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GRCh37/hg19 7p22.1(chr7:4655928-5990874)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 15, 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:
RCV002475747.1

Allele description [Variation Report for GRCh37/hg19 7p22.1(chr7:4655928-5990874)x1]

GRCh37/hg19 7p22.1(chr7:4655928-5990874)x1

Genes:
  • CCZ1:CCZ1 homolog, vacuolar protein trafficking and biogenesis associated [Gene - HGNC]
  • FBXL18:F-box and leucine rich repeat protein 18 [Gene - OMIM - HGNC]
  • RBAK:RB associated KRAB zinc finger [Gene - OMIM - HGNC]
  • RBAK-RBAKDN:RBAK-RBAKDN readthrough [Gene - HGNC]
  • RADIL:Rap associating with DIL domain [Gene - OMIM - HGNC]
  • WIPI2:WD repeat domain, phosphoinositide interacting 2 [Gene - OMIM - HGNC]
  • ACTB:actin beta [Gene - OMIM - HGNC]
  • AP5Z1:adaptor related protein complex 5 subunit zeta 1 [Gene - OMIM - HGNC]
  • FSCN1:fascin actin-bundling protein 1 [Gene - OMIM - HGNC]
  • FOXK1:forkhead box K1 [Gene - OMIM - HGNC]
  • MMD2:monocyte to macrophage differentiation associated 2 [Gene - OMIM - HGNC]
  • OCM:oncomodulin [Gene - OMIM - HGNC]
  • PAPOLB:poly(A) polymerase beta [Gene - OMIM - HGNC]
  • RSPH10B:radial spoke head 10 homolog B [Gene - HGNC]
  • RNF216:ring finger protein 216 [Gene - OMIM - HGNC]
  • SLC29A4:solute carrier family 29 member 4 [Gene - OMIM - HGNC]
  • TNRC18:trinucleotide repeat containing 18 [Gene - HGNC]
Variant type:
copy number loss
Cytogenetic location:
7p22.1
Genomic location:
Chr7: 4655928 - 5990874 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 7p22.1(chr7:4655928-5990874)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
    SCV002773335Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Nov 15, 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, SCV002773335.1

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

    Description

    The copy number loss of 7p22.1 involves several protein-coding genes, including ACTB (OMIM 102630). Deletions overlapping this region are associated with chromosome 7p22.1 deletion syndrome (OMIM 243310; also known as Baraitser-Winter syndrome-1), a severe developmental disorder characterized by intellectual disability; growth retardation; microcephaly; hypotonia; coloboma; sensorineural deafness; typical facial gestalt; and multiple other congenital malformations, including cardiac, skeletal, and urogenital defects. Some patients may develop cortical malformations, seizures, and ventriculomegaly. The pleiotropic malformations associated with this syndrome are thought to be primarily caused by haploinsufficiency of ACTB (Li 2020, Palumbo 2018, Cuvertino 2017, Shimojima 2016, Verloes 2015, Preiksaitiene 2012). Thus, this copy number variant (CNV) isinterpreted as pathogenic. References: Cuvertino et al., Am J Hum Genet. 2017 Dec 7;101(6):1021-1033. PMID:29220674. Li et al., Indian Pediatr. 2020 Jun 15;57(6):580-581. PMID: 32562408.Palumbo et al., Eur J Med Genet. 2018 May;61(5):248-252. PMID:29274487. Preiksaitiene et al., Am J Med Genet A. 2012 May;158A(5):1200-3.PMID: 22495914. Shimojima et al., Eur J Med Genet. 2016 Oct;59(10):502-6. PMID:27633570. Verloes et al., Eur J Hum Genet. 2015 Mar;23(3):292-301. PMID:25052316.

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

    Last Updated: Dec 31, 2022