NC_000023.10:g.(?_153195397)_(153642547_?)dup AND Severe neonatal-onset encephalopathy with microcephaly

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 24, 2022
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:: RCV003113631.2

Allele description

NC_000023.10:g.(?_153195397)_(153642547_?)dup

Genes:

NAA10:N-alpha-acetyltransferase 10, NatA catalytic subunit [Gene - OMIM - HGNC]
DNASE1L1:deoxyribonuclease 1 like 1 [Gene - OMIM - HGNC]
EMD:emerin [Gene - OMIM - HGNC]
FLNA:filamin A [Gene - OMIM - HGNC]
HCFC1:host cell factor C1 [Gene - OMIM - HGNC]
IRAK1:interleukin 1 receptor associated kinase 1 [Gene - OMIM - HGNC]
MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]
OPN1LW:opsin 1, long wave sensitive [Gene - OMIM - HGNC]
OPN1MW2:opsin 1, medium wave sensitive 2 [Gene - HGNC]
OPN1MW:opsin 1, medium wave sensitive [Gene - OMIM - HGNC]
RENBP:renin binding protein [Gene - OMIM - HGNC]
RPL10:ribosomal protein L10 [Gene - OMIM - HGNC]
TAFAZZIN:tafazzin, phospholipid-lysophospholipid transacylase [Gene - OMIM - HGNC]
TEX28:testis expressed 28 [Gene - OMIM - HGNC]
TKTL1:transketolase like 1 [Gene - OMIM - HGNC]
TMEM187:transmembrane protein 187 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

Xq28

Genomic location:

ChrX: 153195397 - 153642547 (on Assembly GRCh37)

Preferred name:

NC_000023.10:g.(?_153195397)_(153642547_?)dup

HGVS:

NC_000023.10:g.(?_153195397)_(153642547_?)dup

Condition(s)

Name:: Severe neonatal-onset encephalopathy with microcephaly
Synonyms:: Encephalopathy, neonatal severe; Encephalopathy, neonatal severe, due to MECP2 mutations
Identifiers:: MONDO: MONDO:0010397; MedGen: C1968556; Orphanet: 209370; OMIM: 300673

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003794712	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 24, 2022)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 17088400, 22679399, 15351775, 15689435, 16080119, 23220634, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003794712

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 24, 2022)

germline

clinical testing

PubMed (7)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Recurrent infections, hypotonia, and mental retardation caused by duplication of MECP2 and adjacent region in Xq28.

Friez MJ, Jones JR, Clarkson K, Lubs H, Abuelo D, Bier JA, Pai S, Simensen R, Williams C, Giampietro PF, Schwartz CE, Stevenson RE.

Pediatrics. 2006 Dec;118(6):e1687-95. Epub 2006 Nov 6.

PubMed [citation]

PMID:: 17088400

MECP2 Duplication Syndrome.

Van Esch H.

Mol Syndromol. 2012 Apr;2(3-5):128-136. Epub 2011 Jul 5.

PubMed [citation]

PMID:: 22679399
PMCID:: PMC3366699

See all PubMed Citations (7)

Details of each submission

From Invitae, SCV003794712.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

A copy number gain of the genomic region encompassing the full coding sequence of the MECP2 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. A similar copy number variant has been observed in individual(s) with MECP2-duplication syndrome (PMID: 17088400, 22679399). It has also been observed to segregate with disease in related individuals. Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that a similar copy number variant affects MECP2 function (PMID: 15351775, 15689435, 16080119, 23220634). For these reasons, this variant has been classified as Pathogenic.

#	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

Last Updated: Feb 18, 2023

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