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GRCh37/hg19 5q33.1-35.2(chr5:150535183-172906793)x3 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 16, 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:
RCV002474507.1

Allele description [Variation Report for GRCh37/hg19 5q33.1-35.2(chr5:150535183-172906793)x3]

GRCh37/hg19 5q33.1-35.2(chr5:150535183-172906793)x3

Genes:
  • ADAM19:ADAM metallopeptidase domain 19 [Gene - OMIM - HGNC]
  • ATP6V0E1:ATPase H+ transporting V0 subunit e1 [Gene - OMIM - HGNC]
  • ATP10B:ATPase phospholipid transporting 10B (putative) [Gene - OMIM - HGNC]
  • BNIP1:BCL2 interacting protein 1 [Gene - OMIM - HGNC]
  • C1QTNF2:C1q and TNF related 2 [Gene - OMIM - HGNC]
  • CNOT8:CCR4-NOT transcription complex subunit 8 [Gene - OMIM - HGNC]
  • CREBRF:CREB3 regulatory factor [Gene - OMIM - HGNC]
  • EBF1:EBF transcription factor 1 [Gene - OMIM - HGNC]
  • EFCAB9:EF-hand calcium binding domain 9 [Gene - OMIM - HGNC]
  • FBXW11:F-box and WD repeat domain containing 11 [Gene - OMIM - HGNC]
  • FAT2:FAT atypical cadherin 2 [Gene - OMIM - HGNC]
  • G3BP1:G3BP stress granule assembly factor 1 [Gene - OMIM - HGNC]
  • ITK:IL2 inducible T cell kinase [Gene - OMIM - HGNC]
  • LSM11:LSM11, U7 small nuclear RNA associated [Gene - OMIM - HGNC]
  • LARP1:La ribonucleoprotein 1, translational regulator [Gene - OMIM - HGNC]
  • NIPAL4:NIPA like domain containing 4 [Gene - OMIM - HGNC]
  • NKX2-5:NK2 homeobox 5 [Gene - OMIM - HGNC]
  • NUDCD2:NudC domain containing 2 [Gene - OMIM - HGNC]
  • PTTG1:PTTG1 regulator of sister chromatid separation, securin [Gene - OMIM - HGNC]
  • PWWP2A:PWWP domain containing 2A [Gene - OMIM - HGNC]
  • RANBP17:RAN binding protein 17 [Gene - OMIM - HGNC]
  • SAP30L:SAP30 like [Gene - OMIM - HGNC]
  • SH3PXD2B:SH3 and PX domains 2B [Gene - OMIM - HGNC]
  • SLU7:SLU7 homolog, splicing factor [Gene - OMIM - HGNC]
  • SOX30:SRY-box transcription factor 30 [Gene - OMIM - HGNC]
  • TIMD4:T cell immunoglobulin and mucin domain containing 4 [Gene - OMIM - HGNC]
  • TLX3:T cell leukemia homeobox 3 [Gene - OMIM - HGNC]
  • WWC1:WW and C2 domain containing 1 [Gene - OMIM - HGNC]
  • ADRA1B:adrenoceptor alpha 1B [Gene - OMIM - HGNC]
  • ANXA6:annexin A6 [Gene - OMIM - HGNC]
  • ATOX1:antioxidant 1 copper chaperone [Gene - OMIM - HGNC]
  • RARS1:arginyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
  • C5orf52:chromosome 5 open reading frame 52 [Gene - HGNC]
  • C5orf58:chromosome 5 open reading frame 58 [Gene - HGNC]
  • CLINT1:clathrin interactor 1 [Gene - OMIM - HGNC]
  • CCDC69:coiled-coil domain containing 69 [Gene - OMIM - HGNC]
  • CCNG1:cyclin G1 [Gene - OMIM - HGNC]
  • CCNJL:cyclin J like [Gene - HGNC]
  • CYFIP2:cytoplasmic FMR1 interacting protein 2 [Gene - OMIM - HGNC]
  • DOCK2:dedicator of cytokinesis 2 [Gene - OMIM - HGNC]
  • DUSP1:dual specificity phosphatase 1 [Gene - OMIM - HGNC]
  • ERGIC1:endoplasmic reticulum-golgi intermediate compartment 1 [Gene - OMIM - HGNC]
  • FAM114A2:family with sequence similarity 114 member A2 [Gene - HGNC]
  • FAM200C:family with sequence similarity 200 member C [Gene - OMIM - HGNC]
  • FABP6:fatty acid binding protein 6 [Gene - OMIM - HGNC]
  • FAXDC2:fatty acid hydroxylase domain containing 2 [Gene - OMIM - HGNC]
  • FGF18:fibroblast growth factor 18 [Gene - OMIM - HGNC]
  • FNDC9:fibronectin type III domain containing 9 [Gene - HGNC]
  • FOXI1:forkhead box I1 [Gene - OMIM - HGNC]
  • GABRA1:gamma-aminobutyric acid type A receptor subunit alpha1 [Gene - OMIM - HGNC]
  • GABRA6:gamma-aminobutyric acid type A receptor subunit alpha6 [Gene - OMIM - HGNC]
