GRCh38/hg38 Xq26.3-28(chrX:137118983-156003242)x1 AND See cases

Clinical significance:Pathogenic (Last evaluated: Mar 21, 2011)

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000137257.3

Allele description [Variation Report for GRCh38/hg38 Xq26.3-28(chrX:137118983-156003242)x1]

GRCh38/hg38 Xq26.3-28(chrX:137118983-156003242)x1

Genes:
  • AFF2:AF4/FMR2 family member 2 [Gene - OMIM - HGNC]
  • ABCD1:ATP binding cassette subfamily D member 1 [Gene - OMIM - HGNC]
  • ATP6AP1:ATPase H+ transporting accessory protein 1 [Gene - OMIM - HGNC]
  • ATP11C:ATPase phospholipid transporting 11C [Gene - OMIM - HGNC]
  • ATP2B3:ATPase plasma membrane Ca2+ transporting 3 [Gene - OMIM - HGNC]
  • BCAP31:B cell receptor associated protein 31 [Gene - OMIM - HGNC]
  • BRCC3:BRCA1/BRCA2-containing complex subunit 3 [Gene - OMIM - HGNC]
  • CMC4:C-X9-C motif containing 4 [Gene - HGNC]
  • CD99L2:CD99 molecule like 2 [Gene - OMIM - HGNC]
  • CSAG2:CSAG family member 2 [Gene - HGNC]
  • CSAG3:CSAG family member 3 [Gene - HGNC]
  • FAM3A:FAM3 metabolism regulating signaling molecule A [Gene - OMIM - HGNC]
  • FGF13-AS1:FGF13 antisense RNA 1 [Gene - HGNC]
  • FMR1-AS1:FMR1 antisense RNA 1 [Gene - OMIM - HGNC]
  • FMR1NB:FMR1 neighbor [Gene - HGNC]
  • FMR1:FMRP translational regulator 1 [Gene - OMIM - HGNC]
  • LOC108684022:FRAXA repeat instability region [Gene]
  • LOC109461475:FRAXE repeat instability region [Gene]
  • LOC109396974:FRAXF repeat instability region [Gene]
  • FUNDC2:FUN14 domain containing 2 [Gene - HGNC]
  • GPR50:G protein-coupled receptor 50 [Gene - OMIM - HGNC]
  • LOC108281126:G6PD and IKBKG intron CAGE-defined low expression enhancer [Gene]
  • GDI1:GDP dissociation inhibitor 1 [Gene - OMIM - HGNC]
  • GPR50-AS1:GPR50 antisense RNA 1 [Gene - HGNC]
  • GAB3:GRB2 associated binding protein 3 [Gene - OMIM - HGNC]
  • H2AB1:H2A.B variant histone 1 [Gene - HGNC]
  • H2AB2:H2A.B variant histone 2 [Gene - HGNC]
  • H2AB3:H2A.B variant histone 3 [Gene - OMIM - HGNC]
  • HAUS7:HAUS augmin like complex subunit 7 [Gene - OMIM - HGNC]
  • HCFC1-AS1:HCFC1 antisense RNA 1 [Gene - HGNC]
  • LOC111589209:HNF4 motif-containing MPRA enhancer 232 [Gene]
  • LOC106050102:IDS recombination region [Gene]
  • LOC106050103:IDSP1 recombination region [Gene]
  • LOC107988022:IKBKG downstream recombination region [Gene]
  • LOC107988021:IKBKG recombination region [Gene]
  • LOC107988024:IKBKGP1 recombination region [Gene]
  • LOC107988025:IKBKGP1 upstream recombination region [Gene]
  • LAGE3:L antigen family member 3 [Gene - OMIM - HGNC]
  • L1CAM:L1 cell adhesion molecule [Gene - OMIM - HGNC]
  • LDOC1:LDOC1 regulator of NFKB signaling [Gene - OMIM - HGNC]
  • MAGEA10:MAGE family member A10 [Gene - OMIM - HGNC]
  • MAGEA11:MAGE family member A11 [Gene - OMIM - HGNC]
  • MAGEA12:MAGE family member A12 [Gene - OMIM - HGNC]
  • MAGEA1:MAGE family member A1 [Gene - OMIM - HGNC]
  • MAGEA2:MAGE family member A2 [Gene - OMIM - HGNC]
  • MAGEA2B:MAGE family member A2B [Gene - OMIM - HGNC]
  • MAGEA3:MAGE family member A3 [Gene - OMIM - HGNC]
  • MAGEA4:MAGE family member A4 [Gene - OMIM - HGNC]
  • MAGEA5:MAGE family member A5 [Gene - OMIM - HGNC]
