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GRCh37/hg19 16p12.2-11.2(chr16:21576802-29351826)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 1, 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:
RCV001006786.3

Allele description [Variation Report for GRCh37/hg19 16p12.2-11.2(chr16:21576802-29351826)x3]

GRCh37/hg19 16p12.2-11.2(chr16:21576802-29351826)x3

Genes:
  • ATP2A1:ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1 [Gene - OMIM - HGNC]
  • CD19:CD19 molecule [Gene - OMIM - HGNC]
  • CLN3:CLN3 lysosomal/endosomal transmembrane protein, battenin [Gene - OMIM - HGNC]
  • GSG1L:GSG1 like [Gene - OMIM - HGNC]
  • NDUFAB1:NADH:ubiquinone oxidoreductase subunit AB1 [Gene - OMIM - HGNC]
  • NSMCE1:NSE1 homolog, SMC5-SMC6 complex component [Gene - OMIM - HGNC]
  • PDZD9:PDZ domain containing 9 [Gene - HGNC]
  • RBBP6:RB binding protein 6, ubiquitin ligase [Gene - OMIM - HGNC]
  • POLR3E:RNA polymerase III subunit E [Gene - OMIM - HGNC]
  • ARHGAP17:Rho GTPase activating protein 17 [Gene - OMIM - HGNC]
  • SGF29:SAGA complex associated factor 29 [Gene - OMIM - HGNC]
  • SH2B1:SH2B adaptor protein 1 [Gene - OMIM - HGNC]
  • SBK1:SH3 domain binding kinase 1 [Gene - OMIM - HGNC]
  • SPNS1:SPNS lysolipid transporter 1, lysophospholipid [Gene - OMIM - HGNC]
  • TUFM:Tu translation elongation factor, mitochondrial [Gene - OMIM - HGNC]
  • APOBR:apolipoprotein B receptor [Gene - OMIM - HGNC]
  • AQP8:aquaporin 8 [Gene - OMIM - HGNC]
  • ATXN2L:ataxin 2 like [Gene - OMIM - HGNC]
  • CHP2:calcineurin like EF-hand protein 2 [Gene - HGNC]
  • CACNG3:calcium voltage-gated channel auxiliary subunit gamma 3 [Gene - OMIM - HGNC]
  • CDR2:cerebellar degeneration related protein 2 [Gene - OMIM - HGNC]
  • C16orf82:chromosome 16 open reading frame 82 [Gene - HGNC]
  • COG7:component of oligomeric golgi complex 7 [Gene - OMIM - HGNC]
  • DCTN5:dynactin subunit 5 [Gene - OMIM - HGNC]
  • ERN2:endoplasmic reticulum to nucleus signaling 2 [Gene - OMIM - HGNC]
  • EEF2K:eukaryotic elongation factor 2 kinase [Gene - OMIM - HGNC]
  • EIF3CL:eukaryotic translation initiation factor 3 subunit C like [Gene - HGNC]
  • EIF3C:eukaryotic translation initiation factor 3 subunit C [Gene - OMIM - HGNC]
  • XPO6:exportin 6 [Gene - OMIM - HGNC]
  • GTF3C1:general transcription factor IIIC subunit 1 [Gene - OMIM - HGNC]
  • EARS2:glutamyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
  • GGA2:golgi associated, gamma adaptin ear containing, ARF binding protein 2 [Gene - OMIM - HGNC]
  • HS3ST2:heparan sulfate-glucosamine 3-sulfotransferase 2 [Gene - OMIM - HGNC]
  • HS3ST4:heparan sulfate-glucosamine 3-sulfotransferase 4 [Gene - OMIM - HGNC]
  • IGSF6:immunoglobulin superfamily member 6 [Gene - OMIM - HGNC]
  • IL21R:interleukin 21 receptor [Gene - OMIM - HGNC]
  • IL27:interleukin 27 [Gene - OMIM - HGNC]
  • IL4R:interleukin 4 receptor [Gene - OMIM - HGNC]
  • KATNIP:katanin interacting protein [Gene - OMIM - HGNC]
  • LCMT1:leucine carboxyl methyltransferase 1 [Gene - OMIM - HGNC]
  • LAT:linker for activation of T cells [Gene - OMIM - HGNC]
  • KDM8:lysine demethylase 8 [Gene - OMIM - HGNC]
  • METTL9:methyltransferase 9, His-X-His N1(pi)-histidine [Gene - OMIM - HGNC]
  • MOSMO:modulator of smoothened [Gene - HGNC]
  • NFATC2IP:nuclear factor of activated T cells 2 interacting protein [Gene - OMIM - HGNC]
  • NPIPB4:nuclear pore complex interacting protein family member B4 [Gene - HGNC]
  • NPIPB5:nuclear pore complex interacting protein family member B5 [Gene - HGNC]
  • NPIPB6:nuclear pore complex interacting protein family member B6 [Gene - HGNC]
  • NUPR1:nuclear protein 1, transcriptional regulator [Gene - OMIM - HGNC]
  • OTOA:otoancorin [Gene - OMIM - HGNC]
  • PALB2:partner and localizer of BRCA2 [Gene - OMIM - HGNC]
  • PLK1:polo like kinase 1 [Gene - OMIM - HGNC]
  • PRKCB:protein kinase C beta [Gene - OMIM - HGNC]
  • RABEP2:rabaptin, RAB GTPase binding effector protein 2 [Gene - OMIM - HGNC]
  • SDR42E2:short chain dehydrogenase/reductase family 42E, member 2 [Gene - HGNC]
  • SCNN1B:sodium channel epithelial 1 subunit beta [Gene - OMIM - HGNC]
  • SCNN1G:sodium channel epithelial 1 subunit gamma [Gene - OMIM - HGNC]
  • SLC5A11:solute carrier family 5 member 11 [Gene - OMIM - HGNC]
  • SULT1A1:sulfotransferase family 1A member 1 [Gene - OMIM - HGNC]
  • SULT1A2:sulfotransferase family 1A member 2 [Gene - OMIM - HGNC]
  • TNRC6A:trinucleotide repeat containing adaptor 6A [Gene - OMIM - HGNC]
  • UQCRC2:ubiquinol-cytochrome c reductase core protein 2 [Gene - OMIM - HGNC]
  • UBFD1:ubiquitin family domain containing 1 [Gene - HGNC]
  • USP31:ubiquitin specific peptidase 31 [Gene - OMIM - HGNC]
  • VWA3A:von Willebrand factor A domain containing 3A [Gene - HGNC]
  • ZKSCAN2:zinc finger with KRAB and SCAN domains 2 [Gene - HGNC]
Variant type:
copy number gain
Cytogenetic location:
16p12.2-11.2
Genomic location:
Chr16: 21576802 - 29351826 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 16p12.2-11.2(chr16:21576802-29351826)x3
HGVS:

