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GRCh38/hg38 Xq28(chrX:154895862-155336084) AND Chromosome Xq28 duplication syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 2, 2022
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:
RCV004555194.1

Allele description [Variation Report for GRCh38/hg38 Xq28(chrX:154895862-155336084)]

GRCh38/hg38 Xq28(chrX:154895862-155336084)

Genes:
  • LOC130068891:ATAC-STARR-seq lymphoblastoid active region 30072 [Gene]
  • LOC130068892:ATAC-STARR-seq lymphoblastoid active region 30073 [Gene]
  • LOC130068895:ATAC-STARR-seq lymphoblastoid active region 30074 [Gene]
  • LOC130068893:ATAC-STARR-seq lymphoblastoid silent region 21120 [Gene]
  • LOC130068894:ATAC-STARR-seq lymphoblastoid silent region 21121 [Gene]
  • LOC130068896:ATAC-STARR-seq lymphoblastoid silent region 21124 [Gene]
  • LOC130068897:ATAC-STARR-seq lymphoblastoid silent region 21125 [Gene]
  • BRCC3:BRCA1/BRCA2-containing complex subunit 3 [Gene - OMIM - HGNC]
  • CMC4:C-X9-C motif containing 4 [Gene - OMIM - HGNC]
  • FUNDC2:FUN14 domain containing 2 [Gene - OMIM - HGNC]
  • H2AB1:H2A.B variant histone 1 [Gene - OMIM - HGNC]
  • H2AB2:H2A.B variant histone 2 [Gene - OMIM - HGNC]
  • H2AB3:H2A.B variant histone 3 [Gene - OMIM - HGNC]
  • LOC126863349:P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:154195537-154196736 [Gene]
  • RAB39B:RAB39B, member RAS oncogene family [Gene - OMIM - HGNC]
  • LOC121627986:Sharpr-MPRA regulatory region 3530 [Gene]
  • LOC125467795:Sharpr-MPRA regulatory region 4209 [Gene]
  • LOC113875016:Sharpr-MPRA regulatory region 7862 [Gene]
  • TMLHE-AS1:TMLHE antisense RNA 1 [Gene - HGNC]
  • VBP1:VHL binding protein 1 [Gene - OMIM - HGNC]
  • CLIC2:chloride intracellular channel 2 [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]
  • 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]
  • MTCP1:mature T cell proliferation 1 [Gene - OMIM - HGNC]
  • MIR1184-1:microRNA 1184-1 [Gene - HGNC]
  • MIR1184-2:microRNA 1184-2 [Gene - HGNC]
  • MIR1184-3:microRNA 1184-3 [Gene - HGNC]
  • TMLHE:trimethyllysine hydroxylase, epsilon [Gene - OMIM - HGNC]
  • LOC101927830:uncharacterized LOC101927830 [Gene]
Variant type:
copy number gain
Cytogenetic location:
Xq28
Genomic location:
ChrX: 154879214 - 155506035 (on Assembly GRCh38)
Preferred name:
GRCh38/hg38 Xq28(chrX:154895862-155336084)
Observations:
1

Condition(s)

Name:
Chromosome Xq28 duplication syndrome
Synonyms:
Xq28 Recurrent Microduplication Syndrome
Identifiers:
MONDO: MONDO:0010436; MedGen: C2749007; Orphanet: 1762; OMIM: 300815

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005044138New York Genome Center - PrenatalSEQ
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Pathogenic
(Sep 2, 2022) 		inheritedclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedunknown1not providednot provided1not providedclinical testing

Citations

PubMed

The int22h1/int22h2-Mediated Xq28 Duplication Syndrome: An Intersection between Neurodevelopment, Immunology, and Cancer.

Ballout RA, El-Hattab AW.

Genes (Basel). 2021 Jun 4;12(6). doi:pii: 860. 10.3390/genes12060860. Review.

PubMed [citation]
PMID:
34199727
PMCID:
PMC8229372

Xq28 Duplication Syndrome, Int22h1/Int22h2 Mediated.

Ballout RA, El-Hattab AW, Schaaf CP, Cheung SW.

2016 Mar 10 [updated 2021 Feb 25]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]
PMID:
26962617
See all PubMed Citations (5)

Details of each submission

From New York Genome Center - PrenatalSEQ, SCV005044138.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (5)

Description

Xq28 duplication syndrome (Int22h1/Int22h2 mediated) is a recurrent duplication syndrome, and has been observed in more than 30 individuals to date (for review [PMID:34199727, 26962617, 32112660, 25927380, 35595445]). The minimal duplication identified here contains 7 OMIM associated genes, including a partial duplication of disease associated gene F8, and full duplication of OMIM disease associated genes RAB39B and CLIC2 which are thought to be responsible for the cognitive and neurobehavioral manifestations of Xq28 duplication syndrome, Int22h1/Int22h2 mediated [GeneReviews; PMID: 26962617]. The Xq28 recurrent region (int22h1/int22h2-flanked) including RAB39B has been curated by the Clinical Genome Resource (ClinGen) Dosage Sensitivity group to have a Triplosensitivity score of 3 (Sufficient evidence for Triplosensitivity; https://search.clinicalgenome.org/kb/gene-dosage/region/ISCA-37494). The inherited Xq28 duplication identified here is reported as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

Last Updated: May 26, 2024