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GRCh38/hg38 Xp11.4-11.23(chrX:41434043-47880733)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:
RCV000053088.5

Allele description [Variation Report for GRCh38/hg38 Xp11.4-11.23(chrX:41434043-47880733)x1]

GRCh38/hg38 Xp11.4-11.23(chrX:41434043-47880733)x1

Genes:
  • ARAF:A-Raf proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]
  • LOC130068162:ATAC-STARR-seq lymphoblastoid active region 29555 [Gene]
  • LOC130068164:ATAC-STARR-seq lymphoblastoid active region 29556 [Gene]
  • LOC130068165:ATAC-STARR-seq lymphoblastoid active region 29557 [Gene]
  • LOC130068166:ATAC-STARR-seq lymphoblastoid active region 29558 [Gene]
  • LOC130068167:ATAC-STARR-seq lymphoblastoid active region 29559 [Gene]
  • LOC130068168:ATAC-STARR-seq lymphoblastoid active region 29560 [Gene]
  • LOC130068171:ATAC-STARR-seq lymphoblastoid active region 29561 [Gene]
  • LOC130068175:ATAC-STARR-seq lymphoblastoid active region 29562 [Gene]
  • LOC130068178:ATAC-STARR-seq lymphoblastoid active region 29565 [Gene]
  • LOC130068179:ATAC-STARR-seq lymphoblastoid active region 29566 [Gene]
  • LOC130068180:ATAC-STARR-seq lymphoblastoid active region 29567 [Gene]
  • LOC130068187:ATAC-STARR-seq lymphoblastoid active region 29568 [Gene]
  • LOC130068188:ATAC-STARR-seq lymphoblastoid active region 29569 [Gene]
  • LOC130068190:ATAC-STARR-seq lymphoblastoid active region 29571 [Gene]
  • LOC130068194:ATAC-STARR-seq lymphoblastoid active region 29572 [Gene]
  • LOC130068195:ATAC-STARR-seq lymphoblastoid active region 29573 [Gene]
  • LOC130068196:ATAC-STARR-seq lymphoblastoid active region 29574 [Gene]
  • LOC130068199:ATAC-STARR-seq lymphoblastoid active region 29575 [Gene]
  • LOC130068200:ATAC-STARR-seq lymphoblastoid active region 29576 [Gene]
  • LOC130068202:ATAC-STARR-seq lymphoblastoid active region 29577 [Gene]
  • LOC130068203:ATAC-STARR-seq lymphoblastoid active region 29578 [Gene]
  • LOC130068205:ATAC-STARR-seq lymphoblastoid active region 29579 [Gene]
  • LOC130068206:ATAC-STARR-seq lymphoblastoid active region 29580 [Gene]
  • LOC130068207:ATAC-STARR-seq lymphoblastoid active region 29581 [Gene]
  • LOC130068208:ATAC-STARR-seq lymphoblastoid active region 29582 [Gene]
  • LOC130068209:ATAC-STARR-seq lymphoblastoid active region 29583 [Gene]
  • LOC130068212:ATAC-STARR-seq lymphoblastoid active region 29586 [Gene]
  • LOC130068213:ATAC-STARR-seq lymphoblastoid active region 29587 [Gene]
  • LOC130068215:ATAC-STARR-seq lymphoblastoid active region 29589 [Gene]
  • LOC130068216:ATAC-STARR-seq lymphoblastoid active region 29590 [Gene]
  • LOC130068217:ATAC-STARR-seq lymphoblastoid active region 29591 [Gene]
  • LOC130068218:ATAC-STARR-seq lymphoblastoid active region 29592 [Gene]
  • LOC130068219:ATAC-STARR-seq lymphoblastoid active region 29593 [Gene]
  • LOC130068226:ATAC-STARR-seq lymphoblastoid active region 29595 [Gene]