    Condition(s)

    Synonyms:
    none provided
    Identifiers:
    MedGen: C3661900

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV001166345Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Nov 1, 2022)     		unknownclinical testing

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

    Help

    Summary from all submissions

    EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
    not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

    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 Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001166345.3

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

    Description

    The copy number gain of 16p12.2p11.2 involves numerous protein-coding genes and includes the atypical 16p11.2 duplication interval referred to as BP2-BP3 or distal 16p11.2 duplication (Coe 2014, Loviglio 2017, Rosenfeld 2013, Sonderby 2020). Most notably, larger copy number gains that include the recurrent 16p11.2 BP2-BP3 duplication region while also extending several Mb distally into 16p12.2 have been associated with broad phenotypes that include language delay, intellectual disability, behavioral difficulties, macrocephaly, and dysmorphic features (Barber 2013, Okamoto 2014). Therefore, based on current medical literature and gene content, this copy number variant (CNV) is classified as pathogenic. References: Barber et al., Eur J Hum Genet. 2013 Feb;21(2):182-9. PMID: 22828807 Coe et al., Nat Genet. 2014 Oct;46(10):1063-71. PMID: 25217958 Loviglio MN, et al. Mol Psychiatry. 2017 Jun;22(6):836-849 PMID: 27240531 Okamoto et al., Am J Med Genet A. 2014 Jan;164A(1):213-9. PMID: 24259393 Rosenfeld JA, Genet Med. 2013 Jun;15(6):478-81 PMID: 23258348 Sonderby et al., Mol Psychiatry. 2020 Mar;25(3):584-602. PMID: 30283035

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

    Last Updated: Feb 4, 2024