GRCh37/hg19 18q11.2-23(chr18:23626739-78014976)x3 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:: RCV001537911.4

Allele description [Variation Report for GRCh37/hg19 18q11.2-23(chr18:23626739-78014976)x3]

GRCh37/hg19 18q11.2-23(chr18:23626739-78014976)x3

Genes:

KDSR:3-ketodihydrosphingosine reductase [Gene - OMIM - HGNC]
ADNP2:ADNP homeobox 2 [Gene - OMIM - HGNC]
ASXL3:ASXL transcriptional regulator 3 [Gene - OMIM - HGNC]
ATP5F1A:ATP synthase F1 subunit alpha [Gene - OMIM - HGNC]
ATP8B1:ATPase phospholipid transporting 8B1 [Gene - OMIM - HGNC]
ATP9B:ATPase phospholipid transporting 9B (putative) [Gene - OMIM - HGNC]
BCL2:BCL2 apoptosis regulator [Gene - OMIM - HGNC]
CD226:CD226 molecule [Gene - OMIM - HGNC]
CTDP1:CTD phosphatase subunit 1 [Gene - OMIM - HGNC]
CELF4:CUGBP Elav-like family member 4 [Gene - OMIM - HGNC]
CXXC1:CXXC finger protein 1 [Gene - OMIM - HGNC]
DCC:DCC netrin 1 receptor [Gene - OMIM - HGNC]
POLI:DNA polymerase iota [Gene - OMIM - HGNC]
FBXO15:F-box protein 15 [Gene - OMIM - HGNC]
GAREM1:GRB2 associated regulator of MAPK1 subtype 1 [Gene - OMIM - HGNC]
HAUS1:HAUS augmin like complex subunit 1 [Gene - OMIM - HGNC]
INO80C:INO80 complex subunit C [Gene - HGNC]
KIAA1328:KIAA1328 [Gene - OMIM - HGNC]
MALT1:MALT1 paracaspase [Gene - OMIM - HGNC]
NEDD4L:NEDD4 like E3 ubiquitin protein ligase [Gene - OMIM - HGNC]
PHLPP1:PH domain and leucine rich repeat protein phosphatase 1 [Gene - OMIM - HGNC]
RELCH:RAB11 binding and LisH domain, coiled-coil and HEAT repeat containing [Gene - OMIM - HGNC]
RAB27B:RAB27B, member RAS oncogene family [Gene - OMIM - HGNC]
RPL17-C18orf32:RPL17-C18orf32 readthrough [Gene - HGNC]
RIT2:Ras like without CAAX 2 [Gene - OMIM - HGNC]
SEC11C:SEC11 homolog C, signal peptidase complex subunit [Gene - HGNC]
SETBP1:SET binding protein 1 [Gene - OMIM - HGNC]
SKOR2:SKI family transcriptional corepressor 2 [Gene - OMIM - HGNC]
SMAD2:SMAD family member 2 [Gene - OMIM - HGNC]
SMAD4:SMAD family member 4 [Gene - OMIM - HGNC]
SMAD7:SMAD family member 7 [Gene - OMIM - HGNC]
SS18:SS18 subunit of BAF chromatin remodeling complex [Gene - OMIM - HGNC]
ST8SIA3:ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3 [Gene - OMIM - HGNC]
ST8SIA5:ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5 [Gene - OMIM - HGNC]
STARD6:StAR related lipid transfer domain containing 6 [Gene - OMIM - HGNC]
TAF4B:TATA-box binding protein associated factor 4b [Gene - OMIM - HGNC]
TNFRSF11A:TNF receptor superfamily member 11a [Gene - OMIM - HGNC]
WDR7:WD repeat domain 7 [Gene - OMIM - HGNC]
ACAA2:acetyl-CoA acyltransferase 2 [Gene - OMIM - HGNC]
ALPK2:alpha kinase 2 [Gene - OMIM - HGNC]
AQP4:aquaporin 4 [Gene - OMIM - HGNC]
ARK2C:arkadia (RNF111) C-terminal like ring finger ubiquitin ligase 2C [Gene - HGNC]
ARK2N:arkadia (RNF111) N-terminal like PKA signaling regulator 2N [Gene - HGNC]
NARS1:asparaginyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
B4GALT6:beta-1,4-galactosyltransferase 6 [Gene - OMIM - HGNC]
BOD1L2:biorientation of chromosomes in cell division 1 like 2 [Gene - HGNC]
CDH19:cadherin 19 [Gene - OMIM - HGNC]
CDH20:cadherin 20 [Gene - OMIM - HGNC]
CDH2:cadherin 2 [Gene - OMIM - HGNC]
CDH7:cadherin 7 [Gene - OMIM - HGNC]
CTIF:cap binding complex dependent translation initiation factor [Gene - OMIM - HGNC]
CHST9:carbohydrate sulfotransferase 9 [Gene - OMIM - HGNC]
CNDP1:carnosine dipeptidase 1 [Gene - OMIM - HGNC]
CNDP2:carnosine dipeptidase 2 [Gene - OMIM - HGNC]
CBLN2:cerebellin 2 precursor [Gene - OMIM - HGNC]
C18orf21:chromosome 18 open reading frame 21 [Gene - HGNC]
