GRCh38/hg38 Xq27.1-28(chrX:139230333-150628474)x1 AND See cases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 12, 2011
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:: RCV000051733.4

Allele description [Variation Report for GRCh38/hg38 Xq27.1-28(chrX:139230333-150628474)x1]

GRCh38/hg38 Xq27.1-28(chrX:139230333-150628474)x1

Genes:

AFF2:ALF transcription elongation factor 2 [Gene - OMIM - HGNC]
LOC130068771:ATAC-STARR-seq lymphoblastoid active region 30004 [Gene]
LOC130068772:ATAC-STARR-seq lymphoblastoid active region 30005 [Gene]
LOC129929048:ATAC-STARR-seq lymphoblastoid active region 30006 [Gene]
LOC129929049:ATAC-STARR-seq lymphoblastoid active region 30007 [Gene]
LOC130068774:ATAC-STARR-seq lymphoblastoid active region 30008 [Gene]
LOC130068775:ATAC-STARR-seq lymphoblastoid active region 30009 [Gene]
LOC130068776:ATAC-STARR-seq lymphoblastoid active region 30010 [Gene]
LOC130068777:ATAC-STARR-seq lymphoblastoid active region 30011 [Gene]
LOC130068778:ATAC-STARR-seq lymphoblastoid active region 30012 [Gene]
LOC130068779:ATAC-STARR-seq lymphoblastoid active region 30013 [Gene]
LOC130068780:ATAC-STARR-seq lymphoblastoid active region 30014 [Gene]
LOC130068781:ATAC-STARR-seq lymphoblastoid active region 30015 [Gene]
LOC130068785:ATAC-STARR-seq lymphoblastoid active region 30016 [Gene]
LOC130068788:ATAC-STARR-seq lymphoblastoid active region 30017 [Gene]
LOC130068789:ATAC-STARR-seq lymphoblastoid active region 30018 [Gene]
LOC130068790:ATAC-STARR-seq lymphoblastoid active region 30019 [Gene]
LOC130068791:ATAC-STARR-seq lymphoblastoid active region 30020 [Gene]
LOC130068797:ATAC-STARR-seq lymphoblastoid active region 30021 [Gene]
LOC130068798:ATAC-STARR-seq lymphoblastoid active region 30022 [Gene]
LOC130068768:ATAC-STARR-seq lymphoblastoid silent region 21035 [Gene]
LOC130068769:ATAC-STARR-seq lymphoblastoid silent region 21036 [Gene]
LOC130068770:ATAC-STARR-seq lymphoblastoid silent region 21037 [Gene]
LOC130068773:ATAC-STARR-seq lymphoblastoid silent region 21038 [Gene]
LOC129929053:ATAC-STARR-seq lymphoblastoid silent region 21039 [Gene]
LOC130068782:ATAC-STARR-seq lymphoblastoid silent region 21041 [Gene]
LOC130068783:ATAC-STARR-seq lymphoblastoid silent region 21042 [Gene]
LOC130068784:ATAC-STARR-seq lymphoblastoid silent region 21043 [Gene]
LOC130068786:ATAC-STARR-seq lymphoblastoid silent region 21044 [Gene]
LOC130068787:ATAC-STARR-seq lymphoblastoid silent region 21045 [Gene]
LOC130068792:ATAC-STARR-seq lymphoblastoid silent region 21046 [Gene]
LOC130068793:ATAC-STARR-seq lymphoblastoid silent region 21047 [Gene]
LOC130068794:ATAC-STARR-seq lymphoblastoid silent region 21048 [Gene]
LOC130068795:ATAC-STARR-seq lymphoblastoid silent region 21049 [Gene]
LOC130068796:ATAC-STARR-seq lymphoblastoid silent region 21050 [Gene]
ATP11C:ATPase phospholipid transporting 11C [Gene - OMIM - HGNC]
LOC126863335:CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:141291591-141292790 [Gene]
LOC126863336:CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:141891706-141892905 [Gene]
LOC126863342:CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:148591963-148593162 [Gene]
EOLA1-DT:EOLA1 divergent transcript [Gene - HGNC]
EOLA2-DT:EOLA2 divergent transcript [Gene - HGNC]
FMR1-AS1:FMR1 antisense RNA 1 [Gene - OMIM - HGNC]
FMR1NB:FMR1 neighbor [Gene - HGNC]
LOC109396974:FRAXF repeat instability region [Gene]
HAPSTR2:HUWE1 associated protein modifying stress responses 2 [Gene - HGNC]
LOC106050102:IDS recombination region [Gene]
LOC106050103:IDSP1 recombination region [Gene]
LDOC1:LDOC1 regulator of NFKB signaling [Gene - OMIM - HGNC]
MAGEA11:MAGE family member A11 [Gene - OMIM - HGNC]
MAGEA8:MAGE family member A8 [Gene - OMIM - HGNC]
MAGEA9:MAGE family member A9 [Gene - OMIM - HGNC]
MAGEA9B:MAGE family member A9B [Gene - OMIM - HGNC]
MAGEC1:MAGE family member C1 [Gene - OMIM - HGNC]
MAGEC2:MAGE family member C2 [Gene - OMIM - HGNC]
MAGEC3:MAGE family member C3 [Gene - OMIM - HGNC]
MAGEA8-AS1:MAGEA8 antisense RNA 1 [Gene - HGNC]
MCF2:MCF.2 cell line derived transforming sequence [Gene - OMIM - HGNC]
LOC126863332:MED14-independent group 3 enhancer GRCh37_chrX:139356271-139357470 [Gene]
LOC126863333:MED14-independent group 3 enhancer GRCh37_chrX:140802566-140803765 [Gene]
