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GRCh37/hg19 11q14.1-22.3(chr11:81478509-104667040)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 19, 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:
RCV002475722.1

Allele description [Variation Report for GRCh37/hg19 11q14.1-22.3(chr11:81478509-104667040)x1]

GRCh37/hg19 11q14.1-22.3(chr11:81478509-104667040)x1

Genes:
  • CREBZF:CREB/ATF bZIP transcription factor [Gene - OMIM - HGNC]
  • CWC15:CWC15 spliceosome associated protein homolog [Gene - HGNC]
  • DDIAS:DNA damage induced apoptosis suppressor [Gene - OMIM - HGNC]
  • DDI1:DNA damage inducible 1 homolog 1 [Gene - HGNC]
  • FAT3:FAT atypical cadherin 3 [Gene - OMIM - HGNC]
  • GPR83:G protein-coupled receptor 83 [Gene - OMIM - HGNC]
  • IZUMO1R:IZUMO1 receptor, JUNO [Gene - OMIM - HGNC]
  • JRKL:JRK like [Gene - OMIM - HGNC]
  • MRE11:MRE11 homolog, double strand break repair nuclease [Gene - OMIM - HGNC]
  • NAALAD2:N-acetylated alpha-linked acidic dipeptidase 2 [Gene - OMIM - HGNC]
  • NOX4:NADPH oxidase 4 [Gene - OMIM - HGNC]
  • PCF11:PCF11 cleavage and polyadenylation factor subunit [Gene - OMIM - HGNC]
  • RAB30:RAB30, member RAS oncogene family [Gene - OMIM - HGNC]
  • RAB38:RAB38, member RAS oncogene family [Gene - OMIM - HGNC]
  • ARHGAP42:Rho GTPase activating protein 42 [Gene - OMIM - HGNC]
  • TAF1D:TATA-box binding protein associated factor, RNA polymerase I subunit D [Gene - OMIM - HGNC]
  • VSTM5:V-set and transmembrane domain containing 5 [Gene - HGNC]
  • YAP1:Yes1 associated transcriptional regulator [Gene - OMIM - HGNC]
  • AMOTL1:angiomotin like 1 [Gene - OMIM - HGNC]
  • ANGPTL5:angiopoietin like 5 [Gene - OMIM - HGNC]
  • ANKRD42:ankyrin repeat domain 42 [Gene - OMIM - HGNC]
  • ANKRD49:ankyrin repeat domain 49 [Gene - OMIM - HGNC]
  • BIRC2:baculoviral IAP repeat containing 2 [Gene - OMIM - HGNC]
  • BIRC3:baculoviral IAP repeat containing 3 [Gene - OMIM - HGNC]
  • CTSC:cathepsin C [Gene - OMIM - HGNC]
  • CEP126:centrosomal protein 126 [Gene - OMIM - HGNC]
  • CEP295:centrosomal protein 295 [Gene - OMIM - HGNC]
  • CEP57:centrosomal protein 57 [Gene - OMIM - HGNC]
  • C11orf54:chromosome 11 open reading frame 54 [Gene - OMIM - HGNC]
  • CFAP300:cilia and flagella associated protein 300 [Gene - OMIM - HGNC]
  • CCDC81:coiled-coil domain containing 81 [Gene - HGNC]
  • CCDC82:coiled-coil domain containing 82 [Gene - OMIM - HGNC]
  • CCDC83:coiled-coil domain containing 83 [Gene - HGNC]
  • CCDC89:coiled-coil domain containing 89 [Gene - HGNC]
  • CCDC90B:coiled-coil domain containing 90B [Gene - HGNC]
  • CNTN5:contactin 5 [Gene - OMIM - HGNC]
  • CHORDC1:cysteine and histidine rich domain containing 1 [Gene - OMIM - HGNC]
  • DCUN1D5:defective in cullin neddylation 1 domain containing 5 [Gene - OMIM - HGNC]
  • DEUP1:deuterosome assembly protein 1 [Gene - OMIM - HGNC]
  • DLG2:discs large MAGUK scaffold protein 2 [Gene - OMIM - HGNC]
  • DYNC2H1:dynein cytoplasmic 2 heavy chain 1 [Gene - OMIM - HGNC]
  • EED:embryonic ectoderm development [Gene - OMIM - HGNC]
  • ENDOD1:endonuclease domain containing 1 [Gene - OMIM - HGNC]
  • FAM181B:family with sequence similarity 181 member B [Gene - HGNC]
  • FAM76B:family with sequence similarity 76 member B [Gene - HGNC]
  • FOLH1B:folate hydrolase 1B [Gene - OMIM - HGNC]
