NM_001110792.2(MECP2):c.414-17del AND not provided

Germline classification:: Benign/Likely benign (6 submissions)
Last evaluated:: Jun 2, 2017
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000144110.10

Allele description [Variation Report for NM_001110792.2(MECP2):c.414-17del]

NM_001110792.2(MECP2):c.414-17del

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.414-17del

HGVS:

NC_000023.11:g.154031469del
NG_007107.3:g.110637del
NM_001110792.2:c.414-17delMANE SELECT
NM_001316337.2:c.99-17del
NM_001369391.2:c.99-17del
NM_001369392.2:c.99-17del
NM_001369393.2:c.99-17del
NM_001369394.2:c.99-17del
NM_001386137.1:c.-183-17del
NM_001386138.1:c.-183-17del
NM_001386139.1:c.-183-17del
NM_004992.4:c.378-17del
LRG_764t1:c.414-17del
LRG_764t2:c.378-17del
AJ132917.1:c.378-17delT
LRG_764:g.110637del
NC_000023.10:g.153296918del
NC_000023.10:g.153296918delA
NC_000023.10:g.153296920del
NG_007107.2:g.110661del
NG_007107.2:g.110661delT
NM_004992.3:c.378-17del
NM_004992.3:c.378-17delT

Links:

dbSNP: rs61753982

NCBI 1000 Genomes Browser:

rs61753982

Molecular consequence:

NM_001110792.2:c.414-17del - intron variant - [Sequence Ontology: SO:0001627]
NM_001316337.2:c.99-17del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369391.2:c.99-17del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369392.2:c.99-17del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369393.2:c.99-17del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369394.2:c.99-17del - intron variant - [Sequence Ontology: SO:0001627]
NM_001386137.1:c.-183-17del - intron variant - [Sequence Ontology: SO:0001627]
NM_001386138.1:c.-183-17del - intron variant - [Sequence Ontology: SO:0001627]
NM_001386139.1:c.-183-17del - intron variant - [Sequence Ontology: SO:0001627]
NM_004992.4:c.378-17del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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TMTC3 [Mesitornis unicolor]
TMTC3 [Mesitornis unicolor]
Gene ID:104547161

Gene
NTM [Mesitornis unicolor]
NTM [Mesitornis unicolor]
Gene ID:104541167

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000609828	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jun 2, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000804263	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia See additional submitters Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	no assertion criteria provided	Benign (Apr 3, 2015)	germline	clinical testing
SCV001742659	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001870203	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Mar 3, 2015)	germline	clinical testing	Citation Link,
SCV004220013	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Benign (Mar 23, 2016)	unknown	clinical testing	PubMed (5) [See all records that cite these PMIDs] 23810759, 20031356, 17387578, 11469283, 26467025

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
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	not provided	not provided	not provided	not provided	not provided	1	not provided	literature only

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

MECP2 gene study in a large cohort: testing of 240 female patients and 861 healthy controls (519 females and 342 males).

Maortua H, Martínez-Bouzas C, García-Ribes A, Martínez MJ, Guillen E, Domingo MR, Calvo MT, Guitart M, Gabau E, Botella MP, Gener B, Rubio I, López-Aríztegui MA, Tejada MI.

J Mol Diagn. 2013 Sep;15(5):723-9. doi: 10.1016/j.jmoldx.2013.05.002. Epub 2013 Jun 26.

PubMed [citation]

PMID:: 23810759

See all PubMed Citations (6)

Details of each submission

From RettBASE, SCV000189186.1

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

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

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000609828.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	0.007883	not provided	not provided

From Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, SCV000804263.1

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

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

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001742659.3

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

#	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

From GeneDx, SCV001870203.1

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

#	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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004220013.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

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

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000189186	RettBASE	flagged submission Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV000189186 appears to be redundant with SCV000222412.	not provided	not provided	not provided

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000189186

RettBASE

flagged submission

Reason: This record appears to be redundant with a more recent record from the same submitter.

Notes: SCV000189186 appears to be redundant with SCV000222412.

not provided

Last Updated: Sep 29, 2024

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