LOC126863334:MED14-independent group 3 enhancer GRCh37_chrX:140991796-140992995 [Gene]
LOC126863338:MED14-independent group 3 enhancer GRCh37_chrX:144556098-144557297 [Gene]
LOC126863339:MED14-independent group 3 enhancer GRCh37_chrX:144939449-144940648 [Gene]
LOC126863341:MED14-independent group 3 enhancer GRCh37_chrX:147636485-147637684 [Gene]
LOC126863337:P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:143882879-143884078 [Gene]
LOC126863340:P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:146645835-146647034 [Gene]
SLITRK2:SLIT and NTRK like family member 2 [Gene - OMIM - HGNC]
SLITRK4:SLIT and NTRK like family member 4 [Gene - OMIM - HGNC]
LOC108281134:SOX3 promoter region [Gene]
SPANXA2:SPANX family member A2 [Gene - OMIM - HGNC]
SPANXB1:SPANX family member B1 [Gene - OMIM - HGNC]
SPANXC:SPANX family member C [Gene - OMIM - HGNC]
SPANXD:SPANX family member D [Gene - OMIM - HGNC]
SPANXN1:SPANX family member N1 [Gene - OMIM - HGNC]
SPANXN2:SPANX family member N2 [Gene - OMIM - HGNC]
SPANXN3:SPANX family member N3 [Gene - OMIM - HGNC]
SPANXN4:SPANX family member N4 [Gene - OMIM - HGNC]
SPANXA2-OT1:SPANXA2 overlapping transcript 1 [Gene - HGNC]
SOX3:SRY-box transcription factor 3 [Gene - OMIM - HGNC]
LOC121627982:Sharpr-MPRA regulatory region 13710 [Gene]
LOC125467789:Sharpr-MPRA regulatory region 14619 [Gene]
LOC121627983:Sharpr-MPRA regulatory region 15241 [Gene]
LOC125467790:Sharpr-MPRA regulatory region 6851 [Gene]
LOC110120680:VISTA enhancer hs427 [Gene]
LOC110120737:VISTA enhancer hs667 [Gene]
CDR1:cerebellar degeneration related 1 [Gene - OMIM - HGNC]
CXorf51A:chromosome X open reading frame 51A [Gene - HGNC]
CXorf51B:chromosome X open reading frame 51B [Gene - HGNC]
CXorf66:chromosome X open reading frame 66 [Gene - HGNC]
F9:coagulation factor IX [Gene - OMIM - HGNC]
EOLA1:endothelium and lymphocyte associated ASCH domain 1 [Gene - OMIM - HGNC]
EOLA2:endothelium and lymphocyte associated ASCH domain 2 [Gene - HGNC]
FMR1:fragile X messenger ribonucleoprotein 1 [Gene - OMIM - HGNC]
FRAXA:fragile site, folic acid type, rare, fra(X)(q27.3) A [Gene - HGNC]
FRAXE:fragile site, folic acid type, rare, fra(X)(q28) E [Gene - HGNC]
HSFX1:heat shock transcription factor family, X-linked 1 [Gene - HGNC]
HSFX2:heat shock transcription factor family, X-linked 2 [Gene - HGNC]
HSFX3:heat shock transcription factor family, X-linked member 3 [Gene - HGNC]
HSFX4:heat shock transcription factor family, X-linked member 4 [Gene - HGNC]
IDS:iduronate 2-sulfatase [Gene - OMIM - HGNC]
LINC00632:long intergenic non-protein coding RNA 632 [Gene - HGNC]
LINC00850:long intergenic non-protein coding RNA 850 [Gene - OMIM - HGNC]
MAMLD1:mastermind like domain containing 1 [Gene - OMIM - HGNC]
MIR2114:microRNA 2114 [Gene - HGNC]
MIR320D2:microRNA 320d-2 [Gene - HGNC]
MIR505:microRNA 505 [Gene - OMIM - HGNC]
MIR506:microRNA 506 [Gene - OMIM - HGNC]
MIR507:microRNA 507 [Gene - HGNC]
MIR508:microRNA 508 [Gene - OMIM - HGNC]
MIR509-1:microRNA 509-1 [Gene - OMIM - HGNC]
MIR509-2:microRNA 509-2 [Gene - HGNC]
MIR509-3:microRNA 509-3 [Gene - OMIM - HGNC]
MIR510:microRNA 510 [Gene - OMIM - HGNC]
MIR513A1:microRNA 513a-1 [Gene - HGNC]
MIR513A2:microRNA 513a-2 [Gene - HGNC]
MIR513B:microRNA 513b [Gene - HGNC]
MIR513C:microRNA 513c [Gene - HGNC]
MIR514A1:microRNA 514a-1 [Gene - HGNC]
MIR514A2:microRNA 514a-2 [Gene - HGNC]
MIR514A3:microRNA 514a-3 [Gene - HGNC]
MIR514B:microRNA 514b [Gene - HGNC]
MIR888:microRNA 888 [Gene - HGNC]
MIR890:microRNA 890 [Gene - HGNC]
MIR891A:microRNA 891a [Gene - HGNC]
MIR891B:microRNA 891b [Gene - HGNC]
MIR892A:microRNA 892a [Gene - HGNC]
MIR892B:microRNA 892b [Gene - HGNC]
MIR892C:microRNA 892c [Gene - HGNC]
MTM1:myotubularin 1 [Gene - OMIM - HGNC]
LOC107048984:origin of replication in 5' region of AFF2/FMR2 [Gene]
LOC107032825:origin of replication in 5' region of FMR1 [Gene]
LOC107048982:origin of replication upstream of FMR1 [Gene]
SPANXA1:sperm protein associated with the nucleus, X-linked, family member A1 [Gene - OMIM - HGNC]
TMEM185A:transmembrane protein 185A [Gene - OMIM - HGNC]
UBE2NL:ubiquitin conjugating enzyme E2 N like (gene/pseudogene) [Gene - HGNC]
LOC122319696:uncharacterized LOC122319696 [Gene]
LOC645188:uncharacterized LOC645188 [Gene]
LOC728660:uncharacterized LOC728660 [Gene]