  • LOC130068227:ATAC-STARR-seq lymphoblastoid active region 29596 [Gene]
  • LOC130068228:ATAC-STARR-seq lymphoblastoid active region 29597 [Gene]
  • LOC130068229:ATAC-STARR-seq lymphoblastoid active region 29598 [Gene]
  • LOC130068163:ATAC-STARR-seq lymphoblastoid silent region 20775 [Gene]
  • LOC130068169:ATAC-STARR-seq lymphoblastoid silent region 20776 [Gene]
  • LOC130068170:ATAC-STARR-seq lymphoblastoid silent region 20777 [Gene]
  • LOC130068172:ATAC-STARR-seq lymphoblastoid silent region 20778 [Gene]
  • LOC130068173:ATAC-STARR-seq lymphoblastoid silent region 20779 [Gene]
  • LOC130068174:ATAC-STARR-seq lymphoblastoid silent region 20780 [Gene]
  • LOC130068176:ATAC-STARR-seq lymphoblastoid silent region 20781 [Gene]
  • LOC130068177:ATAC-STARR-seq lymphoblastoid silent region 20782 [Gene]
  • LOC130068181:ATAC-STARR-seq lymphoblastoid silent region 20783 [Gene]
  • LOC130068182:ATAC-STARR-seq lymphoblastoid silent region 20784 [Gene]
  • LOC130068183:ATAC-STARR-seq lymphoblastoid silent region 20785 [Gene]
  • LOC130068184:ATAC-STARR-seq lymphoblastoid silent region 20786 [Gene]
  • LOC130068185:ATAC-STARR-seq lymphoblastoid silent region 20787 [Gene]
  • LOC130068186:ATAC-STARR-seq lymphoblastoid silent region 20788 [Gene]
  • LOC130068189:ATAC-STARR-seq lymphoblastoid silent region 20789 [Gene]
  • LOC130068191:ATAC-STARR-seq lymphoblastoid silent region 20790 [Gene]
  • LOC130068192:ATAC-STARR-seq lymphoblastoid silent region 20791 [Gene]
  • LOC130068193:ATAC-STARR-seq lymphoblastoid silent region 20792 [Gene]
  • LOC130068197:ATAC-STARR-seq lymphoblastoid silent region 20793 [Gene]
  • LOC130068198:ATAC-STARR-seq lymphoblastoid silent region 20794 [Gene]
  • LOC130068201:ATAC-STARR-seq lymphoblastoid silent region 20795 [Gene]
  • LOC130068204:ATAC-STARR-seq lymphoblastoid silent region 20797 [Gene]
  • LOC130068210:ATAC-STARR-seq lymphoblastoid silent region 20798 [Gene]
  • LOC130068211:ATAC-STARR-seq lymphoblastoid silent region 20799 [Gene]
  • LOC130068214:ATAC-STARR-seq lymphoblastoid silent region 20803 [Gene]
  • LOC130068220:ATAC-STARR-seq lymphoblastoid silent region 20804 [Gene]
  • LOC130068221:ATAC-STARR-seq lymphoblastoid silent region 20805 [Gene]
  • LOC130068222:ATAC-STARR-seq lymphoblastoid silent region 20806 [Gene]
  • LOC130068223:ATAC-STARR-seq lymphoblastoid silent region 20807 [Gene]
  • LOC130068224:ATAC-STARR-seq lymphoblastoid silent region 20808 [Gene]
  • LOC130068225:ATAC-STARR-seq lymphoblastoid silent region 20809 [Gene]
  • LOC126863249:BRD4-independent group 4 enhancer GRCh37_chrX:46186381-46187580 [Gene]
  • LOC126863250:BRD4-independent group 4 enhancer GRCh37_chrX:46404230-46405429 [Gene]
  • LOC126863251:BRD4-independent group 4 enhancer GRCh37_chrX:46569386-46570585 [Gene]
  • CASK-AS1:CASK antisense RNA 1 [Gene - HGNC]
  • LOC126863248:CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:46122614-46123813 [Gene]