  • MAGEA6:MAGE family member A6 [Gene - OMIM - HGNC]
  • MAGEA8:MAGE family member A8 [Gene - OMIM - HGNC]
  • MAGEA9:MAGE family member A9 [Gene - OMIM - HGNC]
  • MAGEA9B:MAGE family member A9B [Gene - OMIM - HGNC]
  • MAGEC1:MAGE family member C1 [Gene - OMIM - HGNC]
  • MAGEC2:MAGE family member C2 [Gene - OMIM - HGNC]
  • MAGEC3:MAGE family member C3 [Gene - OMIM - HGNC]
  • MAGEA10-MAGEA5:MAGEA10-MAGEA5 readthrough [Gene]
  • MAGEA4-AS1:MAGEA4 antisense RNA 1 [Gene - HGNC]
  • MAGEA8-AS1:MAGEA8 antisense RNA 1 [Gene - HGNC]
  • MCF2:MCF.2 cell line derived transforming sequence [Gene - OMIM - HGNC]
  • NAA10:N(alpha)-acetyltransferase 10, NatA catalytic subunit [Gene - OMIM - HGNC]
  • NSDHL:NAD(P) dependent steroid dehydrogenase-like [Gene - OMIM - HGNC]
  • LOC111365170:NFE2L2 motif-containing MPRA enhancer 190/191 [Gene]
  • LOC111429618:NFE2L2 motif-containing MPRA enhancer 215 [Gene]
  • PASD1:PAS domain containing repressor 1 [Gene - OMIM - HGNC]
  • PDZD4:PDZ domain containing 4 [Gene - OMIM - HGNC]
  • PNMA3:PNMA family member 3 [Gene - OMIM - HGNC]
  • PNMA5:PNMA family member 5 [Gene - OMIM - HGNC]
  • PNMA6A:PNMA family member 6A [Gene - OMIM - HGNC]
  • PNMA6E:PNMA family member 6E [Gene - HGNC]
  • PNMA6F:PNMA family member 6F [Gene - HGNC]
  • RAB39B:RAB39B, member RAS oncogene family [Gene - OMIM - OMIM - HGNC]
  • ARHGAP4:Rho GTPase activating protein 4 [Gene - OMIM - HGNC]
  • SLITRK2:SLIT and NTRK like family member 2 [Gene - OMIM - HGNC]
  • SLITRK4:SLIT and NTRK like family member 4 [Gene - OMIM - HGNC]
  • LOC108281134:SOX3 promoter region [Gene]
  • SPANXA2:SPANX family member A2 [Gene - OMIM - HGNC]
  • SPANXB1:SPANX family member B1 [Gene - OMIM - HGNC]
  • SPANXC:SPANX family member C [Gene - OMIM - HGNC]
  • SPANXD:SPANX family member D [Gene - OMIM - OMIM - HGNC]
  • SPANXN1:SPANX family member N1 [Gene - OMIM - HGNC]
  • SPANXN2:SPANX family member N2 [Gene - OMIM - HGNC]
  • SPANXN3:SPANX family member N3 [Gene - OMIM - HGNC]
  • SPANXN4:SPANX family member N4 [Gene - OMIM - HGNC]
  • SPANXA2-OT1:SPANXA2 overlapping transcript 1 [Gene - HGNC]
  • SRPK3:SRSF protein kinase 3 [Gene - OMIM - HGNC]
  • SOX3:SRY-box transcription factor 3 [Gene - OMIM - HGNC]
  • LOC113875015:Sharpr-MPRA regulatory region 12525 [Gene]
  • LOC113875016:Sharpr-MPRA regulatory region 7862 [Gene]
  • LOC113875014:Sharpr-MPRA regulatory region 9358 [Gene]
  • TMLHE-AS1:TMLHE antisense RNA 1 [Gene - HGNC]
  • VBP1:VHL binding protein 1 [Gene - OMIM - HGNC]
  • LOC110121199:VISTA enhancer hs1746 [Gene]
  • LOC110120680:VISTA enhancer hs427 [Gene]
  • LOC110120737:VISTA enhancer hs667 [Gene]
  • LOC110120761:VISTA enhancer hs755 [Gene]
  • LOC107988033:Xq28 distal FLNA-EMD recombination region [Gene]
  • LOC107988032:Xq28 proximal FLNA-EMD recombination region [Gene]
  • ZFP92:ZFP92 zinc finger protein [Gene - HGNC]
  • ZIC3:Zic family member 3 [Gene - OMIM - HGNC]
  • AVPR2:arginine vasopressin receptor 2 [Gene - OMIM - HGNC]
  • BGN:biglycan [Gene - OMIM - HGNC]
  • CTAG1A:cancer/testis antigen 1A [Gene - OMIM - HGNC]
  • CTAG1B:cancer/testis antigen 1B [Gene - OMIM - HGNC]
