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:: 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:: RCV000144758.1

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

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

Gene:

MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

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

Other names:

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

HGVS:

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

Note:

70-nt deletion in exon 4 of gene MECP2.

Protein change:

K154fs

Links:

dbSNP: rs1557135353

NCBI 1000 Genomes Browser:

rs1557135353

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]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000190972	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Dec 11, 2013)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000190972

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Dec 11, 2013)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000190972.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

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).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Aug 4, 2024

ClinVar

Relating variation to medicine