonatal-onset encephalopathy with microcephaly
Allele origin: germline
Invitae
Accession: SCV000645658.4
Submitted: (Jan 29, 2020)
Evidence details
Likely benign
(Apr 12, 2018)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000849969.3
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (1)
Comment:
Does not segregate with disease in family study (genes with incomplete penetrance);In silico models in agreement (benign)
Uncertain significance
(Jun 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001156228.7
Submitted: (Jul 04, 2021)
Evidence details
Benign
(Dec 20, 2002)
no assertion criteria provided
Method: curation
Not specified
Allele origin: maternal, unknown
RettBASE
Accession: SCV000187946.2
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
Mutation analysis of the coding sequence of the MECP2 gene in infantile autism. Beyer KS Human genetics 2002 PMID: 12384770

Text-mined citations for rs61753014...

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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 11, 2021