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GRCh37/hg19 22q11.1-11.21(chr22:16800000-21500000)x4 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 7, 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:
RCV001270641.4

Allele description [Variation Report for GRCh37/hg19 22q11.1-11.21(chr22:16800000-21500000)x4]

GRCh37/hg19 22q11.1-11.21(chr22:16800000-21500000)x4

Genes:
  • ARVCF:ARVCF delta catenin family member [Gene - OMIM - HGNC]
  • ATP6V1E1:ATPase H+ transporting V1 subunit E1 [Gene - OMIM - HGNC]
  • BCL2L13:BCL2 like 13 [Gene - OMIM - HGNC]
  • BID:BH3 interacting domain death agonist [Gene - OMIM - HGNC]
  • CECR2:CECR2 histone acetyl-lysine reader [Gene - OMIM - HGNC]
  • CRKL:CRK like proto-oncogene, adaptor protein [Gene - OMIM - HGNC]
  • DGCR8:DGCR8 microprocessor complex subunit [Gene - OMIM - HGNC]
  • DGCR2:DiGeorge syndrome critical region gene 2 [Gene - OMIM - HGNC]
  • DGCR6L:DiGeorge syndrome critical region gene 6 like [Gene - OMIM - HGNC]
  • DGCR6:DiGeorge syndrome critical region gene 6 [Gene - OMIM - HGNC]
  • GNB1L:G protein subunit beta 1 like [Gene - OMIM - HGNC]
  • GAB4:GRB2 associated binding protein family member 4 [Gene - HGNC]
  • RANBP1:RAN binding protein 1 [Gene - OMIM - HGNC]
  • RIMBP3:RIMS binding protein 3 [Gene - OMIM - HGNC]
  • TBX1:T-box transcription factor 1 [Gene - OMIM - HGNC]
  • THAP7:THAP domain containing 7 [Gene - OMIM - HGNC]
  • XKR3:XK related 3 [Gene - OMIM - HGNC]
  • ADA2:adenosine deaminase 2 [Gene - OMIM - HGNC]
  • AIFM3:apoptosis inducing factor mitochondria associated 3 [Gene - OMIM - HGNC]
  • CECR3:cat eye syndrome chromosome region, candidate 3 [Gene - HGNC]
  • COMT:catechol-O-methyltransferase [Gene - OMIM - HGNC]
  • CDC45:cell division cycle 45 [Gene - OMIM - HGNC]
  • CCT8L2:chaperonin containing TCP1 subunit 8 like 2 [Gene - HGNC]
  • C22orf39:chromosome 22 open reading frame 39 [Gene - HGNC]
  • CLTCL1:clathrin heavy chain like 1 [Gene - OMIM - HGNC]
  • CLDN5:claudin 5 [Gene - OMIM - HGNC]
  • ESS2:ess-2 splicing factor homolog [Gene - OMIM - HGNC]
  • FAM230A:family with sequence similarity 230 member A [Gene - HGNC]
  • GGTLC3:gamma-glutamyltransferase light chain family member 3 [Gene - OMIM - HGNC]
  • GP1BB:glycoprotein Ib platelet subunit beta [Gene - OMIM - HGNC]
  • GSC2:goosecoid homeobox 2 [Gene - OMIM - HGNC]
  • HDHD5:haloacid dehalogenase like hydrolase domain containing 5 [Gene - HGNC]
  • HIRA:histone cell cycle regulator [Gene - OMIM - HGNC]
  • IL17RA:interleukin 17 receptor A [Gene - OMIM - HGNC]
  • KLHL22:kelch like family member 22 [Gene - OMIM - HGNC]
  • LZTR1:leucine zipper like post translational regulator 1 [Gene - OMIM - HGNC]
  • MED15:mediator complex subunit 15 [Gene - OMIM - HGNC]
  • MICAL3:microtubule associated monooxygenase, calponin and LIM domain containing 3 [Gene - OMIM - HGNC]
  • MRPL40:mitochondrial ribosomal protein L40 [Gene - OMIM - HGNC]
  • PEX26:peroxisomal biogenesis factor 26 [Gene - OMIM - HGNC]
  • PI4KA:phosphatidylinositol 4-kinase alpha [Gene - OMIM - HGNC]
  • PRODH:proline dehydrogenase 1 [Gene - OMIM - HGNC]
  • P2RX6:purinergic receptor P2X 6 [Gene - OMIM - HGNC]
  • RTN4R:reticulon 4 receptor [Gene - OMIM - HGNC]
  • RTL10:retrotransposon Gag like 10 [Gene - HGNC]
  • SCARF2:scavenger receptor class F member 2 [Gene - OMIM - HGNC]
  • SEPTIN5:septin 5 [Gene - OMIM - HGNC]
  • SERPIND1:serpin family D member 1 [Gene - OMIM - HGNC]
  • SLC25A18:solute carrier family 25 member 18 [Gene - OMIM - HGNC]
  • SLC25A1:solute carrier family 25 member 1 [Gene - OMIM - HGNC]
  • SLC7A4:solute carrier family 7 member 4 [Gene - OMIM - HGNC]
  • SNAP29:synaptosome associated protein 29 [Gene - OMIM - HGNC]
  • TRMT2A:tRNA methyltransferase 2 homolog A [Gene - OMIM - HGNC]
  • TSSK2:testis specific serine kinase 2 [Gene - OMIM - HGNC]
  • TXNRD2:thioredoxin reductase 2 [Gene - OMIM - HGNC]
  • TMEM121B:transmembrane protein 121B [Gene - HGNC]
  • TMEM191B:transmembrane protein 191B [Gene - HGNC]
  • TANGO2:transport and golgi organization 2 homolog [Gene - OMIM - HGNC]
  • TUBA8:tubulin alpha 8 [Gene - OMIM - HGNC]
  • UFD1:ubiquitin recognition factor in ER associated degradation 1 [Gene - OMIM - HGNC]
  • USP18:ubiquitin specific peptidase 18 [Gene - OMIM - HGNC]
  • USP41:ubiquitin specific peptidase 41 [Gene - HGNC]
  • ZDHHC8:zinc finger DHHC-type palmitoyltransferase 8 [Gene - OMIM - HGNC]
  • ZNF74:zinc finger protein 74 [Gene - OMIM - HGNC]
Variant type:
copy number gain
Cytogenetic location:
22q11.1-11.21
Genomic location:
Chr22: 16800000 - 21500000 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 22q11.1-11.21(chr22:16800000-21500000)x4
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
    SCV001451372Illumina Laboratory Services, Illumina
    criteria provided, single submitter