C18orf32:chromosome 18 open reading frame 32 [Gene - OMIM - HGNC]
C18orf54:chromosome 18 open reading frame 54 [Gene - OMIM - HGNC]
C18orf63:chromosome 18 open reading frame 63 [Gene - HGNC]
CFAP53:cilia and flagella associated protein 53 [Gene - OMIM - HGNC]
CCDC102B:coiled-coil domain containing 102B [Gene - HGNC]
CCDC178:coiled-coil domain containing 178 [Gene - HGNC]
CCDC68:coiled-coil domain containing 68 [Gene - OMIM - HGNC]
CCBE1:collagen and calcium binding EGF domains 1 [Gene - OMIM - HGNC]
CPLX4:complexin 4 [Gene - OMIM - HGNC]
CYB5A:cytochrome b5 type A [Gene - OMIM - HGNC]
DSEL:dermatan sulfate epimerase like [Gene - OMIM - HGNC]
DSC1:desmocollin 1 [Gene - OMIM - HGNC]
DSC2:desmocollin 2 [Gene - OMIM - HGNC]
DSC3:desmocollin 3 [Gene - OMIM - HGNC]
DSG1:desmoglein 1 [Gene - OMIM - HGNC]
DSG2:desmoglein 2 [Gene - OMIM - HGNC]
DSG3:desmoglein 3 [Gene - OMIM - HGNC]
DSG4:desmoglein 4 [Gene - OMIM - HGNC]
DIPK1C:divergent protein kinase domain 1C [Gene - OMIM - HGNC]
DOK6:docking protein 6 [Gene - OMIM - HGNC]
DYM:dymeclin [Gene - OMIM - HGNC]
DYNAP:dynactin associated protein [Gene - OMIM - HGNC]
DTNA:dystrobrevin alpha [Gene - OMIM - HGNC]
EPG5:ectopic P-granules 5 autophagy tethering factor [Gene - OMIM - HGNC]
ELAC1:elaC ribonuclease Z 1 [Gene - OMIM - HGNC]
ELP2:elongator acetyltransferase complex subunit 2 [Gene - OMIM - HGNC]
ELOA2:elongin A2 [Gene - OMIM - HGNC]
FECH:ferrochelatase [Gene - OMIM - HGNC]
FHOD3:formin homology 2 domain containing 3 [Gene - OMIM - HGNC]
GALR1:galanin receptor 1 [Gene - OMIM - HGNC]
GRP:gastrin releasing peptide [Gene - OMIM - HGNC]
HDHD2:haloacid dehalogenase like hydrolase domain containing 2 [Gene - HGNC]
HSBP1L1:heat shock factor binding protein 1 like 1 [Gene - HGNC]
HMSD:histocompatibility minor serpin domain containing [Gene - OMIM - HGNC]
IER3IP1:immediate early response 3 interacting protein 1 [Gene - OMIM - HGNC]
KATNAL2:katanin catalytic subunit A1 like 2 [Gene - OMIM - HGNC]
KLHL14:kelch like family member 14 [Gene - OMIM - HGNC]
LMAN1:lectin, mannose binding 1 [Gene - OMIM - HGNC]
LIPG:lipase G, endothelial type [Gene - OMIM - HGNC]
LOXHD1:lipoxygenase homology PLAT domains 1 [Gene - OMIM - HGNC]
LINC01415:long intergenic non-protein coding RNA 1415 [Gene - HGNC]
LINC01879:long intergenic non-protein coding RNA 1879 [Gene - HGNC]
LINC00683:long intergenic non-protein coding RNA 683 [Gene - HGNC]
LINC-ROR:long intergenic non-protein coding RNA, regulator of reprogramming [Gene - OMIM - HGNC]
MRO:maestro [Gene - OMIM - HGNC]
ME2:malic enzyme 2 [Gene - OMIM - HGNC]
MC4R:melanocortin 4 receptor [Gene - OMIM - HGNC]
MEP1B:meprin A subunit beta [Gene - OMIM - HGNC]
MBD1:methyl-CpG binding domain protein 1 [Gene - OMIM - HGNC]
MBD2:methyl-CpG binding domain protein 2 [Gene - OMIM - HGNC]
MEX3C:mex-3 RNA binding family member C [Gene - OMIM - HGNC]
MIR122:microRNA 122 [Gene - OMIM - HGNC]
MIR187:microRNA 187 [Gene - OMIM - HGNC]
MAPRE2:microtubule associated protein RP/EB family member 2 [Gene - OMIM - HGNC]
MAPK4:mitogen-activated protein kinase 4 [Gene - OMIM - HGNC]
MOCOS:molybdenum cofactor sulfurase [Gene - OMIM - HGNC]
MBP:myelin basic protein [Gene - OMIM - HGNC]
MYO5B:myosin VB [Gene - OMIM - HGNC]
NETO1:neuropilin and tolloid like 1 [Gene - OMIM - HGNC]
NFATC1:nuclear factor of activated T cells 1 [Gene - OMIM - HGNC]
NOL4:nucleolar protein 4 [Gene - OMIM - HGNC]
ONECUT2:one cut homeobox 2 [Gene - OMIM - HGNC]
PARD6G:par-6 family cell polarity regulator gamma [Gene - OMIM - HGNC]