  • CTAG2:cancer/testis antigen 2 [Gene - OMIM - HGNC]
  • CETN2:centrin 2 [Gene - OMIM - HGNC]
  • CDR1:cerebellar degeneration related protein 1 [Gene - OMIM - HGNC]
  • CLIC2:chloride intracellular channel 2 [Gene - OMIM - HGNC]
  • CSAG1:chondrosarcoma associated gene 1 [Gene - OMIM - HGNC]
  • LOC389895:chromosome 16 open reading frame 72-like [Gene]
  • CXorf40A:chromosome X open reading frame 40A [Gene - OMIM - HGNC]
  • CXorf40B:chromosome X open reading frame 40B [Gene - HGNC]
  • CXorf51A:chromosome X open reading frame 51A [Gene - HGNC]
  • CXorf51B:chromosome X open reading frame 51B [Gene - HGNC]
  • CXorf66:chromosome X open reading frame 66 [Gene - HGNC]
  • F9:coagulation factor IX [Gene - OMIM - HGNC]
  • F8A1:coagulation factor VIII associated 1 [Gene - OMIM - HGNC]
  • F8A2:coagulation factor VIII associated 2 [Gene - HGNC]
  • F8A3:coagulation factor VIII associated 3 [Gene - HGNC]
  • F8:coagulation factor VIII [Gene - OMIM - HGNC]
  • CNGA2:cyclic nucleotide gated channel subunit alpha 2 [Gene - OMIM - HGNC]
  • CCNQ:cyclin Q [Gene - OMIM - HGNC]
  • DNASE1L1:deoxyribonuclease 1 like 1 [Gene - OMIM - HGNC]
  • DUSP9:dual specificity phosphatase 9 [Gene - OMIM - HGNC]
  • DKC1:dyskerin pseudouridine synthase 1 [Gene - OMIM - HGNC]
  • EMD:emerin [Gene - OMIM - HGNC]
  • LOC100509091:extracellular matrix protein 2-like [Gene]
  • FAM223A:family with sequence similarity 223 member A [Gene - HGNC]
  • FAM223B:family with sequence similarity 223 member B [Gene - HGNC]
  • FAM50A:family with sequence similarity 50 member A [Gene - OMIM - HGNC]
  • FATE1:fetal and adult testis expressed 1 [Gene - OMIM - HGNC]
  • FGF13:fibroblast growth factor 13 [Gene - OMIM - HGNC]
  • FLNA:filamin A [Gene - OMIM - HGNC]
  • GABRA3:gamma-aminobutyric acid type A receptor alpha3 subunit [Gene - OMIM - HGNC]
  • GABRE:gamma-aminobutyric acid type A receptor epsilon subunit [Gene - OMIM - HGNC]
  • GABRQ:gamma-aminobutyric acid type A receptor theta subunit [Gene - OMIM - HGNC]
  • G6PD:glucose-6-phosphate dehydrogenase [Gene - OMIM - HGNC]
  • HSFX1:heat shock transcription factor family, X-linked 1 [Gene - HGNC]
  • HSFX2:heat shock transcription factor family, X-linked 2 [Gene - HGNC]
  • HSFX3:heat shock transcription factor family, X-linked member 3 [Gene - HGNC]
  • HSFX4:heat shock transcription factor family, X-linked member 4 [Gene - HGNC]
  • HMGB3:high mobility group box 3 [Gene - OMIM - HGNC]
  • HCFC1:host cell factor C1 [Gene - OMIM - HGNC]
  • IDS:iduronate 2-sulfatase [Gene - OMIM - HGNC]
  • IKBKG:inhibitor of nuclear factor kappa B kinase regulatory subunit gamma [Gene - OMIM - HGNC]
  • LOC106146143:int1h-1 recombination region [Gene]
  • LOC106146144:int1h-2 recombination region [Gene]
  • LOC106146150:int22h-1 recombination region [Gene]
  • LOC106146151:int22h-2 recombination region [Gene]
  • LOC106146152:int22h-3 recombination region [Gene]
  • IRAK1:interleukin 1 receptor associated kinase 1 [Gene - OMIM - HGNC]
  • IL9R:interleukin 9 receptor [Gene - OMIM - HGNC]
  • IDH3G:isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gamma [Gene - OMIM - HGNC]
