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Single allele AND Chromosome 15q13.3 microdeletion syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 25, 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:
RCV002280355.2

Allele description [Variation Report for Single allele]

Genes:
  • LOC106736480:15q13 proximal microdeletion recombination region [Gene]
  • LOC130056726:ATAC-STARR-seq lymphoblastoid silent region 6267 [Gene]
  • LOC130056727:ATAC-STARR-seq lymphoblastoid silent region 6268 [Gene]
  • LOC126862088:BRD4-independent group 4 enhancer GRCh37_chr15:31318084-31319283 [Gene]
  • FAN1:FANCD2 and FANCI associated nuclease 1 [Gene - OMIM - HGNC]
  • KLF13:KLF transcription factor 13 [Gene - OMIM - HGNC]
  • LOC127829159:KLF13 promoter region [Gene]
  • LOC128899998:KLF13-II enhancer [Gene]
  • LOC128899999:KLF13-III enhancer [Gene]
  • LOC126862089:MED14-independent group 3 enhancer GRCh37_chr15:31442413-31443612 [Gene]
  • LOC129390679:MPRA-validated peak2284 silencer [Gene]
  • LOC129390680:MPRA-validated peak2285 silencer [Gene]
  • OTUD7A:OTU deubiquitinase 7A [Gene - OMIM - HGNC]
  • ARHGAP11B:Rho GTPase activating protein 11B [Gene - OMIM - HGNC]
  • LOC125078053:Sharpr-MPRA regulatory region 11410 [Gene]
  • LOC112272582:Sharpr-MPRA regulatory region 5138 [Gene]
  • LOC121847941:Sharpr-MPRA regulatory region 8183 [Gene]
  • LOC110121498:VISTA enhancer hs2231 [Gene]
  • CHRNA7:cholinergic receptor nicotinic alpha 7 subunit [Gene - OMIM - HGNC]
  • LOC106736477:distal CHRNA7 low-copy repeat recombination region [Gene]
  • LINC02352:long intergenic non-protein coding RNA 2352 [Gene - HGNC]
  • LINC03034:long intergenic non-protein coding RNA 3034 [Gene - HGNC]
  • MIR211:microRNA 211 [Gene - OMIM - HGNC]
  • MTMR10:myotubularin related protein 10 [Gene - HGNC]
  • LOC106783506:nonconserved acetylation island sequence 49 enhancer [Gene]
  • LOC106736476:proximal CHRNA7 low-copy repeat recombination region [Gene]
  • TRPM1:transient receptor potential cation channel subfamily M member 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
15q13.2-13.3
Genomic location:
Chr15: 30626003 - 32111997 (on Assembly GRCh38)

Condition(s)

Name:
Chromosome 15q13.3 microdeletion syndrome
Synonyms:
CHROMOSOME 15q13.3 DELETION SYNDROME; 15q13.3 microdeletion syndrome; 15q13.3 Microdeletion
Identifiers:
MONDO: MONDO:0012774; MedGen: C2677613; Orphanet: 199318; OMIM: 612001

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002568411Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)		Pathogenic
(Aug 25, 2022) 		germlinecuration

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).

Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL.

Genet Med. 2020 Feb;22(2):245-257. doi: 10.1038/s41436-019-0686-8. Epub 2019 Nov 6. Erratum in: Genet Med. 2021 Nov;23(11):2230. doi: 10.1038/s41436-021-01150-9.

PubMed [citation]
PMID:
31690835
PMCID:
PMC7313390

Details of each submission

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV002568411.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

A confirmed paternally inherited deletion in chromosome 15q13.2-13.3 ([GRCh38]30626003_32111997x1) encompassing 19 genes was identified by whole exome sequencing in one individual with autism, delayed speech and language development, global developmental delay, delayed gross motor development, expressive language delay, and delayed fine motor development via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Neurodev Study (https://www.neurodevproject.org/). Data from large population studies is insufficient to assess the frequency of this variant. There is nearly complete overlap with the 15q13.3 recurrent region (BP4-BP5) (includes CHRNA7), which is known to be haploinsufficient and has been assessed by the ClinGen Dosage Sensitivity Working Group. However, this region does show incomplete penetrance and there are case/control studies demonstrating enrichment in affected individuals (PMID: 25217958; PMID: 21844811). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive Chromosome 15q13.33 Deletion Syndrome. The ACMG/ClinGen evidence codes and points used in this curation are as follows: 1A: 0 points, 2B: 1.0 points, 3A: 0. points, 4: 0. points, 5: 0. points; Total: points; Riggs 2020 (PMID: 31690835).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 30, 2024