U.S. flag

An official website of the United States government

Single allele AND Chromosome 16p11.2 duplication 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:
RCV002280356.2

Allele description [Variation Report for Single allele]

Genes:
  • LOC130058769:ATAC-STARR-seq lymphoblastoid active region 10665 [Gene]
  • LOC130058770:ATAC-STARR-seq lymphoblastoid active region 10667 [Gene]
  • LOC130058772:ATAC-STARR-seq lymphoblastoid active region 10668 [Gene]
  • LOC130058773:ATAC-STARR-seq lymphoblastoid active region 10669 [Gene]
  • LOC130058774:ATAC-STARR-seq lymphoblastoid active region 10670 [Gene]
  • LOC130058775:ATAC-STARR-seq lymphoblastoid active region 10671 [Gene]
  • LOC130058777:ATAC-STARR-seq lymphoblastoid active region 10672 [Gene]
  • LOC130058778:ATAC-STARR-seq lymphoblastoid active region 10673 [Gene]
  • LOC130058780:ATAC-STARR-seq lymphoblastoid active region 10674 [Gene]
  • LOC130058781:ATAC-STARR-seq lymphoblastoid active region 10675 [Gene]
  • LOC130058783:ATAC-STARR-seq lymphoblastoid active region 10676 [Gene]
  • LOC130058787:ATAC-STARR-seq lymphoblastoid active region 10677 [Gene]
  • LOC130058790:ATAC-STARR-seq lymphoblastoid active region 10679 [Gene]
  • LOC130058792:ATAC-STARR-seq lymphoblastoid active region 10680 [Gene]
  • LOC130058793:ATAC-STARR-seq lymphoblastoid active region 10682 [Gene]
  • LOC130058794:ATAC-STARR-seq lymphoblastoid active region 10683 [Gene]
  • LOC130058799:ATAC-STARR-seq lymphoblastoid active region 10684 [Gene]
  • LOC130058802:ATAC-STARR-seq lymphoblastoid active region 10686 [Gene]
  • LOC130058803:ATAC-STARR-seq lymphoblastoid active region 10687 [Gene]
  • LOC130058808:ATAC-STARR-seq lymphoblastoid active region 10688 [Gene]
  • LOC130058810:ATAC-STARR-seq lymphoblastoid active region 10689 [Gene]
  • LOC130058812:ATAC-STARR-seq lymphoblastoid active region 10690 [Gene]
  • LOC130058814:ATAC-STARR-seq lymphoblastoid active region 10691 [Gene]
  • LOC130058815:ATAC-STARR-seq lymphoblastoid active region 10692 [Gene]
  • LOC130058816:ATAC-STARR-seq lymphoblastoid active region 10693 [Gene]
  • LOC130058819:ATAC-STARR-seq lymphoblastoid active region 10695 [Gene]
  • LOC130058768:ATAC-STARR-seq lymphoblastoid silent region 7330 [Gene]
  • LOC130058771:ATAC-STARR-seq lymphoblastoid silent region 7331 [Gene]
  • LOC130058776:ATAC-STARR-seq lymphoblastoid silent region 7332 [Gene]
  • LOC130058779:ATAC-STARR-seq lymphoblastoid silent region 7333 [Gene]
  • LOC130058782:ATAC-STARR-seq lymphoblastoid silent region 7334 [Gene]
  • LOC130058784:ATAC-STARR-seq lymphoblastoid silent region 7335 [Gene]
  • LOC130058785:ATAC-STARR-seq lymphoblastoid silent region 7336 [Gene]
  • LOC130058786:ATAC-STARR-seq lymphoblastoid silent region 7337 [Gene]
  • LOC130058788:ATAC-STARR-seq lymphoblastoid silent region 7338 [Gene]
  • LOC130058789:ATAC-STARR-seq lymphoblastoid silent region 7339 [Gene]
  • LOC130058791:ATAC-STARR-seq lymphoblastoid silent region 7340 [Gene]
  • LOC130058795:ATAC-STARR-seq lymphoblastoid silent region 7341 [Gene]
  • LOC130058796:ATAC-STARR-seq lymphoblastoid silent region 7342 [Gene]
  • LOC130058797:ATAC-STARR-seq lymphoblastoid silent region 7343 [Gene]
  • LOC130058798:ATAC-STARR-seq lymphoblastoid silent region 7344 [Gene]
  • LOC130058800:ATAC-STARR-seq lymphoblastoid silent region 7345 [Gene]
  • LOC130058801:ATAC-STARR-seq lymphoblastoid silent region 7346 [Gene]
  • LOC130058804:ATAC-STARR-seq lymphoblastoid silent region 7347 [Gene]
  • LOC130058805:ATAC-STARR-seq lymphoblastoid silent region 7348 [Gene]
  • LOC130058806:ATAC-STARR-seq lymphoblastoid silent region 7349 [Gene]
  • LOC130058807:ATAC-STARR-seq lymphoblastoid silent region 7350 [Gene]
  • LOC130058809:ATAC-STARR-seq lymphoblastoid silent region 7351 [Gene]
  • LOC130058811:ATAC-STARR-seq lymphoblastoid silent region 7352 [Gene]
  • LOC130058813:ATAC-STARR-seq lymphoblastoid silent region 7356 [Gene]
  • LOC130058817:ATAC-STARR-seq lymphoblastoid silent region 7357 [Gene]
  • LOC130058818:ATAC-STARR-seq lymphoblastoid silent region 7358 [Gene]
  • CDIPTOSP:CDIP transferase opposite strand, pseudogene [Gene - HGNC]
  • CDIPT:CDP-diacylglycerol--inositol 3-phosphatidyltransferase [Gene - OMIM - HGNC]
  • CORO1A-AS1:CORO1A antisense RNA 1 [Gene - HGNC]
  • LOC116276452:CRISPRi-validated cis-regulatory element chr16.2261 [Gene]
  • HIRIP3:HIRA interacting protein 3 [Gene - OMIM - HGNC]
  • INO80E:INO80 complex subunit E [Gene - HGNC]
  • LOC129390783:MPRA-validated peak2562 silencer [Gene]
  • MVP-DT:MVP divergent transcript [Gene - HGNC]
  • MAZ:MYC associated zinc finger protein [Gene - OMIM - HGNC]
  • PAGR1:PAXIP1 associated glutamate rich protein 1 [Gene - OMIM - HGNC]
  • LOC125146440:Sharpr-MPRA regulatory region 10200 [Gene]
  • LOC125146439:Sharpr-MPRA regulatory region 12104 [Gene]
  • LOC121847977:Sharpr-MPRA regulatory region 13449 [Gene]
  • LOC121847976:Sharpr-MPRA regulatory region 1439 [Gene]
  • LOC112352680:Sharpr-MPRA regulatory region 6067 [Gene]
  • LOC121587541:Sharpr-MPRA regulatory region 7413 [Gene]
  • LOC121587540:Sharpr-MPRA regulatory region 8247 [Gene]
  • LOC125146441:Sharpr-MPRA regulatory region 9068 [Gene]
  • TBX6:T-box transcription factor 6 [Gene - OMIM - HGNC]
  • TAOK2:TAO kinase 2 [Gene - OMIM - HGNC]
  • TLCD3B:TLC domain containing 3B [Gene - OMIM - HGNC]
  • YPEL3-DT:YPEL3 divergent transcript [Gene - HGNC]
  • ALDOA:aldolase, fructose-bisphosphate A [Gene - OMIM - HGNC]
  • ASPHD1:aspartate beta-hydroxylase domain containing 1 [Gene - HGNC]
  • C16orf54:chromosome 16 open reading frame 54 [Gene - HGNC]
  • C16orf92:chromosome 16 open reading frame 92 [Gene - OMIM - HGNC]
  • CORO1A:coronin 1A [Gene - OMIM - HGNC]
  • DOC2A:double C2 domain alpha [Gene - OMIM - HGNC]
  • GDPD3:glycerophosphodiester phosphodiesterase domain containing 3 [Gene - OMIM - HGNC]
  • KIF22:kinesin family member 22 [Gene - OMIM - HGNC]
  • MVP:major vault protein [Gene - OMIM - HGNC]
  • MAPK3:mitogen-activated protein kinase 3 [Gene - OMIM - HGNC]
  • KCTD13:potassium channel tetramerization domain containing 13 [Gene - OMIM - HGNC]
  • PRRT2:proline rich transmembrane protein 2 [Gene - OMIM - HGNC]
  • PPP4C:protein phosphatase 4 catalytic subunit [Gene - OMIM - HGNC]
  • QPRT:quinolinate phosphoribosyltransferase [Gene - OMIM - HGNC]
  • SEZ6L2:seizure related 6 homolog like 2 [Gene - OMIM - HGNC]
  • SPN:sialophorin [Gene - OMIM - HGNC]
  • TMEM219:transmembrane protein 219 [Gene - OMIM - HGNC]
  • LOC112694756:uncharaterized LOC112694756 [Gene]
  • YPEL3:yippee like 3 [Gene - OMIM - HGNC]
  • ZG16:zymogen granule protein 16 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16p11.2
Genomic location:
Chr16: 29663598 - 30188229 (on Assembly GRCh38)

