GRCh38/hg38 Xp11.23-11.22(chrX:47859417-52789530)x3 AND See cases

Clinical significance:Pathogenic (Last evaluated: Aug 12, 2011)

Review status:1 star out of maximum of 4 stars

classified by single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000052390.3

Allele description [Variation Report for ]

GRCh38/hg38 Xp11.23-11.22(chrX:47859417-52789530)x3

Genes:
  • CACNA1F:calcium channel, voltage-dependent, L type, alpha 1F subunit [Gene - OMIM]
  • CLCN5:chloride channel, voltage-sensitive 5 [Gene - OMIM]
  • GAGE1:G antigen 1 [Gene - OMIM]
  • GAGE2C:G antigen 2C [Gene - OMIM]
  • GATA1:GATA binding protein 1 (globin transcription factor 1) [Gene - OMIM]
  • ERAS:ES cell expressed Ras [Gene - OMIM]
  • KCND1:potassium channel, voltage gated Shal related subfamily D, member 1 [Gene - OMIM]
  • PRICKLE3:prickle homolog 3 (Drosophila) [Gene - OMIM]
  • TBC1D25:TBC1 domain family, member 25 [Gene - OMIM]
  • PLP2:proteolipid protein 2 (colonic epithelium-enriched) [Gene - OMIM]
  • RBM3:RNA binding motif (RNP1, RRM) protein 3 [Gene - OMIM]
  • SSX1:synovial sarcoma, X breakpoint 1 [Gene - OMIM]
  • SSX2:synovial sarcoma, X breakpoint 2 [Gene - OMIM]
  • SSX5:synovial sarcoma, X breakpoint 5 [Gene - OMIM]
  • SSX4:synovial sarcoma, X breakpoint 4 [Gene - OMIM]
  • SUV39H1:suppressor of variegation 3-9 homolog 1 (Drosophila) [Gene - OMIM]
  • SYP:synaptophysin [Gene - OMIM]
  • TFE3:transcription factor binding to IGHM enhancer 3 [Gene - OMIM]
  • SLC35A2:solute carrier family 35 (UDP-galactose transporter), member A2 [Gene - OMIM]
  • WAS:Wiskott-Aldrich syndrome [Gene - OMIM]
  • ZNF182:zinc finger protein 182 [Gene - OMIM]
  • PAGE1:P antigen family, member 1 (prostate associated) [Gene - OMIM]
  • AKAP4:A kinase (PRKA) anchor protein 4 [Gene - OMIM]
  • BMP15:bone morphogenetic protein 15 [Gene - OMIM]
  • MAGED1:melanoma antigen family D1 [Gene - OMIM]
  • XAGE2:X antigen family, member 2 [Gene - OMIM]
  • PAGE4:P antigen family, member 4 (prostate associated) [Gene - OMIM]
  • HDAC6:histone deacetylase 6 [Gene - OMIM]
  • PQBP1:polyglutamine binding protein 1 [Gene - OMIM]
  • SSX3:synovial sarcoma, X breakpoint 3 [Gene - OMIM]
  • TIMM17B:translocase of inner mitochondrial membrane 17 homolog B (yeast) [Gene - OMIM]
  • EBP:emopamil binding protein (sterol isomerase) [Gene - OMIM]
  • PIM2:Pim-2 proto-oncogene, serine/threonine kinase [Gene - OMIM]
  • WDR45:WD repeat domain 45 [Gene - OMIM]
  • PRAF2:PRA1 domain family, member 2 [Gene - OMIM]
  • GSPT2:G1 to S phase transition 2 [Gene - OMIM]
  • FTSJ1:FtsJ RNA methyltransferase homolog 1 (E. coli) [Gene - OMIM]
  • GAGE12I:G antigen 12I [Gene - OMIM]
  • GAGE2E:G antigen 2E [Gene - OMIM]
  • GPKOW:G patch domain and KOW motifs [Gene]
  • PCSK1N:proprotein convertase subtilisin/kexin type 1 inhibitor [Gene - OMIM]
  • CCDC22:coiled-coil domain containing 22 [Gene - OMIM]
  • FOXP3:forkhead box P3 [Gene - OMIM]
  • NUDT11:nudix (nucleoside diphosphate linked moiety X)-type motif 11 [Gene - OMIM]
  • OTUD5:OTU deubiquitinase 5 [Gene - OMIM]
  • GRIPAP1:GRIP1 associated protein 1 [Gene - OMIM]
  • ZNF630:zinc finger protein 630 [Gene - OMIM]
  • SHROOM4:shroom family member 4 [Gene - OMIM]
  • WDR13:WD repeat domain 13 [Gene - OMIM]
  • PORCN:porcupine homolog (Drosophila) [Gene - OMIM]
  • MAGIX:MAGI family member, X-linked [Gene]
