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NC_000015.10:g.22698177_(23120963_23380983)del AND Chromosome 15q11.2 deletion syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 5, 2021
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:
RCV003221323.1

Allele description [Variation Report for NC_000015.10:g.22698177_(23120963_23380983)del]

NC_000015.10:g.22698177_(23120963_23380983)del

Genes:
  • LOC130056712:ATAC-STARR-seq lymphoblastoid active region 9154 [Gene]
  • LOC130056713:ATAC-STARR-seq lymphoblastoid active region 9155 [Gene]
  • LOC130056714:ATAC-STARR-seq lymphoblastoid active region 9156 [Gene]
  • LOC130056715:ATAC-STARR-seq lymphoblastoid active region 9157 [Gene]
  • LOC130056716:ATAC-STARR-seq lymphoblastoid active region 9158 [Gene]
  • LOC130056717:ATAC-STARR-seq lymphoblastoid active region 9159 [Gene]
  • LOC130056718:ATAC-STARR-seq lymphoblastoid active region 9160 [Gene]
  • LOC130056708:ATAC-STARR-seq lymphoblastoid silent region 6258 [Gene]
  • LOC130056709:ATAC-STARR-seq lymphoblastoid silent region 6259 [Gene]
  • LOC130056710:ATAC-STARR-seq lymphoblastoid silent region 6260 [Gene]
  • LOC130056711:ATAC-STARR-seq lymphoblastoid silent region 6261 [Gene]
  • LOC130056719:ATAC-STARR-seq lymphoblastoid silent region 6262 [Gene]
  • LOC126862074:CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:22990202-22991401 [Gene]
  • NIPA1:NIPA magnesium transporter 1 [Gene - OMIM - HGNC]
  • NIPA2:NIPA magnesium transporter 2 [Gene - OMIM - HGNC]
  • LOC112272576:Sharpr-MPRA regulatory region 3977 [Gene]
  • LOC112272575:Sharpr-MPRA regulatory region 8478 [Gene]
  • CYFIP1:cytoplasmic FMR1 interacting protein 1 [Gene - OMIM - HGNC]
  • GOLGA6L1:golgin A6 family like 1 [Gene - HGNC]
  • GOLGA6L26:golgin A6 family like 26 [Gene - HGNC]
  • GOLGA8S:golgin A8 family member S [Gene - HGNC]
  • MIR4509-1:microRNA 4509-1 [Gene - HGNC]
  • TUBGCP5:tubulin gamma complex component 5 [Gene - OMIM - HGNC]
  • LOC283683:uncharacterized LOC283683 [Gene]
Variant type:
Deletion
Cytogenetic location:
15q11.2
Genomic location:
Chr15: 22698177 - 23380983 (on Assembly GRCh38)
Preferred name:
NC_000015.10:g.22698177_(23120963_23380983)del
HGVS:
NC_000015.10:g.22698177_(23120963_23380983)del
Observations:
1

Condition(s)

Name:
Chromosome 15q11.2 deletion syndrome
Identifiers:
MONDO: MONDO:0014294; MedGen: C3180937; Orphanet: 261183; OMIM: 615656

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003915657New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Pathogenic
(Mar 5, 2021) 		inheritedclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedyes1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV003915657.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The 15q11.2 BP1-BP2 deletion identified here is an interstitial deletion on the long arm of chromosome 15. The 15q proximal region contains a cluster of low copy repeats that lead to recurrent copy number changes in this region. Deletions in this region are associated with 15q11.2 BP1-BP2 recurrent deletion syndrome.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyes1not providednot provided1not providednot providednot provided

Last Updated: Aug 25, 2024