NM_001110792.2(MECP2):c.616_1227del (p.Ser206_Glu409del) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 30, 2021
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:: RCV002254485.2

Allele description [Variation Report for NM_001110792.2(MECP2):c.616_1227del (p.Ser206_Glu409del)]

NM_001110792.2(MECP2):c.616_1227del (p.Ser206_Glu409del)

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.616_1227del (p.Ser206_Glu409del)

HGVS:

NC_000023.11:g.154030638_154031249del
NG_007107.3:g.110856_111467del
NM_001110792.2:c.616_1227delMANE SELECT
NM_001316337.2:c.301_912del
NM_001369391.2:c.301_912del
NM_001369392.2:c.301_912del
NM_001369393.2:c.301_912del
NM_001369394.2:c.301_912del
NM_001386137.1:c.-90_522del
NM_001386138.1:c.-90_522del
NM_001386139.1:c.-90_522del
NM_004992.4:c.580_1191del
NP_001104262.1:p.Ser206_Glu409del
NP_001303266.1:p.Ser101_Glu304del
NP_001356320.1:p.Ser101_Glu304del
NP_001356321.1:p.Ser101_Glu304del
NP_001356322.1:p.Ser101_Glu304del
NP_001356323.1:p.Ser101_Glu304del
NP_001373066.1:p.Met1_Glu174del
NP_001373067.1:p.Met1_Glu174del
NP_001373068.1:p.Met1_Glu174del
NP_004983.1:p.Ser194_Glu397del
LRG_764t1:c.616_1227del
LRG_764t2:c.580_1191del
LRG_764:g.110856_111467del
LRG_764p1:p.Ser206_Glu409del
LRG_764p2:p.Ser194_Glu397del
NC_000023.10:g.153296089_153296700del
NM_004992.3:c.580_1191del612

Links:

dbSNP: rs2148659968

NCBI 1000 Genomes Browser:

rs2148659968

Molecular consequence:

NM_001110792.2:c.616_1227del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001316337.2:c.301_912del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001369391.2:c.301_912del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001369392.2:c.301_912del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001369393.2:c.301_912del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001369394.2:c.301_912del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001386137.1:c.-90_522del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001386138.1:c.-90_522del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001386139.1:c.-90_522del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004992.4:c.580_1191del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001386137.1:c.-90_522del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001386138.1:c.-90_522del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001386139.1:c.-90_522del - initiator_codon_variant - [Sequence Ontology: SO:0001582]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002525694	Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Aug 30, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002525694

Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Aug 30, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital, SCV002525694.2

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

Description

This deletion impacts multiple critical protein regions and is expected to cause a loss of protein function. Variants that cause a loss of function and/or affect the methyl-DNA binding domain (MBD, aa# 90-163) or the transcriptional repressor domain (TRD, aa#207-310) are a common mechanism of disease causation (NBK1497, PMID: 21326358). While it appears that this variant has not been reported before, other pathogenic alterations impacting these domains are documented (PMID: 21326358, PMID: 19914908, and others).

#	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: Dec 24, 2023

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