  • MAGED4B:melanoma antigen family D4B [Gene - OMIM]
  • CCNB3:cyclin B3 [Gene - OMIM]
  • PPP1R3F:protein phosphatase 1, regulatory subunit 3F [Gene]
  • CCDC120:coiled-coil domain containing 120 [Gene - OMIM]
  • SLC38A5:solute carrier family 38, member 5 [Gene - OMIM]
  • DGKK:diacylglycerol kinase, kappa [Gene - OMIM]
  • USP27X-AS1:USP27X antisense RNA 1 (head to head) [Gene]
  • NUDT10:nudix (nucleoside diphosphate linked moiety X)-type motif 10 [Gene - OMIM]
  • SSX6:synovial sarcoma, X breakpoint 6 (pseudogene) [Gene - OMIM]
  • SSX7:synovial sarcoma, X breakpoint 7 [Gene - OMIM]
  • SSX8:synovial sarcoma, X breakpoint 8 [Gene - OMIM]
  • SSX9:synovial sarcoma, X breakpoint 9 [Gene - OMIM]
  • CXorf67:chromosome X open reading frame 67 [Gene]
  • ZNF81:zinc finger protein 81 [Gene - OMIM]
  • SPACA5:sperm acrosome associated 5 [Gene - OMIM]
  • USP27X:ubiquitin specific peptidase 27, X-linked [Gene]
  • GLOD5:glyoxalase domain containing 5 [Gene]
  • MIR188:microRNA 188 [Gene]
  • SSX4B:synovial sarcoma, X breakpoint 4B [Gene]
  • MIR362:microRNA 362 [Gene]
  • MIR500A:microRNA 500a [Gene]
  • MIR501:microRNA 501 [Gene]
  • MIR502:microRNA 502 [Gene - OMIM]
  • GAGE2B:G antigen 2B [Gene - OMIM]
  • GAGE13:G antigen 13 [Gene - OMIM]
  • GAGE12G:G antigen 12G [Gene - OMIM]
  • XAGE1E:X antigen family, member 1E [Gene - OMIM - OMIM]
  • XAGE1B:X antigen family, member 1B [Gene - OMIM - OMIM]
  • MIR532:microRNA 532 [Gene]
  • MIR660:microRNA 660 [Gene]
  • SSX2B:synovial sarcoma, X breakpoint 2B [Gene]
  • MAGED4:melanoma antigen family D4 [Gene - OMIM]
  • SPACA5B:sperm acrosome associated 5B [Gene]
  • GAGE12J:G antigen 12J [Gene - OMIM]
  • GAGE2D:G antigen 2D [Gene - OMIM]
  • GAGE12C:G antigen 12C [Gene - OMIM]
  • GAGE12B:G antigen 12B [Gene]
  • GAGE12E:G antigen 12E [Gene - OMIM]
  • GAGE12H:G antigen 12H [Gene - OMIM]
  • GAGE2A:G antigen 2A [Gene - OMIM]
  • GAGE12F:G antigen 12F [Gene - OMIM]
  • GAGE8:G antigen 8 [Gene - OMIM]
  • SNORA11D:small nucleolar RNA, H/ACA box 11D [Gene]
  • GAGE12D:G antigen 12D [Gene - OMIM]
  • MIR500B:microRNA 500b [Gene]
  • SYP-AS1:SYP antisense RNA 1 [Gene]
  • ZNF630-AS1:ZNF630 antisense RNA 1 [Gene]
  • SNORA11E:small nucleolar RNA, H/ACA box 11E [Gene]
  • LINC01284:long intergenic non-protein coding RNA 1284 [Gene]
  • MIR8088:microRNA 8088 [Gene]
  • LINC01496:long intergenic non-protein coding RNA 1496 [Gene]
  • GAGE10:G antigen 10 [Gene - OMIM]
Variant type:
copy number gain
Cytogenetic location:
Xp11.23-11.22
Genomic location:
Preferred name:
GRCh38/hg38 Xp11.23-11.22(chrX:47859417-52789530)x3
HGVS:
  • NC_000023.11:g.(?_47859417)_(52789530_?)dup
  • NC_000023.10:g.(?_47835880)_(52818575_?)dup
Links:
dbVar: nsv531100
Observations:
1

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview StatusClinical Significance
(Last evaluated)
OriginMethodConsequenceCitations
SCV000079742ISCA site 6classified by single submitterPathogenic
(Aug 12, 2011)
not providedclinical testing

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

Description

Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations. Clinical assertions have been curated as described in Kaminsky et al. 2011.

SCV000079742

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 ISCA site 6, SCV000079742.3

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

Last Updated: Apr 29, 2015