  • LOC126863252:CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:47037923-47039122 [Gene]
  • LOC126863253:CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:47057593-47058792 [Gene]
  • LOC119369038:CRISPRi-FlowFISH-validated HDAC6 regulatory element 1 [Gene]
  • LOC119369039:CRISPRi-FlowFISH-validated HDAC6 regulatory element 2 [Gene]
  • LOC119407397:CRISPRi-FlowFISH-validated PLP2 regulatory element 2 [Gene]
  • LOC116309151:CRISPRi-validated cis-regulatory element chrX.881 [Gene]
  • EFHC2:EF-hand domain containing 2 [Gene - OMIM - HGNC]
  • ELK1:ETS transcription factor ELK1 [Gene - OMIM - HGNC]
  • FUNDC1:FUN14 domain containing 1 [Gene - OMIM - HGNC]
  • GPR34:G protein-coupled receptor 34 [Gene - OMIM - HGNC]
  • GPR82:G protein-coupled receptor 82 [Gene - OMIM - HGNC]
  • KRBOX4:KRAB box domain containing 4 [Gene - OMIM - HGNC]
  • LOC126863241:MED14-independent group 3 enhancer GRCh37_chrX:41944854-41946053 [Gene]
  • LOC126863242:MED14-independent group 3 enhancer GRCh37_chrX:42835354-42836553 [Gene]
  • LOC126863243:MED14-independent group 3 enhancer GRCh37_chrX:43035494-43036693 [Gene]
  • LOC126863244:MED14-independent group 3 enhancer GRCh37_chrX:44834497-44835696 [Gene]
  • LOC126863245:MED14-independent group 3 enhancer GRCh37_chrX:45339311-45340510 [Gene]
  • LOC126863247:MED14-independent group 3 enhancer GRCh37_chrX:45662536-45663735 [Gene]
  • LOC126863254:MED14-independent group 3 enhancer GRCh37_chrX:47675037-47676236 [Gene]
  • LOC129391298:MPRA-validated peak7375 silencer [Gene]
  • LOC129391299:MPRA-validated peak7376 silencer [Gene]
  • LOC129391300:MPRA-validated peak7378 silencer [Gene]
  • NDUFB11:NADH:ubiquinone oxidoreductase subunit B11 [Gene - OMIM - HGNC]
  • NDP-AS1:NDP antisense RNA 1 [Gene - HGNC]
  • LOC126863246:P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:45365739-45366938 [Gene]
  • PPP1R2C:PPP1R2C family member C [Gene - OMIM - HGNC]
  • RBM10:RNA binding motif protein 10 [Gene - OMIM - HGNC]
  • RP2:RP2 activator of ARL3 GTPase [Gene - OMIM - HGNC]
  • LOC113875027:Sharpr-MPRA regulatory region 10799 [Gene]
  • LOC125467746:Sharpr-MPRA regulatory region 11481 [Gene]
  • LOC125467740:Sharpr-MPRA regulatory region 11747 [Gene]
  • LOC121627968:Sharpr-MPRA regulatory region 12888 [Gene]
  • LOC125467739:Sharpr-MPRA regulatory region 13194 [Gene]
  • LOC125467741:Sharpr-MPRA regulatory region 14703 [Gene]
  • LOC125467738:Sharpr-MPRA regulatory region 14962 [Gene]
  • LOC113875026:Sharpr-MPRA regulatory region 2101 [Gene]
  • LOC121853054:Sharpr-MPRA regulatory region 4088 [Gene]
  • LOC113875030:Sharpr-MPRA regulatory region 4668 [Gene]
  • LOC121627969:Sharpr-MPRA regulatory region 5152 [Gene]
  • LOC125467745:Sharpr-MPRA regulatory region 5754 [Gene]
  • LOC113875028:Sharpr-MPRA regulatory region 7060 [Gene]
  • LOC113875029:Sharpr-MPRA regulatory region 8750 [Gene]
  • LOC121853055:Sharpr-MPRA regulatory region 9461 [Gene]