  • LINC00632:long intergenic non-protein coding RNA 632 [Gene - HGNC]
  • LINC00850:long intergenic non-protein coding RNA 850 [Gene - OMIM - HGNC]
  • LINC00889:long intergenic non-protein coding RNA 889 [Gene - HGNC]
  • LINC00893:long intergenic non-protein coding RNA 893 [Gene - HGNC]
  • LINC00894:long intergenic non-protein coding RNA 894 [Gene - HGNC]
  • LCA10:lung carcinoma-associated 10 [Gene]
  • MAMLD1:mastermind like domain containing 1 [Gene - OMIM - HGNC]
  • MTCP1:mature T cell proliferation 1 [Gene - OMIM - HGNC]
  • LOC107522039:meiotic recombination hotspot PAR2 [Gene]
  • LOC107838685:meiotic recombination hotspot PAR2A [Gene]
  • MPP1:membrane palmitoylated protein 1 [Gene - OMIM - HGNC]
  • MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]
  • MIR105-1:microRNA 105-1 [Gene - OMIM - HGNC]
  • MIR105-2:microRNA 105-2 [Gene - OMIM - HGNC]
  • MIR1184-1:microRNA 1184-1 [Gene - HGNC]
  • MIR1184-2:microRNA 1184-2 [Gene - HGNC]
  • MIR1184-3:microRNA 1184-3 [Gene - HGNC]
  • MIR12129:microRNA 12129 [Gene - HGNC]
  • MIR2114:microRNA 2114 [Gene - HGNC]
  • MIR224:microRNA 224 [Gene - OMIM - HGNC]
  • MIR3202-1:microRNA 3202-1 [Gene - HGNC]
  • MIR3202-2:microRNA 3202-2 [Gene - HGNC]
  • MIR320D2:microRNA 320d-2 [Gene - HGNC]
  • MIR4330:microRNA 4330 [Gene - HGNC]
  • MIR452:microRNA 452 [Gene - HGNC]
  • MIR504:microRNA 504 [Gene - HGNC]
  • MIR505:microRNA 505 [Gene - HGNC]
  • MIR506:microRNA 506 [Gene - OMIM - HGNC]
  • MIR507:microRNA 507 [Gene - HGNC]
  • MIR508:microRNA 508 [Gene - OMIM - HGNC]
  • MIR509-1:microRNA 509-1 [Gene - OMIM - HGNC]
  • MIR509-2:microRNA 509-2 [Gene - HGNC]
  • MIR509-3:microRNA 509-3 [Gene - OMIM - HGNC]
  • MIR510:microRNA 510 [Gene - OMIM - HGNC]
  • MIR513A1:microRNA 513a-1 [Gene - HGNC]
  • MIR513A2:microRNA 513a-2 [Gene - HGNC]
  • MIR513B:microRNA 513b [Gene - HGNC]
  • MIR513C:microRNA 513c [Gene - HGNC]
  • MIR514A1:microRNA 514a-1 [Gene - HGNC]
  • MIR514A2:microRNA 514a-2 [Gene - HGNC]
  • MIR514A3:microRNA 514a-3 [Gene - HGNC]
  • MIR514B:microRNA 514b [Gene - HGNC]
  • MIR664B:microRNA 664b [Gene - HGNC]
  • MIR6858:microRNA 6858 [Gene - HGNC]
  • MIR718:microRNA 718 [Gene - OMIM - HGNC]
  • MIR767:microRNA 767 [Gene - HGNC]
  • MIR888:microRNA 888 [Gene - HGNC]
  • MIR890:microRNA 890 [Gene - HGNC]
  • MIR891A:microRNA 891a [Gene - HGNC]
  • MIR891B:microRNA 891b [Gene - HGNC]
  • MIR892A:microRNA 892a [Gene - HGNC]
  • MIR892B:microRNA 892b [Gene - HGNC]
  • MIR892C:microRNA 892c [Gene - HGNC]
  • MTM1:myotubularin 1 [Gene - OMIM - HGNC]
  • MTMR1:myotubularin related protein 1 [Gene - OMIM - HGNC]
  • OPN1LW:opsin 1, long wave sensitive [Gene - OMIM - HGNC]
  • OPN1MW2:opsin 1, medium wave sensitive 2 [Gene - HGNC]
  • OPN1MW3:opsin 1, medium wave sensitive 3 [Gene - HGNC]
  • OPN1MW:opsin 1, medium wave sensitive [Gene - OMIM - HGNC]
  • OPSIN-LCR:opsin locus control region [Gene - OMIM]
  • LOC107048984:origin of replication in 5' region of AFF2/FMR2 [Gene]
  • LOC107032825:origin of replication in 5' region of FMR1 [Gene]
  • LOC107181288:origin of replication in promoter of G6PD [Gene]
  • LOC107048982:origin of replication upstream of FMR1 [Gene]
