GRCh37/hg19 Xq28(chrX:152941303-153549189)x2 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 8, 2023
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:: RCV003483987.1

Allele description [Variation Report for GRCh37/hg19 Xq28(chrX:152941303-153549189)x2]

GRCh37/hg19 Xq28(chrX:152941303-153549189)x2

Genes:

ABCD1:ATP binding cassette subfamily D member 1 [Gene - OMIM - HGNC]
BCAP31:B cell receptor associated protein 31 [Gene - OMIM - HGNC]
L1CAM:L1 cell adhesion molecule [Gene - OMIM - HGNC]
NAA10:N-alpha-acetyltransferase 10, NatA catalytic subunit [Gene - OMIM - HGNC]
PDZD4:PDZ domain containing 4 [Gene - OMIM - HGNC]
ARHGAP4:Rho GTPase activating protein 4 [Gene - OMIM - HGNC]
SRPK3:SRSF protein kinase 3 [Gene - OMIM - HGNC]
AVPR2:arginine vasopressin receptor 2 [Gene - OMIM - HGNC]
HCFC1:host cell factor C1 [Gene - OMIM - HGNC]
IRAK1:interleukin 1 receptor associated kinase 1 [Gene - OMIM - HGNC]
IDH3G:isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gamma [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]
PLXNB3:plexin B3 [Gene - OMIM - HGNC]
RENBP:renin binding protein [Gene - OMIM - HGNC]
SSR4:signal sequence receptor subunit 4 [Gene - OMIM - HGNC]
SLC6A8:solute carrier family 6 member 8 [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:

copy number gain

Cytogenetic location:

Xq28

Genomic location:

ChrX: 152941303 - 153549189 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 Xq28(chrX:152941303-153549189)x2

HGVS:

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
SCV004230407	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Mar 8, 2023)	unknown	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

SCV004230407

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Mar 8, 2023)

unknown

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).

Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL.

Genet Med. 2020 Feb;22(2):245-257. doi: 10.1038/s41436-019-0686-8. Epub 2019 Nov 6. Erratum in: Genet Med. 2021 Nov;23(11):2230. doi: 10.1038/s41436-021-01150-9.

PubMed [citation]

PMID:: 31690835
PMCID:: PMC7313390

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004230407.1

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

Description

This gain involves the entire MECP2 gene (OMIM 300005), which is consistent with MECP2 duplication syndrome (OMIM 300260). Occasionally females have been described with a MECP2 duplication and related clinical findings (Van Esch 2020). There are no similar copy number gains of this region in the general populations of the Database of Genomic Variants. Thus, based on gene content and current medical literature, this copy number variant (CNV) is classified as pathogenic. References: Van Esch et al., GeneReviews [Updated 2020 May 21]. PMID:20301461

#	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

Last Updated: Feb 4, 2024

ClinVar

Relating variation to medicine