PMAIP1:phorbol-12-myristate-13-acetate-induced protein 1 [Gene - OMIM - HGNC]
PIK3C3:phosphatidylinositol 3-kinase catalytic subunit type 3 [Gene - OMIM - HGNC]
PIGN:phosphatidylinositol glycan anchor biosynthesis class N [Gene - OMIM - HGNC]
GALNT1:polypeptide N-acetylgalactosaminyltransferase 1 [Gene - OMIM - HGNC]
KCTD1:potassium channel tetramerization domain containing 1 [Gene - OMIM - HGNC]
KCNG2:potassium voltage-gated channel modifier subfamily G member 2 [Gene - OMIM - HGNC]
PSTPIP2:proline-serine-threonine phosphatase interacting protein 2 [Gene - OMIM - HGNC]
PTGR3:prostaglandin reductase 3 [Gene - HGNC]
PSMA8:proteasome 20S subunit alpha 8 [Gene - OMIM - HGNC]
PIAS2:protein inhibitor of activated STAT 2 [Gene - OMIM - HGNC]
RPRD1A:regulation of nuclear pre-mRNA domain containing 1A [Gene - OMIM - HGNC]
RAX:retina and anterior neural fold homeobox [Gene - OMIM - HGNC]
RPL17:ribosomal protein L17 [Gene - OMIM - HGNC]
RBFA:ribosome binding factor A [Gene - HGNC]
RNF125:ring finger protein 125 [Gene - OMIM - HGNC]
RNF138:ring finger protein 138 [Gene - OMIM - HGNC]
RNF152:ring finger protein 152 [Gene - OMIM - HGNC]
RTTN:rotatin [Gene - OMIM - HGNC]
SERPINB10:serpin family B member 10 [Gene - OMIM - HGNC]
SERPINB11:serpin family B member 11 [Gene - OMIM - HGNC]
SERPINB12:serpin family B member 12 [Gene - OMIM - HGNC]
SERPINB13:serpin family B member 13 [Gene - OMIM - HGNC]
SERPINB2:serpin family B member 2 [Gene - OMIM - HGNC]
SERPINB3:serpin family B member 3 [Gene - OMIM - HGNC]
SERPINB4:serpin family B member 4 [Gene - OMIM - HGNC]
SERPINB5:serpin family B member 5 [Gene - OMIM - HGNC]
SERPINB7:serpin family B member 7 [Gene - OMIM - HGNC]
SERPINB8:serpin family B member 8 [Gene - OMIM - HGNC]
SIGLEC15:sialic acid binding Ig like lectin 15 [Gene - OMIM - HGNC]
SMIM21:small integral membrane protein 21 [Gene - HGNC]
SLC14A1:solute carrier family 14 member 1 (Kidd blood group) [Gene - OMIM - HGNC]
SLC14A2:solute carrier family 14 member 2 [Gene - OMIM - HGNC]
SLC25A52:solute carrier family 25 member 52 [Gene - OMIM - HGNC]
SLC39A6:solute carrier family 39 member 6 [Gene - OMIM - HGNC]
SLC66A2:solute carrier family 66 member 2 [Gene - HGNC]
SALL3:spalt like transcription factor 3 [Gene - OMIM - HGNC]
SKA1:spindle and kinetochore associated complex subunit 1 [Gene - OMIM - HGNC]
SOCS6:suppressor of cytokine signaling 6 [Gene - OMIM - HGNC]
SYT4:synaptotagmin 4 [Gene - OMIM - HGNC]
TSHZ1:teashirt zinc finger homeobox 1 [Gene - OMIM - HGNC]
TXNL1:thioredoxin like 1 [Gene - OMIM - HGNC]
TXNL4A:thioredoxin like 4A [Gene - OMIM - HGNC]
TMX3:thioredoxin related transmembrane protein 3 [Gene - OMIM - HGNC]
TRAPPC8:trafficking protein particle complex subunit 8 [Gene - OMIM - HGNC]
TCF4:transcription factor 4 [Gene - OMIM - HGNC]
TIMM21:translocase of inner mitochondrial membrane 21 [Gene - OMIM - HGNC]
TTR:transthyretin [Gene - OMIM - HGNC]
TPGS2:tubulin polyglutamylase complex subunit 2 [Gene - HGNC]
VPS4B:vacuolar protein sorting 4 homolog B [Gene - OMIM - HGNC]
ZCCHC2:zinc finger CCHC-type containing 2 [Gene - OMIM - HGNC]
ZBTB7C:zinc finger and BTB domain containing 7C [Gene - OMIM - HGNC]
ZSCAN30:zinc finger and SCAN domain containing 30 [Gene - HGNC]
ZNF236:zinc finger protein 236 [Gene - OMIM - HGNC]
ZNF24:zinc finger protein 24 [Gene - OMIM - HGNC]
ZNF396:zinc finger protein 396 [Gene - OMIM - HGNC]
ZNF397:zinc finger protein 397 [Gene - OMIM - HGNC]
ZNF407:zinc finger protein 407 [Gene - OMIM - HGNC]
ZNF516:zinc finger protein 516 [Gene - OMIM - HGNC]
ZNF532:zinc finger protein 532 [Gene - OMIM - HGNC]

