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GRCh38/hg38 Xq27.3-28(chrX:143293592-149749234) AND Mucopolysaccharidosis, MPS-II

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 30, 2023
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:
RCV003448583.1

Allele description [Variation Report for GRCh38/hg38 Xq27.3-28(chrX:143293592-149749234)]

GRCh38/hg38 Xq27.3-28(chrX:143293592-149749234)

Genes:
  • AFF2:ALF transcription elongation factor 2 [Gene - OMIM - HGNC]
  • LOC129929048:ATAC-STARR-seq lymphoblastoid active region 30006 [Gene]
  • LOC129929049:ATAC-STARR-seq lymphoblastoid active region 30007 [Gene]
  • LOC130068774:ATAC-STARR-seq lymphoblastoid active region 30008 [Gene]
  • LOC130068775:ATAC-STARR-seq lymphoblastoid active region 30009 [Gene]
  • LOC130068776:ATAC-STARR-seq lymphoblastoid active region 30010 [Gene]
  • LOC130068777:ATAC-STARR-seq lymphoblastoid active region 30011 [Gene]
  • LOC130068778:ATAC-STARR-seq lymphoblastoid active region 30012 [Gene]
  • LOC130068779:ATAC-STARR-seq lymphoblastoid active region 30013 [Gene]
  • LOC130068780:ATAC-STARR-seq lymphoblastoid active region 30014 [Gene]
  • LOC130068781:ATAC-STARR-seq lymphoblastoid active region 30015 [Gene]
  • LOC130068785:ATAC-STARR-seq lymphoblastoid active region 30016 [Gene]
  • LOC129929053:ATAC-STARR-seq lymphoblastoid silent region 21039 [Gene]
  • LOC130068782:ATAC-STARR-seq lymphoblastoid silent region 21041 [Gene]
  • LOC130068783:ATAC-STARR-seq lymphoblastoid silent region 21042 [Gene]
  • LOC130068784:ATAC-STARR-seq lymphoblastoid silent region 21043 [Gene]
  • LOC130068786:ATAC-STARR-seq lymphoblastoid silent region 21044 [Gene]
  • LOC130068787:ATAC-STARR-seq lymphoblastoid silent region 21045 [Gene]
  • LOC126863342:CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:148591963-148593162 [Gene]
  • EOLA1-DT:EOLA1 divergent transcript [Gene - HGNC]
  • FMR1-AS1:FMR1 antisense RNA 1 [Gene - OMIM - HGNC]
  • FMR1NB:FMR1 neighbor [Gene - HGNC]
  • LOC109396974:FRAXF repeat instability region [Gene]
  • LOC106050102:IDS recombination region [Gene]
  • LOC106050103:IDSP1 recombination region [Gene]
  • MAGEA11:MAGE family member A11 [Gene - OMIM - HGNC]
  • MAGEA9B:MAGE family member A9B [Gene - OMIM - HGNC]
  • LOC126863338:MED14-independent group 3 enhancer GRCh37_chrX:144556098-144557297 [Gene]
  • LOC126863339:MED14-independent group 3 enhancer GRCh37_chrX:144939449-144940648 [Gene]
  • LOC126863341:MED14-independent group 3 enhancer GRCh37_chrX:147636485-147637684 [Gene]
  • LOC126863337:P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:143882879-143884078 [Gene]
  • LOC126863340:P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:146645835-146647034 [Gene]
  • SLITRK2:SLIT and NTRK like family member 2 [Gene - OMIM - HGNC]
  • SLITRK4:SLIT and NTRK like family member 4 [Gene - 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]
  • LOC121627983:Sharpr-MPRA regulatory region 15241 [Gene]
  • LOC125467790:Sharpr-MPRA regulatory region 6851 [Gene]
  • CXorf51A:chromosome X open reading frame 51A [Gene - HGNC]
  • CXorf51B:chromosome X open reading frame 51B [Gene - HGNC]
  • EOLA1:endothelium and lymphocyte associated ASCH domain 1 [Gene - OMIM - HGNC]
  • FMR1:fragile X messenger ribonucleoprotein 1 [Gene - OMIM - HGNC]
  • FRAXA:fragile site, folic acid type, rare, fra(X)(q27.3) A [Gene - HGNC]
  • FRAXE:fragile site, folic acid type, rare, fra(X)(q28) E [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]
  • IDS:iduronate 2-sulfatase [Gene - OMIM - 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]
  • 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]
  • LOC107048984:origin of replication in 5' region of AFF2/FMR2 [Gene]
  • LOC107032825:origin of replication in 5' region of FMR1 [Gene]
  • LOC107048982:origin of replication upstream of FMR1 [Gene]
  • TMEM185A:transmembrane protein 185A [Gene - OMIM - HGNC]
  • UBE2NL:ubiquitin conjugating enzyme E2 N like (gene/pseudogene) [Gene - HGNC]
  • LOC122319696:uncharacterized LOC122319696 [Gene]
Variant type:
copy number gain
Cytogenetic location:
Xq27.3-28
Genomic location:
ChrX: 143183118 - 149755404 (on Assembly GRCh38)
Preferred name:
GRCh38/hg38 Xq27.3-28(chrX:143293592-149749234)
Observations:
1

Condition(s)

Name:
Mucopolysaccharidosis, MPS-II (MPS2)
Synonyms:
Mucopolysaccharidosis type II; Attenuated MPS (subtype; formerly known as mild MPS II); Severe MPS II; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010674; MedGen: C0026705; Orphanet: 580; OMIM: 309900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004176094New York Genome Center
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(May 30, 2023) 		inheritedclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center, SCV004176094.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

Last Updated: Dec 17, 2023