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GRCh37/hg19 16q23.2-24.3(chr16:80386595-90163348)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 1, 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:
RCV001795551.4

Allele description [Variation Report for GRCh37/hg19 16q23.2-24.3(chr16:80386595-90163348)x3]

GRCh37/hg19 16q23.2-24.3(chr16:80386595-90163348)x3

Genes:
  • ATMIN:ATM interactor [Gene - OMIM - HGNC]
  • ATP2C2:ATPase secretory pathway Ca2+ transporting 2 [Gene - OMIM - HGNC]
  • BANP:BTG3 associated nuclear protein [Gene - OMIM - HGNC]
  • CMC2:C-X9-C motif containing 2 [Gene - HGNC]
  • CBFA2T3:CBFA2/RUNX1 partner transcriptional co-repressor 3 [Gene - OMIM - HGNC]
  • CIBAR2:CBY1 interacting BAR domain containing 2 [Gene - OMIM - HGNC]
  • CENPBD1:CENPB DNA-binding domain containing 1 [Gene - HGNC]
  • EMC8:ER membrane protein complex subunit 8 [Gene - OMIM - HGNC]
  • FBXO31:F-box protein 31 [Gene - OMIM - HGNC]
  • FANCA:FA complementation group A [Gene - OMIM - HGNC]
  • FENDRR:FOXF1 adjacent non-coding developmental regulatory RNA [Gene - OMIM - HGNC]
  • GAS8-AS1:GAS8 antisense RNA 1 [Gene - OMIM - HGNC]
  • GINS2:GINS complex subunit 2 [Gene - OMIM - HGNC]
  • GSE1:Gse1 coiled-coil protein [Gene - OMIM - HGNC]
  • KIAA0513:KIAA0513 [Gene - OMIM - HGNC]
  • MPHOSPH6:M-phase phosphoprotein 6 [Gene - OMIM - HGNC]
  • MEAK7:MTOR associated protein, eak-7 homolog [Gene - OMIM - HGNC]
  • NECAB2:N-terminal EF-hand calcium binding protein 2 [Gene - OMIM - HGNC]
  • PABPN1L:PABPN1 like, cytoplasmic [Gene - HGNC]
  • PRDM7:PR/SET domain 7 [Gene - OMIM - HGNC]
  • SPG7:SPG7 matrix AAA peptidase subunit, paraplegin [Gene - OMIM - HGNC]
  • TAF1C:TATA-box binding protein associated factor, RNA polymerase I subunit C [Gene - OMIM - HGNC]
  • VPS9D1:VPS9 domain containing 1 [Gene - OMIM - HGNC]
  • WFDC1:WAP four-disulfide core domain 1 [Gene - OMIM - HGNC]
  • ZCCHC14-DT:ZCCHC14 divergent transcript [Gene - HGNC]
  • ACSF3:acyl-CoA synthetase family member 3 [Gene - OMIM - HGNC]
  • APRT:adenine phosphoribosyltransferase [Gene - OMIM - HGNC]
  • ADAD2:adenosine deaminase domain containing 2 [Gene - OMIM - HGNC]
  • ANKRD11:ankyrin repeat domain containing 11 [Gene - OMIM - HGNC]
  • BCO1:beta-carotene oxygenase 1 [Gene - OMIM - HGNC]
  • CMIP:c-Maf inducing protein [Gene - OMIM - HGNC]
  • CDH13:cadherin 13 [Gene - OMIM - HGNC]
  • CDH15:cadherin 15 [Gene - OMIM - HGNC]
  • CA5A:carbonic anhydrase 5A [Gene - OMIM - HGNC]
  • CENPN:centromere protein N [Gene - OMIM - HGNC]
  • CHMP1A:charged multivesicular body protein 1A [Gene - OMIM - HGNC]
  • CDT1:chromatin licensing and DNA replication factor 1 [Gene - OMIM - HGNC]
  • CDYL2:chromodomain Y like 2 [Gene - OMIM - HGNC]
  • C16orf46:chromosome 16 open reading frame 46 [Gene - HGNC]
  • C16orf74:chromosome 16 open reading frame 74 [Gene - HGNC]
  • C16orf95:chromosome 16 open reading frame 95 [Gene - HGNC]
  • COTL1:coactosin like F-actin binding protein 1 [Gene - OMIM - HGNC]
  • CPNE7:copine 7 [Gene - OMIM - HGNC]
  • CDK10:cyclin dependent kinase 10 [Gene - OMIM - HGNC]
  • CRISPLD2:cysteine rich secretory protein LCCL domain containing 2 [Gene - OMIM - HGNC]
  • CYBA:cytochrome b-245 alpha chain [Gene - OMIM - HGNC]
  • COX4I1:cytochrome c oxidase subunit 4I1 [Gene - OMIM - HGNC]
  • CTU2:cytosolic thiouridylase subunit 2 [Gene - OMIM - HGNC]
  • DEF8:differentially expressed in FDCP 8 homolog [Gene - HGNC]
  • DPEP1:dipeptidase 1 [Gene - OMIM - HGNC]
  • DNAAF1:dynein axonemal assembly factor 1 [Gene - OMIM - HGNC]
  • DYNLRB2:dynein light chain roadblock-type 2 [Gene - OMIM - HGNC]