  • FZD4:frizzled class receptor 4 [Gene - OMIM - HGNC]
  • FUT4:fucosyltransferase 4 [Gene - OMIM - HGNC]
  • GRM5:glutamate metabotropic receptor 5 [Gene - OMIM - HGNC]
  • HIKESHI:heat shock protein nuclear import factor hikeshi [Gene - OMIM - HGNC]
  • HEPHL1:hephaestin like 1 [Gene - OMIM - HGNC]
  • KDM4D:lysine demethylase 4D [Gene - OMIM - HGNC]
  • KDM4E:lysine demethylase 4E [Gene - OMIM - HGNC]
  • ME3:malic enzyme 3 [Gene - OMIM - HGNC]
  • MAML2:mastermind like transcriptional coactivator 2 [Gene - OMIM - HGNC]
  • LOC100128088:matrix metallopeptidase 1-like [Gene]
  • MMP10:matrix metallopeptidase 10 [Gene - OMIM - HGNC]
  • MMP12:matrix metallopeptidase 12 [Gene - OMIM - HGNC]
  • MMP13:matrix metallopeptidase 13 [Gene - OMIM - HGNC]
  • MMP1:matrix metallopeptidase 1 [Gene - OMIM - HGNC]
  • MMP20:matrix metallopeptidase 20 [Gene - OMIM - HGNC]
  • MMP27:matrix metallopeptidase 27 [Gene - OMIM - HGNC]
  • MMP3:matrix metallopeptidase 3 [Gene - OMIM - HGNC]
  • MMP7:matrix metallopeptidase 7 [Gene - OMIM - HGNC]
  • MMP8:matrix metallopeptidase 8 [Gene - OMIM - HGNC]
  • MED17:mediator complex subunit 17 [Gene - OMIM - HGNC]
  • MTNR1B:melatonin receptor 1B [Gene - OMIM - HGNC]
  • MTMR2:myotubularin related protein 2 [Gene - OMIM - HGNC]
  • PANX1:pannexin 1 [Gene - OMIM - HGNC]
  • PICALM:phosphatidylinositol binding clathrin assembly protein [Gene - OMIM - HGNC]
  • PIWIL4:piwi like RNA-mediated gene silencing 4 [Gene - OMIM - HGNC]
  • PDGFD:platelet derived growth factor D [Gene - OMIM - HGNC]
  • PGR:progesterone receptor [Gene - OMIM - HGNC]
  • PRCP:prolylcarboxypeptidase [Gene - OMIM - HGNC]
  • SRSF8:serine and arginine rich splicing factor 8 [Gene - OMIM - HGNC]
  • PRSS23:serine protease 23 [Gene - OMIM - HGNC]
  • SESN3:sestrin 3 [Gene - OMIM - HGNC]
  • SMCO4:single-pass membrane protein with coiled-coil domains 4 [Gene - OMIM - HGNC]
  • SLC36A4:solute carrier family 36 member 4 [Gene - OMIM - HGNC]
  • SYTL2:synaptotagmin like 2 [Gene - OMIM - HGNC]
  • TRPC6:transient receptor potential cation channel subfamily C member 6 [Gene - OMIM - HGNC]
  • TMEM123:transmembrane protein 123 [Gene - OMIM - HGNC]
  • TMEM126A:transmembrane protein 126A [Gene - OMIM - HGNC]
  • TMEM126B:transmembrane protein 126B [Gene - OMIM - HGNC]
  • TMEM133:transmembrane protein 133 [Gene - HGNC]
  • TMEM135:transmembrane protein 135 [Gene - OMIM - HGNC]
  • TRIM49:tripartite motif containing 49 [Gene - OMIM - HGNC]
  • TRIM49C:tripartite motif containing 49C [Gene - HGNC]
  • TRIM49D1:tripartite motif containing 49D1 [Gene - HGNC]
  • TRIM49D2:tripartite motif containing 49D2 [Gene - HGNC]
  • TRIM64:tripartite motif containing 64 [Gene - HGNC]
  • TRIM64B:tripartite motif containing 64B [Gene - HGNC]
  • TRIM77:tripartite motif containing 77 [Gene - HGNC]
  • TYR:tyrosinase [Gene - OMIM - HGNC]
  • UBTFL1:upstream binding transcription factor like 1 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
11q14.1-22.3
Genomic location:
Chr11: 81478509 - 104667040 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 11q14.1-22.3(chr11:81478509-104667040)x1
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
    SCV002772950Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Oct 19, 2021)     		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, SCV002772950.1