Variant type:

copy number gain

Cytogenetic location:

18q11.2-23

Genomic location:

Chr18: 23626739 - 78014976 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 18q11.2-23(chr18:23626739-78014976)x3

HGVS:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Burkholderia sp. AD27 16S ribosomal RNA gene, partial sequence
Burkholderia sp. AD27 16S ribosomal RNA gene, partial sequence
gi|670736715|gb|KJ685242.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001754839	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL CNVClassificationCriteria Jul2020Prior)	Pathogenic (Jan 9, 2019)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001754839

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL CNVClassificationCriteria Jul2020Prior)

Pathogenic
(Jan 9, 2019)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

The trisomy 18 syndrome.

Cereda A, Carey JC.

Orphanet J Rare Dis. 2012 Oct 23;7:81. doi: 10.1186/1750-1172-7-81. Review.

PubMed [citation]

PMID:: 23088440
PMCID:: PMC3520824

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001754839.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This CNV is a 54.4 Mb duplication of 18q11.2-q23 on chromosome 18, (seq[GRCh37]dup(18)(q11.2q23, chr18:g.23626739_78014976dup), found in a de novo state. This CNV constitutes a gain encompassing at least 173 genes. The CNV overlaps the well-described trisomy 18 syndrome, also referred to as Edwards syndrome. This syndrome has an estimated population prevalence of 1 in 8000 live births and a female to male prevalence of 3:1, with better survival rates in females (Cereda and Carey 2012). Unbalanced translocations were seen in affected individuals and were inherited from a parent with a balanced translocation, however some also occurred de novo. Around 94% of cases show full trisomy and 5% show mosaic or partial trisomy. The phenotype of partial trisomy 18 is extremely variable and clinical features include growth delay, microcephaly, genitourinary malformations (cryptorchidism and hypotrophic labia), gastrointestinal malformations, characteristic facial features (prominent occiput, micrognathia, and ear abnormalities), structural heart defects, developmental delay, and intellectual disability. Based on the collective evidence, this CNV is classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 9, 2023

ClinVar

Relating variation to medicine