GRCh38/hg38 Xp22.33-22.31(chrX:10679-6495923)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:: RCV000052969.5

Allele description [Variation Report for GRCh38/hg38 Xp22.33-22.31(chrX:10679-6495923)x1]

GRCh38/hg38 Xp22.33-22.31(chrX:10679-6495923)x1

Genes:

AKAP17A:A-kinase anchoring protein 17A [Gene - OMIM - OMIM - HGNC]
ARSD-AS1:ARSD antisense RNA 1 [Gene - HGNC]
ASMTL-AS1:ASMTL antisense RNA 1 [Gene - HGNC]
LOC130067892:ATAC-STARR-seq lymphoblastoid active region 29373 [Gene]
LOC130067893:ATAC-STARR-seq lymphoblastoid active region 29374 [Gene]
LOC130067894:ATAC-STARR-seq lymphoblastoid active region 29375 [Gene]
LOC130067895:ATAC-STARR-seq lymphoblastoid active region 29376 [Gene]
LOC130067901:ATAC-STARR-seq lymphoblastoid active region 29377 [Gene]
LOC130067906:ATAC-STARR-seq lymphoblastoid active region 29379 [Gene]
LOC130067907:ATAC-STARR-seq lymphoblastoid active region 29380 [Gene]
LOC130067890:ATAC-STARR-seq lymphoblastoid silent region 20638 [Gene]
LOC130067891:ATAC-STARR-seq lymphoblastoid silent region 20639 [Gene]
LOC130067896:ATAC-STARR-seq lymphoblastoid silent region 20640 [Gene]
LOC130067897:ATAC-STARR-seq lymphoblastoid silent region 20641 [Gene]
LOC130067898:ATAC-STARR-seq lymphoblastoid silent region 20642 [Gene]
LOC130067899:ATAC-STARR-seq lymphoblastoid silent region 20643 [Gene]
LOC130067900:ATAC-STARR-seq lymphoblastoid silent region 20644 [Gene]
LOC130067902:ATAC-STARR-seq lymphoblastoid silent region 20645 [Gene]
LOC130067903:ATAC-STARR-seq lymphoblastoid silent region 20646 [Gene]
LOC130067904:ATAC-STARR-seq lymphoblastoid silent region 20647 [Gene]
LOC130067905:ATAC-STARR-seq lymphoblastoid silent region 20648 [Gene]
LOC126863190:BRD4-independent group 4 enhancer GRCh37_chrX:3445471-3446670 [Gene]
LOC126863191:BRD4-independent group 4 enhancer GRCh37_chrX:3650386-3651585 [Gene]
LOC126863194:BRD4-independent group 4 enhancer GRCh37_chrX:4872887-4874086 [Gene]
LOC126863196:BRD4-independent group 4 enhancer GRCh37_chrX:5224281-5225480 [Gene]
CD99:CD99 molecule (Xg blood group) [Gene - OMIM - OMIM - HGNC]
LOC126863189:CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:2722445-2723644 [Gene]
LOC126863192:CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:4463784-4464983 [Gene]
CNE-2:CNE-2 enhancer upstream of SHOX [Gene]
CNE-3:CNE-3 enhancer upstream of SHOX [Gene]
CNE-5:CNE-5 enhancer upstream of SHOX [Gene]
CNE4:CNE4 enhancer downstream of SHOX [Gene]
CNE5:CNE5 enhancer downstream of SHOX [Gene]
CNE6:CNE6 enhancer downstream of SHOX [Gene]
CNE7:CNE7 enhancer downstream of SHOX [Gene]
CNE8:CNE8 enhancer downstream of SHOX [Gene]
CNE9:CNE9 enhancer downstream of SHOX [Gene]
GTPBP6:GTP binding protein 6 (putative) [Gene - OMIM - HGNC]
LOC126863193:MED14-independent group 3 enhancer GRCh37_chrX:4628486-4629685 [Gene]
LOC129391292:MPRA-validated peak7351 silencer [Gene]
P2RY8:P2Y receptor family member 8 [Gene - OMIM - HGNC]
LOC126863195:P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:4969484-4970683 [Gene]
PRKX-AS1:PRKX antisense RNA 1 [Gene - HGNC]
LOC108251802:SHOX downstream enhancer, distal recombination region [Gene]
LOC108251803:SHOX downstream enhancer, proximal recombination region [Gene]
SHOX:SHOX homeobox [Gene - OMIM - OMIM - HGNC]
LOC125446265:Sharpr-MPRA regulatory region 13686 [Gene]
XG:Xg glycoprotein (Xg blood group) [Gene - OMIM - HGNC]