  • GABRB2:gamma-aminobutyric acid type A receptor subunit beta2 [Gene - OMIM - HGNC]
  • GABRG2:gamma-aminobutyric acid type A receptor subunit gamma2 [Gene - OMIM - HGNC]
  • GABRP:gamma-aminobutyric acid type A receptor subunit pi [Gene - OMIM - HGNC]
  • GM2A:ganglioside GM2 activator [Gene - OMIM - HGNC]
  • GEMIN5:gem nuclear organelle associated protein 5 [Gene - OMIM - HGNC]
  • GRIA1:glutamate ionotropic receptor AMPA type subunit 1 [Gene - OMIM - HGNC]
  • GLRA1:glycine receptor alpha 1 [Gene - OMIM - HGNC]
  • GARIN3:golgi associated RAB2B interactor family member 3 [Gene - OMIM - HGNC]
  • HAND1:heart and neural crest derivatives expressed 1 [Gene - OMIM - HGNC]
  • HAVCR1:hepatitis A virus cellular receptor 1 [Gene - OMIM - HGNC]
  • HAVCR2:hepatitis A virus cellular receptor 2 [Gene - OMIM - HGNC]
  • HMMR:hyaluronan mediated motility receptor [Gene - OMIM - HGNC]
  • INSYN2B:inhibitory synaptic factor family member 2B [Gene - HGNC]
  • IL12B:interleukin 12B [Gene - OMIM - HGNC]
  • KIF4B:kinesin family member 4B [Gene - OMIM - HGNC]
  • LCP2:lymphocyte cytosolic protein 2 [Gene - OMIM - HGNC]
  • MED7:mediator complex subunit 7 [Gene - OMIM - HGNC]
  • MAT2B:methionine adenosyltransferase 2 non-catalytic beta subunit [Gene - OMIM - HGNC]
  • MIR103A1:microRNA 103a-1 [Gene - OMIM - HGNC]
  • MIR146A:microRNA 146a [Gene - OMIM - HGNC]
  • MFAP3:microfibril associated protein 3 [Gene - OMIM - HGNC]
  • MRPL22:mitochondrial ribosomal protein L22 [Gene - OMIM - HGNC]
  • NEURL1B:neuralized E3 ubiquitin protein ligase 1B [Gene - OMIM - HGNC]
  • NMUR2:neuromedin U receptor 2 [Gene - OMIM - HGNC]
  • NPM1:nucleophosmin 1 [Gene - OMIM - HGNC]
  • PANK3:pantothenate kinase 3 [Gene - OMIM - HGNC]
  • GALNT10:polypeptide N-acetylgalactosaminyltransferase 10 [Gene - OMIM - HGNC]
  • KCNMB1:potassium calcium-activated channel subfamily M regulatory beta subunit 1 [Gene - OMIM - HGNC]
  • KCNIP1:potassium voltage-gated channel interacting protein 1 [Gene - OMIM - HGNC]
  • RPL26L1:ribosomal protein L26 like 1 [Gene - HGNC]
  • RNF145:ring finger protein 145 [Gene - HGNC]
  • SGCD:sarcoglycan delta [Gene - OMIM - HGNC]
  • SPARC:secreted protein acidic and cysteine rich [Gene - OMIM - HGNC]
  • STK10:serine/threonine kinase 10 [Gene - OMIM - HGNC]
  • SLIT3:slit guidance ligand 3 [Gene - OMIM - HGNC]
  • SMIM23:small integral membrane protein 23 [Gene - HGNC]
  • SNORA74B:small nucleolar RNA, H/ACA box 74B [Gene - OMIM - HGNC]
  • SLC36A1:solute carrier family 36 member 1 [Gene - OMIM - HGNC]
  • SLC36A2:solute carrier family 36 member 2 [Gene - OMIM - HGNC]
  • SLC36A3:solute carrier family 36 member 3 [Gene - OMIM - HGNC]
  • SPDL1:spindle apparatus coiled-coil protein 1 [Gene - OMIM - HGNC]
  • STC2:stanniocalcin 2 [Gene - OMIM - HGNC]
  • THG1L:tRNA-histidine guanylyltransferase 1 like [Gene - OMIM - HGNC]
  • TENM2:teneurin transmembrane protein 2 [Gene - OMIM - HGNC]
  • TTC1:tetratricopeptide repeat domain 1 [Gene - OMIM - HGNC]
  • UBTD2:ubiquitin domain containing 2 [Gene - OMIM - HGNC]
  • UBLCP1:ubiquitin like domain containing CTD phosphatase 1 [Gene - OMIM - HGNC]
  • LOC100128059:uncharacterized LOC100128059 [Gene]
  • LOC100288254:uncharacterized LOC100288254 [Gene]
Variant type:
copy number gain
Cytogenetic location:
5q33.1-35.2
Genomic location:
Chr5: 150535183 - 172906793 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 5q33.1-35.2(chr5:150535183-172906793)x3
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
    SCV002771903Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (May 16, 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.