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

    Description

    This large interstitial deletion, based on size and gene content, is expected to cause phenotypic and/or developmental abnormalities. This deletion involves numerous genes including FZD4 (OMIM 604579) and YAP1 (OMIM 606608) and DLG2 (OMIM 603583). Haploinsufficiency of FZD4 is associated with autosomal dominant familial exudative vitreoretinopathy-1 (OMIM 133780; Li et al., Invest Ophthalmol Vis Sci. 2018 Nov 1;59(13):5368-5381. PMID: 30452590; Tian et al., Mol Vis. 2019 Feb 7;25:60-69. PMID: 30820142), an inherited disorder characterized by the incomplete development of the retinal vasculature. Heterozygous sequence variants, as well as one large deletion involving YAP1 have been associated with autosomal dominant ocular coloboma with or without hearing impairment, cleft lip/palate, and/or intellectual disability (OMIM 120433; Williamson KA et al., Am J Hum Genet. 2014 Feb 6;94(2):295-302. PMID: 24462371; Holt et al., Sci Rep. 2017 Aug 11;7(1):7975. PMID: 28801591). In addition, there is emerging information suggesting deletions of this gene maybe a risk factor for neurodevelopmental disorders (Reggiani et al.Genome Med. 2017 Jul 19;9(1):67. PMID: 28724449; Di Gregorio et al.,Clin Genet. 2017 Oct;92(4):415-422., PMID: 28295210). Sequence variations and intragenic deletions of DLG2 are also being evaluated with regard to schizophrenia (Kushima et al., Mol Psychiatry. 2017 Mar;22(3):430-440., PMID: 27240532; Ingason et al. Transl Psychiatry. 2015 Oct 13;5:e656. PMID: 26460480; Georgieva et al. Hum Mol Genet. 2014 Dec 15;23(24):6677-83. PMID: 25055870). A single publication identified a similar de novo deletion of 11q14.2q22.1 in a 13-year-old boy with severe learning difficulties, intellectual disability and mild heart defects (Papoulidis et al., Mol Cytogenet.2015 Sep 17;8:71. PMID: 26388939). The authors summarized previously published deletions over this region of variable size and gene content. They implicated GRM5 (encompassed in this deletion) and GRIA4 (not encompassed) in association with severity of developmental delay. The other features were variable and genotype-phenotype correlation could not be established. Further, this deletion interval includes genes that are associated with autosomal dominant phenotypes: TYR (OMIM 601800), TRPC6 (OMIM 603965) and autosomal recessive phenotypes: CTSC (OMIM 245010, 245000, 170650), MRE11 (OMIM 604391), and MTMR2 (OMIM 601382).

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

    Last Updated: Mar 26, 2023