  • TIMP1:TIMP metallopeptidase inhibitor 1 [Gene - OMIM - HGNC]
  • UXT-AS1:UXT antisense RNA 1 [Gene - HGNC]
  • ZNF674-AS1:ZNF674 antisense RNA 1 (head to head) [Gene - HGNC]
  • CASK:calcium/calmodulin dependent serine protein kinase [Gene - OMIM - HGNC]
  • CHST7:carbohydrate sulfotransferase 7 [Gene - OMIM - HGNC]
  • CFP:complement factor properdin [Gene - OMIM - HGNC]
  • CDK16:cyclin dependent kinase 16 [Gene - OMIM - HGNC]
  • DIPK2B:divergent protein kinase domain 2B [Gene - OMIM - HGNC]
  • DUSP21:dual specificity phosphatase 21 [Gene - OMIM - HGNC]
  • INE1:inactivation escape 1 [Gene - OMIM - HGNC]
  • JADE3:jade family PHD finger 3 [Gene - OMIM - HGNC]
  • LINC01186:long intergenic non-protein coding RNA 1186 [Gene - HGNC]
  • LINC01204:long intergenic non-protein coding RNA 1204 [Gene - HGNC]
  • LINC01545:long intergenic non-protein coding RNA 1545 [Gene - HGNC]
  • LINC01560:long intergenic non-protein coding RNA 1560 [Gene - HGNC]
  • LINC02595:long intergenic non-protein coding RNA 2595 [Gene - HGNC]
  • KDM6A:lysine demethylase 6A [Gene - OMIM - HGNC]
  • MIR222HG:miR222/221 cluster host gene [Gene - HGNC]
  • MIR221:microRNA 221 [Gene - OMIM - HGNC]
  • MIR222:microRNA 222 [Gene - OMIM - HGNC]
  • MIR4769:microRNA 4769 [Gene - HGNC]
  • MAOA:monoamine oxidase A [Gene - OMIM - HGNC]
  • MAOB:monoamine oxidase B [Gene - OMIM - HGNC]
  • NDP:norrin cystine knot growth factor NDP [Gene - OMIM - HGNC]
  • NYX:nyctalopin [Gene - OMIM - HGNC]
  • PINCR:p53-induced noncoding RNA [Gene - HGNC]
  • RGN:regucalcin [Gene - OMIM - HGNC]
  • SNORA11C:small nucleolar RNA, H/ACA box 11C [Gene - HGNC]
  • SLC9A7:solute carrier family 9 member A7 [Gene - OMIM - HGNC]
  • SYN1:synapsin I [Gene - OMIM - HGNC]
  • UBA1:ubiquitin like modifier activating enzyme 1 [Gene - OMIM - HGNC]
  • USP11:ubiquitin specific peptidase 11 [Gene - OMIM - HGNC]
  • UXT:ubiquitously expressed prefoldin like chaperone [Gene - OMIM - HGNC]
  • ZNF157:zinc finger protein 157 [Gene - OMIM - HGNC]
  • ZNF41:zinc finger protein 41 [Gene - OMIM - HGNC]
  • ZNF674:zinc finger protein 674 [Gene - OMIM - HGNC]
  • ZNF81:zinc finger protein 81 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
Xp11.4-11.23
Genomic location:
Preferred name:
GRCh38/hg38 Xp11.4-11.23(chrX:41434043-47880733)x1
HGVS:
  • NC_000023.11:g.(?_41434043)_(47880733_?)del
  • NC_000023.10:g.(?_41293296)_(47619970_?)del
  • NC_000023.9:g.(?_41178240)_(47625076_?)del
Links:
dbVar: nssv578433; dbVar: nsv531778
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
SCV000080443GeneDx
criteria provided, single submitter

(Kaminsky et al. (Genet Med. 2011))		Pathogenic
(Aug 12, 2011) 		not providedclinical 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

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, SCV000080443.5

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

Last Updated: Sep 1, 2024