Variant type:

copy number loss

Cytogenetic location:

Xq27.1-28

Genomic location:

Preferred name:

GRCh38/hg38 Xq27.1-28(chrX:139230333-150628474)x1

HGVS:

NC_000023.11:g.(?_139230333)_(150628474_?)del
NC_000023.10:g.(?_138312495)_(149782550_?)del
NC_000023.9:g.(?_138140161)_(149547605_?)del

Links:

dbVar: nssv578469; dbVar: nsv530254

Observations:

Condition(s)

Name:: See cases [See the Variation display for details]
Identifiers:

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Cyrtonyx montezumae ultra conserved element locus uce-1014 genomic sequence
Cyrtonyx montezumae ultra conserved element locus uce-1014 genomic sequence
gi|667514910|gb|KJ968382.1|

Nucleotide
Homo sapiens chromosome 19 clone LLNLR-259H9, complete sequence
Homo sapiens chromosome 19 clone LLNLR-259H9, complete sequence
gi|28416072|gnl|lanlchgs|259H9|gb|A 30.2|

Nucleotide
Homo sapiens zinc finger protein 516 (ZNF516), mRNA
Homo sapiens zinc finger protein 516 (ZNF516), mRNA
gi|1519315766|ref|NM_014643.4|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000079081	GeneDx	criteria provided, single submitter (Kaminsky et al. (Genet Med. 2011))	Pathogenic (Aug 12, 2011)	not provided	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

SCV000079081

GeneDx

criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))

Pathogenic
(Aug 12, 2011)

not provided

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	not provided	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities.

Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, Kunig D, Moreno-De-Luca D, Moreno-De-Luca A, Mulle JG, Warren ST, Richard G, Compton JG, Fuller AE, Gliem TJ, Huang S, Collinson MN, Beal SJ, Ackley T, Pickering DL, Golden DM, Aston E, Whitby H, et al.

Genet Med. 2011 Sep;13(9):777-84. doi: 10.1097/GIM.0b013e31822c79f9.

PubMed [citation]

PMID:: 21844811
PMCID:: PMC3661946

Details of each submission

From GeneDx, SCV000079081.4

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

Last Updated: Oct 14, 2023

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