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NM_001110792.2(MECP2):c.*13C>T AND not specified

Germline classification:
Benign/Likely benign (2 submissions)
Last evaluated:
Mar 6, 2019
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000443181.2

Allele description [Variation Report for NM_001110792.2(MECP2):c.*13C>T]

NM_001110792.2(MECP2):c.*13C>T

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.*13C>T
HGVS:
  • NC_000023.11:g.154030354G>A
  • NG_007107.3:g.111750C>T
  • NM_001110792.2:c.*13C>TMANE SELECT
  • NM_001316337.2:c.*13C>T
  • NM_001369391.2:c.*13C>T
  • NM_001369392.2:c.*13C>T
  • NM_001369393.2:c.*13C>T
  • NM_001369394.2:c.*13C>T
  • NM_001386137.1:c.*13C>T
  • NM_001386138.1:c.*13C>T
  • NM_001386139.1:c.*13C>T
  • NM_004992.4:c.*13C>T
  • LRG_764t1:c.*13C>T
  • LRG_764t2:c.*13C>T
  • LRG_764:g.111750C>T
  • NC_000023.10:g.153295805G>A
  • NG_007107.2:g.111774C>T
  • NM_004992.3:c.*13C>T
Links:
dbSNP: rs782334844
NCBI 1000 Genomes Browser:
rs782334844
Molecular consequence:
  • NM_001110792.2:c.*13C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001316337.2:c.*13C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001369391.2:c.*13C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001369392.2:c.*13C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001369393.2:c.*13C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001369394.2:c.*13C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001386137.1:c.*13C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001386138.1:c.*13C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001386139.1:c.*13C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_004992.4:c.*13C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000513578GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely benign
(Apr 22, 2016) 		germlineclinical testing

Citation Link,

SCV001362154Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Benign
(Mar 6, 2019) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000513578.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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 a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001362154.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: MECP2 c.*13C>T is located in the untranslated mRNA region downstream of the termination codon. The variant allele was found at a frequency of 0.0001 in 200351 control chromosomes (gnomAD), including 6 hemizygotes. The observed variant frequency is approximately 12 fold of the estimated maximal expected allele frequency for a pathogenic variant in MECP2 causing Rett Syndrome phenotype (8.3e-06), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.*13C>T in individuals affected with Rett Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cites the variant as likely benign. Based on the evidence outlined above, the variant was classified as benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2024