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GRCh37/hg19 4p16.3-15.1(chr4:69671-29702595)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 24, 2020
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:
RCV001537928.4

Allele description [Variation Report for GRCh37/hg19 4p16.3-15.1(chr4:69671-29702595)x3]

GRCh37/hg19 4p16.3-15.1(chr4:69671-29702595)x3

Genes:
  • ATP5ME:ATP synthase membrane subunit e [Gene - OMIM - HGNC]
  • CTBP1:C-terminal binding protein 1 [Gene - OMIM - HGNC]
  • C1QTNF7:C1q and TNF related 7 [Gene - HGNC]
  • CD38:CD38 molecule [Gene - OMIM - HGNC]
  • DCAF16:DDB1 and CUL4 associated factor 16 [Gene - HGNC]
  • DHX15:DEAH-box helicase 15 [Gene - OMIM - HGNC]
  • POLN:DNA polymerase nu [Gene - OMIM - HGNC]
  • EVC:EvC ciliary complex subunit 1 [Gene - OMIM - HGNC]
  • EVC2:EvC ciliary complex subunit 2 [Gene - OMIM - HGNC]
  • FBXL5:F-box and leucine rich repeat protein 5 [Gene - OMIM - HGNC]
  • GPR78:G protein-coupled receptor 78 [Gene - OMIM - HGNC]
  • GRK4:G protein-coupled receptor kinase 4 [Gene - OMIM - HGNC]
  • GRPEL1:GrpE like 1, mitochondrial [Gene - OMIM - HGNC]
  • HMX1:H6 family homeobox 1 [Gene - OMIM - HGNC]
  • HAUS3:HAUS augmin like complex subunit 3 [Gene - OMIM - HGNC]
  • HGFAC:HGF activator [Gene - OMIM - HGNC]
  • HTRA3:HtrA serine peptidase 3 [Gene - OMIM - HGNC]
  • KIAA0232:KIAA0232 [Gene - OMIM - HGNC]
  • LRPAP1:LDL receptor related protein associated protein 1 [Gene - OMIM - HGNC]
  • LDB2:LIM domain binding 2 [Gene - OMIM - HGNC]
  • LYAR:Ly1 antibody reactive [Gene - OMIM - HGNC]
  • MXD4:MAX dimerization protein 4 [Gene - OMIM - HGNC]
  • MRFAP1L1:Morf4 family associated protein 1 like 1 [Gene - HGNC]
  • MRFAP1:Morf4 family associated protein 1 [Gene - OMIM - HGNC]
  • MSANTD1:Myb/SANT DNA binding domain containing 1 [Gene - HGNC]
  • NAT8L:N-acetyltransferase 8 like [Gene - OMIM - HGNC]
  • NKX1-1:NK1 homeobox 1 [Gene - OMIM - HGNC]
  • NKX3-2:NK3 homeobox 2 [Gene - OMIM - HGNC]
  • NOP14:NOP14 nucleolar protein [Gene - OMIM - HGNC]
  • PPARGC1A:PPARG coactivator 1 alpha [Gene - OMIM - HGNC]
  • RAB28:RAB28, member RAS oncogene family [Gene - OMIM - HGNC]
  • S100P:S100 calcium binding protein P [Gene - OMIM - HGNC]
  • SEL1L3:SEL1L family member 3 [Gene - OMIM - HGNC]
  • SH3TC1:SH3 domain and tetratricopeptide repeats 1 [Gene - HGNC]
  • SH3BP2:SH3 domain binding protein 2 [Gene - OMIM - HGNC]
  • SEPSECS:Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase [Gene - OMIM - HGNC]
  • TBC1D14:TBC1 domain family member 14 [Gene - OMIM - HGNC]
  • TBC1D19:TBC1 domain family member 19 [Gene - HGNC]
  • TNIP2:TNFAIP3 interacting protein 2 [Gene - OMIM - HGNC]
  • UVSSA:UV stimulated scaffold protein A [Gene - OMIM - HGNC]
  • WDR1:WD repeat domain 1 [Gene - OMIM - HGNC]
  • ABLIM2:actin binding LIM protein family member 2 [Gene - OMIM - HGNC]
  • AFAP1:actin filament associated protein 1 [Gene - OMIM - HGNC]
  • ACOX3:acyl-CoA oxidase 3, pristanoyl [Gene - OMIM - HGNC]
  • ADD1:adducin 1 [Gene - OMIM - HGNC]
  • ADGRA3:adhesion G protein-coupled receptor A3 [Gene - OMIM - HGNC]
  • ADRA2C:adrenoceptor alpha 2C [Gene - OMIM - HGNC]
  • IDUA:alpha-L-iduronidase [Gene - OMIM - HGNC]
  • ANAPC4:anaphase promoting complex subunit 4 [Gene - OMIM - HGNC]
  • BLOC1S4:biogenesis of lysosomal organelles complex 1 subunit 4 [Gene - OMIM - HGNC]
  • BOD1L1:biorientation of chromosomes in cell division 1 like 1 [Gene - OMIM - HGNC]
  • BST1:bone marrow stromal cell antigen 1 [Gene - OMIM - HGNC]
  • CPZ:carboxypeptidase Z [Gene - OMIM - HGNC]
  • CCKAR:cholecystokinin A receptor [Gene - OMIM - HGNC]
  • C4orf48:chromosome 4 open reading frame 48 [Gene - OMIM - HGNC]