  • DBNDD1:dysbindin domain containing 1 [Gene - OMIM - HGNC]
  • FOXC2:forkhead box C2 [Gene - OMIM - HGNC]
  • FOXF1:forkhead box F1 [Gene - OMIM - HGNC]
  • FOXL1:forkhead box L1 [Gene - OMIM - HGNC]
  • GALNS:galactosamine (N-acetyl)-6-sulfatase [Gene - OMIM - HGNC]
  • GAN:gigaxonin [Gene - OMIM - HGNC]
  • GCSH:glycine cleavage system protein H [Gene - OMIM - HGNC]
  • GAS8:growth arrest specific 8 [Gene - OMIM - HGNC]
  • HSBP1:heat shock factor binding protein 1 [Gene - OMIM - HGNC]
  • HSD17B2:hydroxysteroid 17-beta dehydrogenase 2 [Gene - OMIM - HGNC]
  • HSDL1:hydroxysteroid dehydrogenase like 1 [Gene - OMIM - HGNC]
  • IRF8:interferon regulatory factor 8 [Gene - OMIM - HGNC]
  • IL17C:interleukin 17C [Gene - OMIM - HGNC]
  • JPH3:junctophilin 3 [Gene - OMIM - HGNC]
  • KLHDC4:kelch domain containing 4 [Gene - OMIM - HGNC]
  • KLHL36:kelch like family member 36 [Gene - HGNC]
  • LINC01082:long intergenic non-protein coding RNA 1082 [Gene - OMIM - HGNC]
  • MLYCD:malonyl-CoA decarboxylase [Gene - OMIM - HGNC]
  • MC1R:melanocortin 1 receptor [Gene - OMIM - HGNC]
  • MBTPS1:membrane bound transcription factor peptidase, site 1 [Gene - OMIM - HGNC]
  • MTHFSD:methenyltetrahydrofolate synthetase domain containing [Gene - OMIM - HGNC]
  • MVD:mevalonate diphosphate decarboxylase [Gene - OMIM - HGNC]
  • MAP1LC3B:microtubule associated protein 1 light chain 3 beta [Gene - OMIM - HGNC]
  • OSGIN1:oxidative stress induced growth inhibitor 1 [Gene - OMIM - HGNC]
  • PLCG2:phospholipase C gamma 2 [Gene - OMIM - HGNC]
  • PIEZO1:piezo type mechanosensitive ion channel component 1 (Er blood group) [Gene - OMIM - HGNC]
  • PKD1L2:polycystin 1 like 2 (gene/pseudogene) [Gene - OMIM - HGNC]
  • KCNG4:potassium voltage-gated channel modifier subfamily G member 4 [Gene - OMIM - HGNC]
  • RPL13:ribosomal protein L13 [Gene - OMIM - HGNC]
  • RNF166:ring finger protein 166 [Gene - OMIM - HGNC]
  • SDR42E1:short chain dehydrogenase/reductase family 42E, member 1 [Gene - OMIM - HGNC]
  • SNAI3:snail family transcriptional repressor 3 [Gene - OMIM - HGNC]
  • SLC22A31:solute carrier family 22 member 31 [Gene - HGNC]
  • SLC38A8:solute carrier family 38 member 8 [Gene - OMIM - HGNC]
  • SLC7A5:solute carrier family 7 member 5 [Gene - OMIM - HGNC]
  • SPATA2L:spermatogenesis associated 2 like [Gene - HGNC]
  • SPATA33:spermatogenesis associated 33 [Gene - OMIM - HGNC]
  • SPIRE2:spire type actin nucleation factor 2 [Gene - OMIM - HGNC]
  • LOC654780:splicing factor proline/glutamine-rich [Gene]
  • TRAPPC2L:trafficking protein particle complex subunit 2L [Gene - OMIM - HGNC]
  • TCF25:transcription factor 25 [Gene - OMIM - HGNC]
  • TUBB3:tubulin beta 3 class III [Gene - OMIM - HGNC]
  • USP10:ubiquitin specific peptidase 10 [Gene - OMIM - HGNC]
  • LOC101927817:uncharacterized LOC101927817 [Gene]
  • LOC101928417:uncharacterized LOC101928417 [Gene]
  • ZC3H18:zinc finger CCCH-type containing 18 [Gene - HGNC]
  • ZCCHC14:zinc finger CCHC-type containing 14 [Gene - OMIM - HGNC]
  • ZDHHC7:zinc finger DHHC-type palmitoyltransferase 7 [Gene - OMIM - HGNC]
  • ZNF276:zinc finger protein 276 [Gene - OMIM - HGNC]
  • ZNF469:zinc finger protein 469 [Gene - OMIM - HGNC]
  • ZNF778:zinc finger protein 778 [Gene - HGNC]
  • ZFPM1:zinc finger protein, FOG family member 1 [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
16q23.2-24.3
Genomic location:
Chr16: 80386595 - 90163348 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 16q23.2-24.3(chr16:80386595-90163348)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
    SCV002034754Illumina Laboratory Services, Illumina
    criteria provided, single submitter

