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GRCh37/hg19 5p15.33(chr5:13200-4012072)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 9, 2019
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:
RCV001537929.4

Allele description [Variation Report for GRCh37/hg19 5p15.33(chr5:13200-4012072)x1]

GRCh37/hg19 5p15.33(chr5:13200-4012072)x1

Genes:
  • CLPTM1L:CLPTM1 like [Gene - OMIM - HGNC]
  • EXOC3-AS1:EXOC3 antisense RNA 1 [Gene - HGNC]
  • IRX2-DT:IRX2 divergent transcript [Gene - OMIM - HGNC]
  • NDUFS6:NADH:ubiquinone oxidoreductase subunit S6 [Gene - OMIM - HGNC]
  • NKD2:NKD inhibitor of WNT signaling pathway 2 [Gene - OMIM - HGNC]
  • AHRR:aryl hydrocarbon receptor repressor [Gene - OMIM - HGNC]
  • BRD9:bromodomain containing 9 [Gene - OMIM - HGNC]
  • CEP72:centrosomal protein 72 [Gene - OMIM - HGNC]
  • CCDC127:coiled-coil domain containing 127 [Gene - HGNC]
  • EXOC3:exocyst complex component 3 [Gene - OMIM - HGNC]
  • IRX1:iroquois homeobox 1 [Gene - OMIM - HGNC]
  • IRX2:iroquois homeobox 2 [Gene - OMIM - HGNC]
  • IRX4:iroquois homeobox 4 [Gene - OMIM - HGNC]
  • LRRC14B:leucine rich repeat containing 14B [Gene - HGNC]
  • LPCAT1:lysophosphatidylcholine acyltransferase 1 [Gene - OMIM - HGNC]
  • MRPL36:mitochondrial ribosomal protein L36 [Gene - OMIM - HGNC]
  • PLEKHG4B:pleckstrin homology and RhoGEF domain containing G4B [Gene - HGNC]
  • PDCD6:programmed cell death 6 [Gene - OMIM - HGNC]
  • SLC12A7:solute carrier family 12 member 7 [Gene - OMIM - HGNC]
  • SLC6A18:solute carrier family 6 member 18 [Gene - OMIM - HGNC]
  • SLC6A19:solute carrier family 6 member 19 [Gene - OMIM - HGNC]
  • SLC6A3:solute carrier family 6 member 3 [Gene - OMIM - HGNC]
  • SLC9A3:solute carrier family 9 member A3 [Gene - OMIM - HGNC]
  • SDHA:succinate dehydrogenase complex flavoprotein subunit A [Gene - OMIM - HGNC]
  • TERT:telomerase reverse transcriptase [Gene - OMIM - HGNC]
  • TRIP13:thyroid hormone receptor interactor 13 [Gene - OMIM - HGNC]
  • TPPP:tubulin polymerization promoting protein [Gene - OMIM - HGNC]
  • ZDHHC11:zinc finger DHHC-type containing 11 [Gene - HGNC]
  • ZDHHC11B:zinc finger DHHC-type containing 11B [Gene - HGNC]
Variant type:
copy number loss
Cytogenetic location:
5p15.33
Genomic location:
Chr5: 13200 - 4012072 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 5p15.33(chr5:13200-4012072)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
    SCV001754857Illumina Laboratory Services, Illumina
    criteria provided, single submitter

    (ICSL CNVClassificationCriteria Jul2020Prior)    		Pathogenic
    (Jan 9, 2019)     		unknownclinical testing

    PubMed (6)
    [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

    Clinical and molecular characterisation of 80 patients with 5p deletion: genotype-phenotype correlation.

    Mainardi PC, Perfumo C, Calì A, Coucourde G, Pastore G, Cavani S, Zara F, Overhauser J, Pierluigi M, Bricarelli FD.

    J Med Genet. 2001 Mar;38(3):151-8.

    PubMed [citation]
    PMID:
    11238681
    PMCID:
    PMC1734829

    Cri du Chat syndrome.

    Cerruti Mainardi P.

    Orphanet J Rare Dis. 2006 Sep 5;1:33. Review.

    PubMed [citation]
    PMID:
    16953888
    PMCID:
    PMC1574300
    See all PubMed Citations (6)

    Details of each submission

    From Illumina Laboratory Services, Illumina, SCV001754857.1

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1not providednot providednot providednot providedclinical testing PubMed (6)

    Description

    This CNV is a 4 Mb deletion of 5p15.33, on chromosome 5, (seq[GRCh37]del(5)(p15.33); chr5:g.13200_4012072del), found in a de novo state. The CNV constitutes a loss encompassing 60 genes and overlaps the well-described 5p deletion syndrome, also known as cri du chat syndrome (CdCS). CdCS has an estimated population prevalence of 1:15,000 to 1:50,000 and has been reported in more than 200 probands. Unbalanced translocations have been reported in affected individuals who inherited the derivative chromosome from a parent with a balanced translocation. Deletions ranging in size from 560 kb to 40 Mb have been observed in individuals with CdCS, and phenotypic variability has been noted in relation to the location and size of the deletion. Terminal deletions are frequently observed in affected individuals (Mainardi et al. 2001; Mainardi 2006; Nguyen et al. 2016). Common features of the syndrome include high-pitched monochromatic cry, microcephaly, broad nasal bridge, epicanthal folds, micrognathia, abnormal dermatoglyphics, and severe psychomotor and mental retardation. Additional variable features include cardiac, neurological and renal abnormalities, preauricular tags, syndactyly, hypospadias, and cryptorchidism. 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