  • C4orf50:chromosome 4 open reading frame 50 [Gene - HGNC]
  • CLRN2:clarin 2 [Gene - OMIM - HGNC]
  • CC2D2A:coiled-coil and C2 domain containing 2A [Gene - OMIM - HGNC]
  • CCDC149:coiled-coil domain containing 149 [Gene - HGNC]
  • CCDC96:coiled-coil domain containing 96 [Gene - OMIM - HGNC]
  • CRMP1:collapsin response mediator protein 1 [Gene - OMIM - HGNC]
  • CPLX1:complexin 1 [Gene - OMIM - HGNC]
  • GAK:cyclin G associated kinase [Gene - OMIM - HGNC]
  • CRIPAK:cysteine rich PAK1 inhibitor [Gene - OMIM - HGNC]
  • CLNK:cytokine dependent hematopoietic cell linker [Gene - OMIM - HGNC]
  • CYTL1:cytokine like 1 [Gene - OMIM - HGNC]
  • CPEB2:cytoplasmic polyadenylation element binding protein 2 [Gene - OMIM - HGNC]
  • DEFB131A:defensin beta 131A [Gene - HGNC]
  • DGKQ:diacylglycerol kinase theta [Gene - OMIM - HGNC]
  • DOK7:docking protein 7 [Gene - OMIM - HGNC]
  • DRD5:dopamine receptor D5 [Gene - OMIM - HGNC]
  • FAM184B:family with sequence similarity 184 member B [Gene - OMIM - HGNC]
  • FAM193A:family with sequence similarity 193 member A [Gene - OMIM - HGNC]
  • FAM200B:family with sequence similarity 200 member B [Gene - HGNC]
  • FAM53A:family with sequence similarity 53 member A [Gene - OMIM - HGNC]
  • FGFBP1:fibroblast growth factor binding protein 1 [Gene - OMIM - HGNC]
  • FGFBP2:fibroblast growth factor binding protein 2 [Gene - OMIM - HGNC]
  • FGFR3:fibroblast growth factor receptor 3 [Gene - OMIM - HGNC]
  • FGFRL1:fibroblast growth factor receptor like 1 [Gene - OMIM - HGNC]
  • GBA3:glucosylceramidase beta 3 (gene/pseudogene) [Gene - OMIM - HGNC]
  • HS3ST1:heparan sulfate-glucosamine 3-sulfotransferase 1 [Gene - OMIM - HGNC]
  • HTT:huntingtin [Gene - OMIM - HGNC]
  • JAKMIP1:janus kinase and microtubule interacting protein 1 [Gene - OMIM - HGNC]
  • LAP3:leucine aminopeptidase 3 [Gene - OMIM - HGNC]
  • LGI2:leucine rich repeat LGI family member 2 [Gene - OMIM - HGNC]
  • LETM1:leucine zipper and EF-hand containing transmembrane protein 1 [Gene - OMIM - HGNC]
  • LCORL:ligand dependent nuclear receptor corepressor like [Gene - OMIM - HGNC]
  • LINC01587:long intergenic non-protein coding RNA 1587 [Gene - HGNC]
  • MAEA:macrophage erythroblast attacher, E3 ubiquitin ligase [Gene - OMIM - HGNC]
  • MFSD10:major facilitator superfamily domain containing 10 [Gene - OMIM - HGNC]
  • MAN2B2:mannosidase alpha class 2B member 2 [Gene - OMIM - HGNC]
  • MED28:mediator complex subunit 28 [Gene - OMIM - HGNC]
  • MIR95:microRNA 95 [Gene - OMIM - HGNC]
  • MSX1:msh homeobox 1 [Gene - OMIM - HGNC]
  • MYL5:myosin light chain 5 [Gene - OMIM - HGNC]
  • NELFA:negative elongation factor complex member A [Gene - OMIM - HGNC]
  • NSG1:neuronal vesicle trafficking associated 1 [Gene - OMIM - HGNC]
  • NCAPG:non-SMC condensin I complex subunit G [Gene - OMIM - HGNC]
  • NSD2:nuclear receptor binding SET domain protein 2 [Gene - OMIM - HGNC]
  • OTOP1:otopetrin 1 [Gene - OMIM - HGNC]
  • PACRGL:parkin coregulated like [Gene - HGNC]
  • PI4K2B:phosphatidylinositol 4-kinase type 2 beta [Gene - OMIM - HGNC]
  • PIGG:phosphatidylinositol glycan anchor biosynthesis class G [Gene - OMIM - HGNC]
  • PDE6B:phosphodiesterase 6B [Gene - OMIM - HGNC]
  • PCGF3:polycomb group ring finger 3 [Gene - OMIM - HGNC]
  • KCNIP4:potassium voltage-gated channel interacting protein 4 [Gene - OMIM - HGNC]
  • PROM1:prominin 1 [Gene - OMIM - HGNC]
  • PSAPL1:prosaposin like 1 [Gene - HGNC]
  • PPP2R2C:protein phosphatase 2 regulatory subunit Bgamma [Gene - OMIM - HGNC]
  • QDPR:quinoid dihydropteridine reductase [Gene - OMIM - HGNC]
  • RBPJ:recombination signal binding protein for immunoglobulin kappa J region [Gene - OMIM - HGNC]
  • RGS12:regulator of G protein signaling 12 [Gene - OMIM - HGNC]