  • PLXNA3:plexin A3 [Gene - OMIM - HGNC]
  • PLXNB3:plexin B3 [Gene - OMIM - HGNC]
  • PNCK:pregnancy up-regulated nonubiquitous CaM kinase [Gene - OMIM - HGNC]
  • PRRG3:proline rich and Gla domain 3 [Gene - OMIM - HGNC]
  • RENBP:renin binding protein [Gene - OMIM - HGNC]
  • RPL10:ribosomal protein L10 [Gene - OMIM - HGNC]
  • SSR4:signal sequence receptor subunit 4 [Gene - OMIM - HGNC]
  • SMIM9:small integral membrane protein 9 [Gene - HGNC]
  • SNORA36A:small nucleolar RNA, H/ACA box 36A [Gene - HGNC]
  • SNORA56:small nucleolar RNA, H/ACA box 56 [Gene - HGNC]
  • SNORA70:small nucleolar RNA, H/ACA box 70 [Gene - HGNC]
  • SLC10A3:solute carrier family 10 member 3 [Gene - OMIM - HGNC]
  • SLC6A8:solute carrier family 6 member 8 [Gene - OMIM - HGNC]
  • SPANXA1:sperm protein associated with the nucleus, X-linked, family member A1 [Gene - OMIM - HGNC]
  • SPRY3:sprouty RTK signaling antagonist 3 [Gene - OMIM - HGNC]
  • TAZ:tafazzin [Gene - OMIM - HGNC]
  • TEX28:testis expressed 28 [Gene - OMIM - HGNC]
  • TREX2:three prime repair exonuclease 2 [Gene - OMIM - HGNC]
  • TKTL1:transketolase like 1 [Gene - OMIM - HGNC]
  • TMEM185A:transmembrane protein 185A [Gene - OMIM - HGNC]
  • TMEM187:transmembrane protein 187 [Gene - OMIM - HGNC]
  • TMLHE:trimethyllysine hydroxylase, epsilon [Gene - OMIM - HGNC]
  • UBE2NL:ubiquitin conjugating enzyme E2 N like (gene/pseudogene) [Gene - HGNC]
  • UBL4A:ubiquitin like 4A [Gene - OMIM - HGNC]
  • LOC101927830:uncharacterized LOC101927830 [Gene]
  • LOC105373378:uncharacterized LOC105373378 [Gene]
  • LOC105373383:uncharacterized LOC105373383 [Gene]
  • LOC105377213:uncharacterized LOC105377213 [Gene]
  • LOC645188:uncharacterized LOC645188 [Gene]
  • LOC728660:uncharacterized LOC728660 [Gene]
  • CH17-340M24.3:uncharacterized protein BC009467 [Gene]
  • VMA21:vacuolar ATPase assembly factor VMA21 [Gene - OMIM - HGNC]
  • VAMP7:vesicle associated membrane protein 7 [Gene - OMIM - HGNC]
  • ZNF185:zinc finger protein 185 with LIM domain [Gene - OMIM - HGNC]
  • ZNF275:zinc finger protein 275 [Gene - HGNC]
Variant type:
copy number loss
Cytogenetic location:
Xq26.3-28
Genomic location:
Preferred name:
GRCh38/hg38 Xq26.3-28(chrX:137118983-156003242)x1
HGVS:
  • NC_000023.11:g.(?_137118983)_(156003242_?)del
  • NC_000023.10:g.(?_136201142)_(155232907_?)del
  • NC_000023.9:g.(?_136028808)_(154886101_?)del
Links:
dbVar: nssv1415044; dbVar: nsv817179
Observations:
1

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000177473ISCA site 1

See additional submitters

no assertion criteria providedPathogenic
(Mar 21, 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, with clinical assertions as classified by the original submitter.

SCV000177473

Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter. For data from the original published study, [Kaminsky, et al. 2011|/pubmed/21844811], please see [nstd101|/dbvar/studies/nstd101/].

SCV000177473

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, SCV000177473.4

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

Last Updated: Oct 4, 2019

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