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GRCh37/hg19 18p11.32-11.21(chr18:136227-14585159)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 23, 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:
RCV003483328.1

Allele description [Variation Report for GRCh37/hg19 18p11.32-11.21(chr18:136227-14585159)x1]

GRCh37/hg19 18p11.32-11.21(chr18:136227-14585159)x1

Genes:
  • AKAIN1:A-kinase anchor inhibitor 1 [Gene - OMIM - HGNC]
  • AFG3L2:AFG3 like matrix AAA peptidase subunit 2 [Gene - OMIM - HGNC]
  • APCDD1:APC down-regulated 1 [Gene - OMIM - HGNC]
  • DLGAP1:DLG associated protein 1 [Gene - OMIM - HGNC]
  • DLGAP1-AS2:DLGAP1 antisense RNA 2 [Gene - HGNC]
  • GNAL:G protein subunit alpha L [Gene - OMIM - HGNC]
  • L3MBTL4:L3MBTL histone methyl-lysine binding protein 4 [Gene - OMIM - HGNC]
  • NDUFV2:NADH:ubiquinone oxidoreductase core subunit V2 [Gene - OMIM - HGNC]
  • NDC80:NDC80 kinetochore complex component [Gene - OMIM - HGNC]
  • NAPG:NSF attachment protein gamma [Gene - OMIM - HGNC]
  • POTEC:POTE ankyrin domain family member C [Gene - HGNC]
  • PRELID3A:PRELI domain containing 3A [Gene - OMIM - HGNC]
  • RAB12:RAB12, member RAS oncogene family [Gene - OMIM - HGNC]
  • RAB31:RAB31, member RAS oncogene family [Gene - OMIM - HGNC]
  • RNMT:RNA guanine-7 methyltransferase [Gene - OMIM - HGNC]
  • ARHGAP28:Rho GTPase activating protein 28 [Gene - OMIM - HGNC]
  • SEH1L:SEH1 like nucleoporin [Gene - OMIM - HGNC]
  • TGIF1:TGFB induced factor homeobox 1 [Gene - OMIM - HGNC]
  • THOC1:THO complex subunit 1 [Gene - OMIM - HGNC]
  • TYMSOS:TYMS opposite strand RNA [Gene - HGNC]
  • VAPA:VAMP associated protein A [Gene - OMIM - HGNC]
  • YES1:YES proto-oncogene 1, Src family tyrosine kinase [Gene - OMIM - HGNC]
  • ADCYAP1:adenylate cyclase activating polypeptide 1 [Gene - OMIM - HGNC]
  • ANKRD12:ankyrin repeat domain 12 [Gene - OMIM - HGNC]
  • ANKRD62:ankyrin repeat domain 62 [Gene - HGNC]
  • CIDEA:cell death inducing DFFA like effector a [Gene - OMIM - HGNC]
  • CETN1:centrin 1 [Gene - OMIM - HGNC]
  • CEP192:centrosomal protein 192 [Gene - OMIM - HGNC]
  • CEP76:centrosomal protein 76 [Gene - HGNC]
  • CHMP1B:charged multivesicular body protein 1B [Gene - OMIM - HGNC]
  • CLUL1:clusterin like 1 [Gene - OMIM - HGNC]
  • COLEC12:collectin subfamily member 12 [Gene - OMIM - HGNC]
  • EMILIN2:elastin microfibril interfacer 2 [Gene - OMIM - HGNC]
  • ENOSF1:enolase superfamily member 1 [Gene - OMIM - HGNC]
  • EPB41L3:erythrocyte membrane protein band 4.1 like 3 [Gene - OMIM - HGNC]
  • FAM210A:family with sequence similarity 210 member A [Gene - OMIM - HGNC]
  • IMPA2:inositol monophosphatase 2 [Gene - OMIM - HGNC]
  • LAMA1:laminin subunit alpha 1 [Gene - OMIM - HGNC]
  • LRRC30:leucine rich repeat containing 30 [Gene - HGNC]
  • LPIN2:lipin 2 [Gene - OMIM - HGNC]
  • LDLRAD4:low density lipoprotein receptor class A domain containing 4 [Gene - OMIM - HGNC]
  • MC2R:melanocortin 2 receptor [Gene - OMIM - HGNC]