Condition(s)

Name:
Chromosome 16p11.2 duplication syndrome
Identifiers:
MONDO: MONDO:0013847; MedGen: C3553407; OMIM: 614671

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002568412Broad 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, SCV002568412.1

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

Description

A confirmed de novo heterozygous deletion of 16p11.2 ([GRCh38] 29663598_30188229x1) encompassing 30 genes was identified by whole exome sequencing of one individual with autism, delayed speech and language development, global developmental delay and abnormal social behavior via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Neurodev Study (https://www.neurodevproject.org/). There is complete overlap with the PRRT2 gene which is known to be haploinsufficient and has been assessed by the ClinGen Dosage Sensitivity Working Group. The additional gene, TAOK2, also has evidence supporting haploinsufficiency, but has not yet been curated by the clingen dosage sensitivity group (PMID: 29467497). Data from large population studies is insufficient to assess the frequency of this variant. In summary, this variant meets criteria to be classified as pathogenic for Chromosome 16p11.2 Deletion Syndrome, 593-KB. The ACMG/ClinGen evidence codes and points used in this curation are as follows: 1A: 0 points, 2A: 1.00 points, 3C: 0.45 points, 4: 0.0 points, 5A: 0.15 points; Total: 1.60 points; Riggs 2020 (PMID: 31690835).

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

Last Updated: Mar 30, 2024