    (ICSL CNVClassificationCriteria Aug2020)    		Pathogenic
    (Oct 1, 2021)     		unknownclinical testing

    PubMed (2)
    [See all records that cite these PMIDs]

    Citation Link

    Help

    Summary from all submissions

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

    Citations

    PubMed

    DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.

    Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM, Carter NP.

    Am J Hum Genet. 2009 Apr;84(4):524-33. doi: 10.1016/j.ajhg.2009.03.010. Epub 2009 Apr 2.

    PubMed [citation]
    PMID:
    19344873
    PMCID:
    PMC2667985

    Trisomy 16q21 --> qter: Seven-year follow-up of a girl with unusually long survival.

    de Carvalho AF, da Silva Bellucco FT, dos Santos NP, Pellegrino R, de Azevedo Moreira LM, Toralles MB, Kulikowski LD, Melaragno MI.

    Am J Med Genet A. 2010 Aug;152A(8):2074-8. doi: 10.1002/ajmg.a.33524.

    PubMed [citation]
    PMID:
    20635361

    Details of each submission

    From Illumina Laboratory Services, Illumina, SCV002034754.1

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1not providednot providednot providednot providedclinical testing PubMed (2)

    Description

    This CNV is a 9.8Mb duplication of 16q23.2q24.3 on chromosome 16, (seq[GRCh37]dup(16)(q23.2q24.3); chr16:80386595_90163348dup) found in a de novo state. This CNV constitutes a gain of 96 protein-coding genes. Several individuals have been reported in the literature and in the DECIPHER database with various sizes of terminal duplications of the q arm of chromosome 16 (Firth et al. 2009; de Carvalho et al. 2010). Most reported cases also have a monosomy of another chromosome due to an inherited unbalanced chromosome translocation. Common features among reported individuals include intellectual disability, developmental delay, microcephaly, hypotonia, high/prominent forehead, thin upper lip, micrognathia, abnormal palmar creases, urogenital anomalies, and respiratory distress. Based on the collective evidence, this variant is classified as pathogenic.

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

    Last Updated: Sep 1, 2024