  • MC5R:melanocortin 5 receptor [Gene - OMIM - HGNC]
  • MPPE1:metallophosphoesterase 1 [Gene - OMIM - HGNC]
  • METTL4:methyltransferase 4, N6-adenosine [Gene - OMIM - HGNC]
  • MTCL1:microtubule crosslinking factor 1 [Gene - OMIM - HGNC]
  • MYOM1:myomesin 1 [Gene - OMIM - HGNC]
  • MYL12A:myosin light chain 12A [Gene - HGNC]
  • MYL12B:myosin light chain 12B [Gene - OMIM - HGNC]
  • PIEZO2:piezo type mechanosensitive ion channel component 2 [Gene - OMIM - HGNC]
  • PSMG2:proteasome assembly chaperone 2 [Gene - OMIM - HGNC]
  • PPP4R1:protein phosphatase 4 regulatory subunit 1 [Gene - OMIM - HGNC]
  • PTPN2:protein tyrosine phosphatase non-receptor type 2 [Gene - OMIM - HGNC]
  • PTPRM:protein tyrosine phosphatase receptor type M [Gene - OMIM - HGNC]
  • RALBP1:ralA binding protein 1 [Gene - OMIM - HGNC]
  • SLC35G4:solute carrier family 35 member G4 [Gene - HGNC]
  • SPIRE1:spire type actin nucleation factor 1 [Gene - OMIM - HGNC]
  • SMCHD1:structural maintenance of chromosomes flexible hinge domain containing 1 [Gene - OMIM - HGNC]
  • TXNDC2:thioredoxin domain containing 2 [Gene - OMIM - HGNC]
  • TYMS:thymidylate synthetase [Gene - OMIM - HGNC]
  • TMEM200C:transmembrane protein 200C [Gene - HGNC]
  • TUBB6:tubulin beta 6 class V [Gene - OMIM - HGNC]
  • TWSG1:twisted gastrulation BMP signaling modulator 1 [Gene - OMIM - HGNC]
  • USP14:ubiquitin specific peptidase 14 [Gene - OMIM - HGNC]
  • ZBTB14:zinc finger and BTB domain containing 14 [Gene - OMIM - HGNC]
  • ZNF519:zinc finger protein 519 [Gene - HGNC]
Variant type:
copy number loss
Cytogenetic location:
18p11.32-11.21
Genomic location:
Chr18: 136227 - 14585159 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 18p11.32-11.21(chr18:136227-14585159)x1
HGVS:

    Condition(s)

    Synonyms:
    none provided
    Identifiers:
    MedGen: C3661900

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV004230243Quest Diagnostics Nichols Institute San Juan Capistrano
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Nov 23, 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, SCV004230243.1

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

    Description

    This loss is consistent with chromosome 18p deletion syndrome (OMIM 146390), which has a rather broad and variable phenotype (Deletion 18p syndrome, in: Kenneth Lyons Jones, Smith's Recognizable Patterns of Human Malformation, Sixth edition, pages 60-61, Elsevier Saunders; Verrotti et al. Cytogenet Genome Res. 2015;146(2):115-9. PMID: 26278570). Further, haploinsufficiency for TGIF1 (OMIM 602630) through either loss of function mutation or deletion can result in variable expressivity and reduced penetrance for autosomal dominant holoprosencephaly-4 (HPE4; OMIM 142946, Poelmans et al. Am J Med Genet A. 2015 Oct;167A(10):2451-8. PMID: 26080100, Rehm et al., N Engl J Med. 2015 Jun 4;372(23):2235-42. PMID: 26014595 (HGNC:11776)).

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

    Last Updated: Feb 4, 2024