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NM_001110792.2(MECP2):c.1165_1234del (p.Lys389fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 11, 2013
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:

Allele description [Variation Report for NM_001110792.2(MECP2):c.1165_1234del (p.Lys389fs)]

NM_001110792.2(MECP2):c.1165_1234del (p.Lys389fs)

MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]
Variant type:
Cytogenetic location:
Genomic location:
Preferred name:
NM_001110792.2(MECP2):c.1165_1234del (p.Lys389fs)
Other names:
NM_001110792.2(MECP2):c.1165_1234del; p.Lys389fs
  • NC_000023.11:g.154030635_154030704del
  • NG_007107.3:g.111405_111474del
  • NM_001110792.2:c.1165_1234delMANE SELECT
  • NM_001316337.2:c.850_919del
  • NM_001369391.2:c.850_919del
  • NM_001369392.2:c.850_919del
  • NM_001369393.2:c.850_919del
  • NM_001369394.2:c.850_919del
  • NM_001386137.1:c.460_529del
  • NM_001386138.1:c.460_529del
  • NM_001386139.1:c.460_529del
  • NM_004992.3:c.1129_1198del
  • NM_004992.4:c.1129_1198del
  • NP_001104262.1:p.Lys389fs
  • NP_001303266.1:p.Lys284fs
  • NP_001356320.1:p.Lys284fs
  • NP_001356321.1:p.Lys284fs
  • NP_001356322.1:p.Lys284fs
  • NP_001356323.1:p.Lys284fs
  • NP_001373066.1:p.Lys154fs
  • NP_001373067.1:p.Lys154fs
  • NP_001373068.1:p.Lys154fs
  • NP_004983.1:p.Lys377fs
  • LRG_764t1:c.1165_1234del
  • LRG_764t2:c.1129_1198del
  • LRG_764:g.111405_111474del
  • LRG_764p1:p.Lys389fs
  • LRG_764p2:p.Lys377fs
  • NC_000023.10:g.153296086_153296155del
  • NG_007107.2:g.111429_111498del
  • NM_004992.3:c.1129_1198del70
  • p.K377Pfsx9
70-nt deletion in exon 4 of gene MECP2.
Protein change:
dbSNP: rs1557135353
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001110792.2:c.1165_1234del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001316337.2:c.850_919del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369391.2:c.850_919del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369392.2:c.850_919del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369393.2:c.850_919del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369394.2:c.850_919del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001386137.1:c.460_529del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001386138.1:c.460_529del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001386139.1:c.460_529del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004992.4:c.1129_1198del - frameshift variant - [Sequence Ontology: SO:0001589]


none provided
MedGen: CN517202

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Assertion and evidence details

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

(GeneDx Variant Classification (06012015))
(Dec 11, 2013)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000190972.2

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


The c.1129_1198del70 mutation results in a deletion of 70 base pairs located in the deletion-prone region at the 3' end of the MECP2 gene. This deletion causes a frameshift starting with codon Lysine 377, changes this amino acid to a Proline residue, and creates a premature Stop codon at position 9 of the new reading frame, denoted p.Lys377ProfsX9. This deletion results in the replacement of the last 110 amino acids of the protein with 8 aberrant amino acids and is predicted to cause loss of normal protein function through protein truncation. This mutation has not been reported previously to our knowledge, although large deletions in this region of the gene have been identified in patients with classic and atypical Rett syndrome. The variant is found in INFANT-EPI panel(s).

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

Last Updated: Aug 5, 2023