    PubMed [citation]
    PMID:
    31690835
    PMCID:
    PMC7313390

    Details of each submission

    From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002771903.1

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

    Description

    The copy number gain of 5q33.1q35.2 involves numerous protein-coding genes, many of which are associated with autosomal dominant phenotypes in OMIM: SLC36A2 (OMIM 608331), FAT2 (OMIM 604269), GLRA1 (OMIM 138491), CYFIP2 (OMIM 606323), GABRB2 (OMIM 600232), GABRA1 (OMIM 137160), GABRG2 (OMIM 137164), HMMR (OMIM 600936), KCNMB1 (OMIM 603951), FBXW11 (OMIM 605651), and NKX2-5 (OMIM 600584). Additionally, there are multiple reports of smaller copy-number-gains within the current interval; however, there is little overlap between gene content and/or phenotypes between these reports (Bestetti 2019, Dabkowska-Huc 2013, Faguer 2011, Fujita 2013, Glessner 2010, Koolen 2006, Krutzke 2016, Yu 2011). A report by Koolen et al. (2006) identified a 1.25 Mb duplication in an individual with holoprosencephaly and preaxial polydactyly. They proposed that FBXW11 is a candidate gene to explain this phenotype. Thus, based on current medical literature and gene content, this copy number variant (CNV) is interpreted as pathogenic. References: Bestetti et al., Hum Reprod. 2019 Mar 1;34(3):574-583. PMID: 30689869 Dabkowska-Huc et al., Case Rep Genet. 2013;2013:105052. PMID: 23476832 Faguer et al., Eur J Med Genet. May-Jun 2011;54(3):310-3. PMID: 21276880 Fujita et al., Am J Med Genet A. 2013 Aug;161A(8):1904-9. PMID: 23824987 Glessner et al., PLoS One. 2010 Dec 1;5(12):e15463. PMID: 21152026 Koolen et al., J Hum Genet. 2006;51(8):721-726. PMID: 16865294 Krutzke et al., Birth Defects Res A Clin Mol Teratol. 2016 Jan;106(1):16-26. PMID: 26680650 Yu et al., Rheumatology (Oxford). 2011 Jul;50(7):1201-5. PMID: 21278068

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

    Last Updated: Mar 26, 2023