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GRCh38/hg38 Xp22.33-22.31(chrX:10679-9459643)x1 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 18, 2010
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000134136.6

Allele description [Variation Report for GRCh38/hg38 Xp22.33-22.31(chrX:10679-9459643)x1]

GRCh38/hg38 Xp22.33-22.31(chrX:10679-9459643)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]
  • LOC130067908:ATAC-STARR-seq lymphoblastoid active region 29381 [Gene]
  • LOC130067909:ATAC-STARR-seq lymphoblastoid active region 29382 [Gene]
  • LOC130067910:ATAC-STARR-seq lymphoblastoid active region 29383 [Gene]
  • LOC130067911:ATAC-STARR-seq lymphoblastoid active region 29384 [Gene]
  • LOC130067912:ATAC-STARR-seq lymphoblastoid active region 29385 [Gene]
  • LOC130067913:ATAC-STARR-seq lymphoblastoid active region 29386 [Gene]
  • LOC130067914:ATAC-STARR-seq lymphoblastoid active region 29387 [Gene]
  • LOC130067916:ATAC-STARR-seq lymphoblastoid active region 29389 [Gene]
  • LOC130067917:ATAC-STARR-seq lymphoblastoid active region 29390 [Gene]
  • LOC130067918:ATAC-STARR-seq lymphoblastoid active region 29391 [Gene]
  • LOC130067919:ATAC-STARR-seq lymphoblastoid active region 29393 [Gene]
  • LOC130067920:ATAC-STARR-seq lymphoblastoid active region 29394 [Gene]
  • LOC130067921:ATAC-STARR-seq lymphoblastoid active region 29395 [Gene]
  • LOC130067922:ATAC-STARR-seq lymphoblastoid active region 29396 [Gene]
  • LOC130067923:ATAC-STARR-seq lymphoblastoid active region 29397 [Gene]
  • LOC130067924:ATAC-STARR-seq lymphoblastoid active region 29398 [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]
  • LOC130067915:ATAC-STARR-seq lymphoblastoid silent region 20649 [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]
  • LOC126863198:BRD4-independent group 4 enhancer GRCh37_chrX:7889540-7890739 [Gene]
  • LOC126863204:BRD4-independent group 4 enhancer GRCh37_chrX:9374111-9375310 [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]
  • LOC126863201:CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:8725279-8726478 [Gene]
  • LOC126863202:CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:9098527-9099726 [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]
  • LOC126863197:MED14-independent group 3 enhancer GRCh37_chrX:7290864-7292063 [Gene]
  • LOC126863203:MED14-independent group 3 enhancer GRCh37_chrX:9320474-9321673 [Gene]
  • LOC129391292:MPRA-validated peak7351 silencer [Gene]
  • LOC129391293:MPRA-validated peak7356 silencer [Gene]
  • P2RY8:P2Y receptor family member 8 [Gene - OMIM - HGNC]
  • LOC126863195:P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:4969484-4970683 [Gene]
  • LOC126863199:P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:8313181-8314380 [Gene]
  • LOC126863200:P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:8462508-8463707 [Gene]
  • PRKX-AS1:PRKX antisense RNA 1 [Gene - HGNC]
  • LOC106029241:S232-VCX2 recombination region [Gene]
  • LOC106029240:S232-VCX3A recombination region [Gene]
  • 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]
  • LOC125446268:Sharpr-MPRA regulatory region 2097 [Gene]
  • LOC121627957:Sharpr-MPRA regulatory region 2843 [Gene]
  • LOC113875037:Sharpr-MPRA regulatory region 5189 [Gene]
  • LOC125446266:Sharpr-MPRA regulatory region 9499 [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]
  • ANOS1:anosmin 1 [Gene - 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]
  • FAM9A:family with sequence similarity 9 member A [Gene - OMIM - HGNC]
  • FAM9B:family with sequence similarity 9 member B [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]
  • MIR4767:microRNA 4767 [Gene - HGNC]
  • MIR4770:microRNA 4770 [Gene - HGNC]
  • MIR6089:microRNA 6089 [Gene - HGNC]
  • MIR651:microRNA 651 [Gene - HGNC]
  • NLGN4X:neuroligin 4 X-linked [Gene - OMIM - HGNC]
  • PNPLA4:patatin like phospholipase domain containing 4 [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]
  • PUDP:pseudouridine 5'-phosphatase [Gene - OMIM - HGNC]
  • SNORA48B:small nucleolar RNA, H/ACA box 48B [Gene - HGNC]
  • SLC25A6:solute carrier family 25 member 6 [Gene - OMIM - OMIM - HGNC]
  • STS:steroid sulfatase [Gene - 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]
  • VCX2:variable charge X-linked 2 [Gene - OMIM - HGNC]
  • VCX3A:variable charge X-linked 3A [Gene - OMIM - HGNC]
  • VCX3B:variable charge X-linked 3B [Gene - OMIM - HGNC]
  • VCX:variable charge X-linked [Gene - OMIM - HGNC]
  • 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:10679-9459643)x1
HGVS:
  • NC_000023.11:g.(?_10679)_(9459643_?)del
  • NC_000023.10:g.(?_60679)_(9427683_?)del
  • NC_000023.9:g.(?_679)_(9387683_?)del
Links:
dbVar: nssv576286; dbVar: nsv492223
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
SCV000173629ISCA site 1

See additional submitters

no assertion criteria provided
Pathogenic
(Aug 18, 2010) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot providedyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.

Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, et al.

Am J Hum Genet. 2010 May 14;86(5):749-64. doi: 10.1016/j.ajhg.2010.04.006. Review.

PubMed [citation]
PMID:
20466091
PMCID:
PMC2869000

Details of each submission

From ISCA site 1, SCV000173629.4

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

Last Updated: May 7, 2024