NM_001110792.2(MECP2):c.138del (p.Asp46fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 1, 2017
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:: RCV000519737.1

Allele description [Variation Report for NM_001110792.2(MECP2):c.138del (p.Asp46fs)]

NM_001110792.2(MECP2):c.138del (p.Asp46fs)

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.138del (p.Asp46fs)

HGVS:

NC_000023.11:g.154032482del
NG_007107.2:g.109646del
NG_007107.3:g.109622del
NM_001110792.2:c.138delMANE SELECT
NM_001316337.2:c.-178del
NM_001369391.2:c.-178del
NM_001369392.2:c.-178del
NM_001369393.2:c.-178del
NM_001369394.2:c.-178del
NM_001386137.1:c.-459del
NM_001386138.1:c.-459del
NM_001386139.1:c.-459del
NM_004992.4:c.102del
NP_001104262.1:p.Asp46fs
NP_004983.1:p.Asp34fs
LRG_764t1:c.138del
LRG_764t2:c.102del
LRG_764:g.109622del
LRG_764p1:p.Asp46fs
LRG_764p2:p.Asp34fs
NC_000023.10:g.153297933del
NM_004992.3:c.102delT

Protein change:

D34fs

Links:

dbSNP: rs1557137983

NCBI 1000 Genomes Browser:

rs1557137983

Molecular consequence:

NM_001316337.2:c.-178del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001369391.2:c.-178del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001369392.2:c.-178del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001369393.2:c.-178del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001369394.2:c.-178del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001386137.1:c.-459del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001386138.1:c.-459del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001386139.1:c.-459del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001110792.2:c.138del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004992.4:c.102del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000619620	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Aug 1, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000619620

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Aug 1, 2017)

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, SCV000619620.2

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

Description

The c.102delT variant in the MECP2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.102delT variant causes a frameshift starting with codon Aspartic acid 34, changes this amino acid to a Glutamic acid residue, and creates a premature Stop codon at position 91 of the new reading frame, denoted p.Asp34GlufsX91. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.102delT variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.102delT as a pathogenic variant.

#	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: Sep 17, 2022

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