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GRCh38/hg38 Xp22.33-22.32(chrX:40904-4469489)x3 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:
RCV000052326.7

Allele description [Variation Report for GRCh38/hg38 Xp22.33-22.32(chrX:40904-4469489)x3]

GRCh38/hg38 Xp22.33-22.32(chrX:40904-4469489)x3

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]
  • 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]
  • CD99:CD99 molecule (Xg blood group) [Gene - OMIM - OMIM - HGNC]
  • LOC126863189:CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:2722445-2723644 [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]
  • LOC129391292:MPRA-validated peak7351 silencer [Gene]
  • P2RY8:P2Y receptor family member 8 [Gene - OMIM - HGNC]
  • 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]
  • MIR6089:microRNA 6089 [Gene - 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]
  • ZBED1:zinc finger BED-type containing 1 [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
Xp22.33-22.32
Genomic location:
Preferred name:
GRCh38/hg38 Xp22.33-22.32(chrX:40904-4469489)x3
HGVS:
  • NC_000023.11:g.(?_40904)_(4469489_?)dup
  • NC_000023.10:g.(?_90904)_(4387530_?)dup
  • NC_000023.9:g.(?_30904)_(4397530_?)dup
Links:
dbVar: nssv579186; dbVar: nsv531038
Observations:
1

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000079678ISCA site 17

See additional submitters

criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))		Pathogenic
(Aug 12, 2011) 		maternalclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedmaternalyes1not providednot providednot providednot providedclinical 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 17, SCV000079678.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: May 7, 2024