ASMTL:acetylserotonin O-methyltransferase like [Gene - OMIM - OMIM - HGNC]
ASMT:acetylserotonin O-methyltransferase [Gene - OMIM - OMIM - HGNC]
ARSD:arylsulfatase D [Gene - OMIM - HGNC]
ARSF:arylsulfatase F [Gene - OMIM - HGNC]
ARSL:arylsulfatase L [Gene - OMIM - HGNC]
ARSH:arylsulfatase family member H [Gene - OMIM - HGNC]
CSF2RA:colony stimulating factor 2 receptor subunit alpha [Gene - OMIM - OMIM - HGNC]
CRLF2:cytokine receptor like factor 2 [Gene - OMIM - OMIM - HGNC]
DHRSX:dehydrogenase/reductase X-linked [Gene - OMIM - HGNC]
GYG2:glycogenin 2 [Gene - OMIM - HGNC]
IL3RA:interleukin 3 receptor subunit alpha [Gene - OMIM - OMIM - HGNC]
LINC00102:long intergenic non-protein coding RNA 102 [Gene - HGNC]
LINC00106:long intergenic non-protein coding RNA 106 [Gene - HGNC]
LINC01546:long intergenic non-protein coding RNA 1546 [Gene - HGNC]
LINC00685:long intergenic non-protein coding RNA 685 [Gene - HGNC]
MXRA5:matrix remodeling associated 5 [Gene - OMIM - HGNC]
LOC107652445:meiotic recombination hotspot SHOX [Gene]
MIR3690:microRNA 3690 [Gene - HGNC]
MIR4770:microRNA 4770 [Gene - HGNC]
MIR6089:microRNA 6089 [Gene - HGNC]
NLGN4X:neuroligin 4 X-linked [Gene - OMIM - HGNC]
PLCXD1:phosphatidylinositol specific phospholipase C X domain containing 1 [Gene - OMIM - HGNC]
PRKX:protein kinase cAMP-dependent X-linked catalytic subunit [Gene - OMIM - HGNC]
PPP2R3B:protein phosphatase 2 regulatory subunit B''beta [Gene - OMIM - HGNC]
SNORA48B:small nucleolar RNA, H/ACA box 48B [Gene - HGNC]
SLC25A6:solute carrier family 25 member 6 [Gene - OMIM - OMIM - HGNC]
TRI-GAT1-1:tRNA-Ile (anticodon GAT) 1-1 [Gene - HGNC]
TRI-GAT1-2:tRNA-Ile (anticodon GAT) 1-2 [Gene - HGNC]
TRI-GAT1-3:tRNA-Ile (anticodon GAT) 1-3 [Gene - HGNC]
LOC101928201:uncharacterized LOC101928201 [Gene]
LOC105373156:uncharacterized LOC105373156 [Gene]
ZBED1:zinc finger BED-type containing 1 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

Xp22.33-22.31

Genomic location:

Preferred name:

GRCh38/hg38 Xp22.33-22.31(chrX:10679-6495923)x1

HGVS:

NC_000023.11:g.(?_10679)_(6495923_?)del
NC_000023.10:g.(?_60679)_(6413964_?)del
NC_000023.9:g.(?_679)_(6423964_?)del

Links:

dbVar: nssv578379; dbVar: nsv531682

Observations:

Condition(s)

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

Recent activity

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GCF_000313255.1
GCF_000313255.1

biosample
txid75463[Organism:noexp] (2)
Nucleotide
Lung PEComa
Lung PEComa

MedGen

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000080323	ISCA site 14 See additional submitters International Standards For Cytogenomic Arrays Consortium (ISCA)	criteria provided, single submitter (Kaminsky et al. (Genet Med. 2011))	Pathogenic (Aug 12, 2011)	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

SCV000080323

ISCA site 14

See additional submitters

criteria provided, single submitter

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

Pathogenic
(Aug 12, 2011)

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	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 ISCA site 14, SCV000080323.4

#	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	unknown	yes	not provided	not provided	Discovery		1	not provided	not provided	not provided

Last Updated: May 7, 2024

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