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GRCh37/hg19 5p15.33-15.1(chr5:113577-17654787)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 22, 2022
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:
RCV002473919.1

Allele description [Variation Report for GRCh37/hg19 5p15.33-15.1(chr5:113577-17654787)x1]

GRCh37/hg19 5p15.33-15.1(chr5:113577-17654787)x1

Genes:
  • MTRR:5-methyltetrahydrofolate-homocysteine methyltransferase reductase [Gene - OMIM - HGNC]
  • ADAMTS16:ADAM metallopeptidase with thrombospondin type 1 motif 16 [Gene - OMIM - HGNC]
  • ANKH:ANKH inorganic pyrophosphate transport regulator [Gene - OMIM - HGNC]
  • ATPSCKMT:ATP synthase c subunit lysine N-methyltransferase [Gene - OMIM - HGNC]
  • CLPTM1L:CLPTM1 like [Gene - OMIM - HGNC]
  • EXOC3-AS1:EXOC3 antisense RNA 1 [Gene - HGNC]
  • FBXL7:F-box and leucine rich repeat protein 7 [Gene - OMIM - HGNC]
  • FASTKD3:FAST kinase domains 3 [Gene - OMIM - 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]
  • NSUN2:NOP2/Sun RNA methyltransferase 2 [Gene - OMIM - HGNC]
  • OTULINL:OTU deubiquitinase with linear linkage specificity like [Gene - HGNC]
  • OTULIN:OTU deubiquitinase with linear linkage specificity [Gene - OMIM - HGNC]
  • OTULIN-DT:OTULIN divergent transcript [Gene - HGNC]
  • ADCY2:adenylate cyclase 2 [Gene - OMIM - HGNC]
  • ANKRD33B:ankyrin repeat domain 33B [Gene - HGNC]
  • AHRR:aryl hydrocarbon receptor repressor [Gene - OMIM - HGNC]
  • BASP1:brain abundant membrane attached signal protein 1 [Gene - OMIM - HGNC]
  • BRD9:bromodomain containing 9 [Gene - OMIM - HGNC]
  • CMBL:carboxymethylenebutenolidase homolog [Gene - OMIM - HGNC]
  • CTNND2:catenin delta 2 [Gene - OMIM - HGNC]
  • CEP72:centrosomal protein 72 [Gene - OMIM - HGNC]
  • CCT5:chaperonin containing TCP1 subunit 5 [Gene - OMIM - HGNC]
  • CFAP90:cilia and flagella associated protein 90 [Gene - HGNC]
  • CCDC127:coiled-coil domain containing 127 [Gene - HGNC]
  • DAP:death associated protein [Gene - OMIM - HGNC]
  • DNAH5:dynein axonemal heavy chain 5 [Gene - OMIM - HGNC]
  • EXOC3:exocyst complex component 3 [Gene - OMIM - HGNC]
  • ICE1:interactor of little elongation complex ELL subunit 1 [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]
  • LINC01194:long intergenic non-protein coding RNA 1194 [Gene - OMIM - HGNC]
  • LPCAT1:lysophosphatidylcholine acyltransferase 1 [Gene - OMIM - HGNC]
  • MED10:mediator complex subunit 10 [Gene - OMIM - HGNC]
  • MARCHF11:membrane associated ring-CH-type finger 11 [Gene - OMIM - HGNC]
  • MARCHF6:membrane associated ring-CH-type finger 6 [Gene - OMIM - HGNC]
  • MRPL36:mitochondrial ribosomal protein L36 [Gene - OMIM - HGNC]
  • MYO10:myosin X [Gene - OMIM - HGNC]
  • PLEKHG4B:pleckstrin homology and RhoGEF domain containing G4B [Gene - HGNC]
  • PDCD6:programmed cell death 6 [Gene - OMIM - HGNC]
  • RETREG1:reticulophagy regulator 1 [Gene - OMIM - HGNC]
  • ROPN1L:rhophilin associated tail protein 1 like [Gene - OMIM - HGNC]
  • SEMA5A:semaphorin 5A [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]
  • SRD5A1:steroid 5 alpha-reductase 1 [Gene - OMIM - HGNC]
  • SDHA:succinate dehydrogenase complex flavoprotein subunit A [Gene - OMIM - HGNC]
  • TAS2R1:taste 2 receptor member 1 [Gene - OMIM - HGNC]
  • TERT:telomerase reverse transcriptase [Gene - OMIM - HGNC]
  • TENT4A:terminal nucleotidyltransferase 4A [Gene - OMIM - HGNC]
  • TRIP13:thyroid hormone receptor interactor 13 [Gene - OMIM - HGNC]
  • TRIO:trio Rho guanine nucleotide exchange factor [Gene - OMIM - HGNC]
  • TPPP:tubulin polymerization promoting protein [Gene - OMIM - HGNC]
  • UBE2QL1:ubiquitin conjugating enzyme E2 Q family like 1 [Gene - OMIM - HGNC]
  • ZDHHC11:zinc finger DHHC-type containing 11 [Gene - HGNC]
  • ZDHHC11B:zinc finger DHHC-type containing 11B [Gene - HGNC]
  • ZNF622:zinc finger protein 622 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
5p15.33-15.1
Genomic location:
Chr5: 113577 - 17654787 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 5p15.33-15.1(chr5:113577-17654787)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
    SCV002773785Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Mar 22, 2022)     		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, SCV002773785.1

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

    Description

    This terminal deletion of 5p is consistent with the clinical diagnosis of Cri-du-chat syndrome (OMIM 123450). The main clinical features include a distinctive high-pitched cry, characteristic facial dysmorphism, slow growth, microcephaly, and intellectual disability. The severity of the phenotype varies, and there is some correlation between clinical features and the size of the deletion (GeneReviews: https://www.ncbi.nlm.nih.gov/books/NBK482460/)

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

    Last Updated: Mar 26, 2023