  • RNF212:ring finger protein 212 [Gene - OMIM - HGNC]
  • RNF4:ring finger protein 4 [Gene - OMIM - HGNC]
  • STK32B:serine/threonine kinase 32B [Gene - HGNC]
  • SLIT2:slit guidance ligand 2 [Gene - OMIM - HGNC]
  • SMIM20:small integral membrane protein 20 [Gene - OMIM - HGNC]
  • SLC2A9:solute carrier family 2 member 9 [Gene - OMIM - HGNC]
  • SLC26A1:solute carrier family 26 member 1 [Gene - OMIM - HGNC]
  • SLC34A2:solute carrier family 34 member 2 [Gene - OMIM - HGNC]
  • SLC49A3:solute carrier family 49 member 3 [Gene - HGNC]
  • SORCS2:sortilin related VPS10 domain containing receptor 2 [Gene - OMIM - HGNC]
  • SPON2:spondin 2 [Gene - OMIM - HGNC]
  • SLBP:stem-loop binding protein [Gene - OMIM - HGNC]
  • STIM2:stromal interaction molecule 2 [Gene - OMIM - HGNC]
  • SOD3:superoxide dismutase 3 [Gene - OMIM - HGNC]
  • STX18:syntaxin 18 [Gene - OMIM - HGNC]
  • TRMT44:tRNA methyltransferase 44 homolog [Gene - OMIM - HGNC]
  • TADA2B:transcriptional adaptor 2B [Gene - OMIM - HGNC]
  • TACC3:transforming acidic coiled-coil containing protein 3 [Gene - OMIM - HGNC]
  • TAPT1:transmembrane anterior posterior transformation 1 [Gene - OMIM - HGNC]
  • TMEM128:transmembrane protein 128 [Gene - HGNC]
  • TMEM129:transmembrane protein 129, E3 ubiquitin ligase [Gene - OMIM - HGNC]
  • TMEM175:transmembrane protein 175 [Gene - OMIM - HGNC]
  • USP17L10:ubiquitin specific peptidase 17 like family member 10 [Gene - HGNC]
  • USP17L11:ubiquitin specific peptidase 17 like family member 11 [Gene - HGNC]
  • USP17L12:ubiquitin specific peptidase 17 like family member 12 [Gene - HGNC]
  • USP17L13:ubiquitin specific peptidase 17 like family member 13 [Gene - HGNC]
  • USP17L15:ubiquitin specific peptidase 17 like family member 15 [Gene - HGNC]
  • USP17L17:ubiquitin specific peptidase 17 like family member 17 [Gene - HGNC]
  • USP17L18:ubiquitin specific peptidase 17 like family member 18 [Gene - HGNC]
  • USP17L19:ubiquitin specific peptidase 17 like family member 19 [Gene - HGNC]
  • USP17L20:ubiquitin specific peptidase 17 like family member 20 [Gene - HGNC]
  • USP17L21:ubiquitin specific peptidase 17 like family member 21 [Gene - HGNC]
  • USP17L22:ubiquitin specific peptidase 17 like family member 22 [Gene - HGNC]
  • USP17L24:ubiquitin specific peptidase 17 like family member 24 [Gene - HGNC]
  • USP17L25:ubiquitin specific peptidase 17 like family member 25 [Gene - HGNC]
  • USP17L26:ubiquitin specific peptidase 17 like family member 26 [Gene - HGNC]
  • USP17L27:ubiquitin specific peptidase 17 like family member 27 [Gene - HGNC]
  • USP17L28:ubiquitin specific peptidase 17 like family member 28 [Gene - HGNC]
  • USP17L29:ubiquitin specific peptidase 17 like family member 29 [Gene - HGNC]
  • USP17L30:ubiquitin specific peptidase 17 like family member 30 [Gene - HGNC]
  • USP17L5:ubiquitin specific peptidase 17 like family member 5 [Gene - HGNC]
  • WFS1:wolframin ER transmembrane glycoprotein [Gene - OMIM - HGNC]
  • ZCCHC4:zinc finger CCHC-type containing 4 [Gene - OMIM - HGNC]
  • ZFYVE28:zinc finger FYVE-type containing 28 [Gene - OMIM - HGNC]
  • ZBTB49:zinc finger and BTB domain containing 49 [Gene - OMIM - HGNC]
  • ZNF141:zinc finger protein 141 [Gene - OMIM - HGNC]
  • ZNF518B:zinc finger protein 518B [Gene - OMIM - HGNC]
  • ZNF595:zinc finger protein 595 [Gene - HGNC]
  • ZNF718:zinc finger protein 718 [Gene - HGNC]
  • ZNF721:zinc finger protein 721 [Gene - HGNC]
  • ZNF732:zinc finger protein 732 [Gene - HGNC]
Variant type:
copy number gain
Cytogenetic location:
4p16.3-15.1
Genomic location:
Chr4: 69671 - 29702595 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 4p16.3-15.1(chr4:69671-29702595)x3
HGVS:

