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NM_001110792.2(MECP2):c.331dup (p.Thr111fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 18, 2019
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001008640.1

Allele description [Variation Report for NM_001110792.2(MECP2):c.331dup (p.Thr111fs)]

NM_001110792.2(MECP2):c.331dup (p.Thr111fs)

Gene:
MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_001110792.2(MECP2):c.331dup (p.Thr111fs)
HGVS:
  • NC_000023.11:g.154032289dup
  • NG_007107.2:g.109839dup
  • NG_007107.3:g.109815dup
  • NM_001110792.2:c.331dupMANE SELECT
  • NM_001316337.2:c.16dup
  • NM_001369391.2:c.16dup
  • NM_001369392.2:c.16dup
  • NM_001369393.2:c.16dup
  • NM_001369394.2:c.16dup
  • NM_001386137.1:c.-266dup
  • NM_001386138.1:c.-266dup
  • NM_001386139.1:c.-266dup
  • NM_004992.4:c.295dup
  • NP_001104262.1:p.Thr111fs
  • NP_001303266.1:p.Thr6fs
  • NP_001356320.1:p.Thr6fs
  • NP_001356321.1:p.Thr6fs
  • NP_001356322.1:p.Thr6fs
  • NP_001356323.1:p.Thr6fs
  • NP_004983.1:p.Thr99fs
  • LRG_764t1:c.331dup
  • LRG_764t2:c.295dup
  • LRG_764:g.109815dup
  • LRG_764p1:p.Thr111fs
  • LRG_764p2:p.Thr99fs
  • NC_000023.10:g.153297740dup
  • NM_004992.3:c.295dupA
Protein change:
T111fs
Links:
dbSNP: rs1603310755
NCBI 1000 Genomes Browser:
rs1603310755
Molecular consequence:
  • NM_001386137.1:c.-266dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386138.1:c.-266dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386139.1:c.-266dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001110792.2:c.331dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001316337.2:c.16dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369391.2:c.16dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369392.2:c.16dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369393.2:c.16dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369394.2:c.16dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004992.4:c.295dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001168414GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Mar 18, 2019) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV001168414.1

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

Description

The c.295dupA variant in the MECP2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.295dupA variant causes a frameshift starting with codon Threonine 99, changes this amino acid to an Asparagine residue, and creates a premature Stop codon at position 4 of the new reading frame, denoted p.Thr99AsnfsX4. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.295dupA variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.295dupA as a pathogenic variant.

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

Last Updated: Sep 17, 2022