    (ICSL CNVClassificationCriteria Aug2020)    		Pathogenic
    (Oct 7, 2020)     		unknownclinical testing

    PubMed (4)
    [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

    Phenotypic variability of the cat eye syndrome. Case report and review of the literature.

    Rosias PR, Sijstermans JM, Theunissen PM, Pulles-Heintzberger CF, De Die-Smulders CE, Engelen JJ, Van Der Meer SB.

    Genet Couns. 2001;12(3):273-82. Review.

    PubMed [citation]
    PMID:
    11693792

    Genomic disorders on 22q11.

    McDermid HE, Morrow BE.

    Am J Hum Genet. 2002 May;70(5):1077-88. Epub 2002 Mar 29. Review.

    PubMed [citation]
    PMID:
    11925570
    PMCID:
    PMC447586
    See all PubMed Citations (4)

    Details of each submission

    From Illumina Laboratory Services, Illumina, SCV001451372.2

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1not providednot providednot providednot providedclinical testing PubMed (4)

    Description

    This CNV is a 4.7 Mb duplication of chromosome 22 at 22q11.1-q11.21 resulting in four copies of the region, (seq[GRCh37](dup)(22)(q11.1q11.21);chr22:g.16800000_21500000dup). This CNV constitutes a gain encompassing 63 protein coding genes. Partial tetrasomy of this region is associated with cat eye syndrome (CES) and usually takes the form of a supernumerary, bisatellited marker chromosome 22, or inv dup(22)(pter-q11.2) (Rosias et al. 2001; McDermid and Morrow 2002). Over 100 patients with CES have described in the literature. Considerable phenotypic variability is observed. Major features include preauricular skin tags/pits or other ear malformations, anorectal malformations, urogenital malformations, eye anomalies, and congenital heart defects. More variable minor features include dysmorphic facial features such as hypertelorism and micrognathia, orthopedic malformations such as digit anomalies, and abdominal malformations. Intellectual disability and other neurological findings may also be present (Rosias et al. 2001; McDermid and Morrow 2002; Denavit et al. 2004). The CES critical region has been narrowed to the most proximal 2 - 2.5 Mb of 22q11. Within this region, the CECR1 gene is a candidate for the heart and facial defects, while the CECR2 gene is a candidate for eye anomalies. Due to the presence of low-copy repeats in the region, two clusters of chromosomal duplication breakpoints are observed, producing three different CES gains defined by copy number of the nearby 22q11.2 deletion syndrome region (McTaggart et al. 1998). It is noted though that disease severity and specific phenotypic features do not seem to be linked to gain size. Similar gains have not been reported in 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