    Condition(s)

    Synonyms:
    none provided
    Identifiers:
    MedGen: CN517202

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV001754856Illumina Laboratory Services, Illumina
    criteria provided, single submitter

    (ICSL CNVClassificationCriteria Jul2020Prior)    		Pathogenic
    (Apr 24, 2020)     		unknownclinical testing

    PubMed (7)
    [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

    Partial monosomy Xq(Xq23 --> qter) and trisomy 4p(4p15.33 --> pter) in a woman with intractable focal epilepsy, borderline intellectual functioning, and dysmorphic features.

    Bartocci A, Striano P, Mancardi MM, Fichera M, Castiglia L, Galesi O, Michelucci R, Elia M.

    Brain Dev. 2008 Jun;30(6):425-9. doi: 10.1016/j.braindev.2007.11.004. Epub 2007 Dec 31.

    PubMed [citation]
    PMID:
    18166284

    Duplication of the Wolf-Hirschhorn syndrome critical region causes neurodevelopmental delay.

    Hannes F, Drozniewska M, Vermeesch JR, Haus O.

    Eur J Med Genet. 2010 May-Jun;53(3):136-40. doi: 10.1016/j.ejmg.2010.02.004. Epub 2010 Mar 1.

    PubMed [citation]
    PMID:
    20197130
    See all PubMed Citations (7)

    Details of each submission

    From Illumina Laboratory Services, Illumina, SCV001754856.1

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1not providednot providednot providednot providedclinical testing PubMed (7)

    Description

    This CNV is a 29.6 Mb duplication of 4p16.3-4p15.1 on chromosome 4, (seq[GRCh37]dup(4)(p16.3p15.1); chr4:g.69671_29702595dup), which is found in a de novo state. This CNV constitutes a gain encompassing 229 genes and overlaps the well-described partial trisomy 4p syndrome region. This duplication fully encompasses the 4p16.3 duplication region that has been described in affected individuals in the literature (Partington et al. 1997; Bartocci et al. 2008; Hannes et al. 2010; Schönewolf-Greulich et al. 2013; Bi et al. 2016; Sagar et al. 2017; Wang et al. 2018). The 4p15.1-pter duplication has not been reported in published controls. Based on the collective evidence, this CNV is classified as pathogenic.

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

    Last Updated: Apr 9, 2023