GRCh37/hg19 18q12.1-12.3(chr18:26595964-38643072)x1 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 13, 2023
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:: RCV003483335.1

Allele description [Variation Report for GRCh37/hg19 18q12.1-12.3(chr18:26595964-38643072)x1]

GRCh37/hg19 18q12.1-12.3(chr18:26595964-38643072)x1

Genes:

ASXL3:ASXL transcriptional regulator 3 [Gene - OMIM - HGNC]
CELF4:CUGBP Elav-like family member 4 [Gene - OMIM - HGNC]
GAREM1:GRB2 associated regulator of MAPK1 subtype 1 [Gene - OMIM - HGNC]
INO80C:INO80 complex subunit C [Gene - HGNC]
KIAA1328:KIAA1328 [Gene - OMIM - HGNC]
B4GALT6:beta-1,4-galactosyltransferase 6 [Gene - OMIM - HGNC]
C18orf21:chromosome 18 open reading frame 21 [Gene - HGNC]
CCDC178:coiled-coil domain containing 178 [Gene - 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]
DTNA:dystrobrevin alpha [Gene - OMIM - HGNC]
ELP2:elongator acetyltransferase complex subunit 2 [Gene - OMIM - HGNC]
FHOD3:formin homology 2 domain containing 3 [Gene - OMIM - HGNC]
KLHL14:kelch like family member 14 [Gene - OMIM - HGNC]
MEP1B:meprin A subunit beta [Gene - OMIM - HGNC]
MIR187:microRNA 187 [Gene - OMIM - HGNC]
MAPRE2:microtubule associated protein RP/EB family member 2 [Gene - OMIM - HGNC]
MOCOS:molybdenum cofactor sulfurase [Gene - OMIM - HGNC]
NOL4:nucleolar protein 4 [Gene - OMIM - HGNC]
GALNT1:polypeptide N-acetylgalactosaminyltransferase 1 [Gene - OMIM - HGNC]
RPRD1A:regulation of nuclear pre-mRNA domain containing 1A [Gene - OMIM - HGNC]
RNF125:ring finger protein 125 [Gene - OMIM - HGNC]
RNF138:ring finger protein 138 [Gene - OMIM - HGNC]
SLC25A52:solute carrier family 25 member 52 [Gene - OMIM - HGNC]
SLC39A6:solute carrier family 39 member 6 [Gene - OMIM - HGNC]
TRAPPC8:trafficking protein particle complex subunit 8 [Gene - OMIM - HGNC]
TTR:transthyretin [Gene - OMIM - HGNC]
TPGS2:tubulin polyglutamylase complex subunit 2 [Gene - HGNC]
ZSCAN30:zinc finger and SCAN domain containing 30 [Gene - 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]

Variant type:

copy number loss

Cytogenetic location:

18q12.1-12.3

Genomic location:

Chr18: 26595964 - 38643072 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 18q12.1-12.3(chr18:26595964-38643072)x1

HGVS:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004230250	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Feb 13, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004230250

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Feb 13, 2023)

unknown

clinical testing

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

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

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, SCV004230250.1

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

Description

This loss involves several protein-coding genes. Smaller and partially overlapping deletions of this region have been described in individuals with variable features (Barone 2017, Brown 2018, Martinez-Granero 2021, Tenorio 2014). Haploinsufficiency of ASXL3 has been associated with Bainbridge-Ropers syndrome (BRPS; OMIM 615485, Rehm 2015). There are no similar copy number losses of this region in the general populations of the Database of Genomic Variants. Thus, based on gene content and current medical literature, this copy number variant (CNV) is classified as pathogenic. References: Barone et al., Am J Med Genet A. 2017 Jun;173(6):1649-1655. PMID: 28407444 Brown et al., Br J Dermatol. 2018 Jan;178(1):284-285. PMID: 28407214 Martinez-Granero et al., NPJ Genom Med. 2021 Mar 25;6(1):25. PMID: 33767182 Rehm et al., N Engl J Med. 2015 Jun 4;372(23):2235-42. PMID: 26014595 HGNC:29357 Tenorio et al., Hum Mutat. 2014 Dec;35(12):1436-41. PMID: 25196541

#	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: Feb 4, 2024

ClinVar

Relating variation to medicine