GRCh37/hg19 18p11.32-11.22(chr18:136227-8513569)x1 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 10, 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:: RCV003483329.1

Allele description [Variation Report for GRCh37/hg19 18p11.32-11.22(chr18:136227-8513569)x1]

GRCh37/hg19 18p11.32-11.22(chr18:136227-8513569)x1

Genes:

AKAIN1:A-kinase anchor inhibitor 1 [Gene - OMIM - HGNC]
DLGAP1:DLG associated protein 1 [Gene - OMIM - HGNC]
DLGAP1-AS2:DLGAP1 antisense RNA 2 [Gene - HGNC]
L3MBTL4:L3MBTL histone methyl-lysine binding protein 4 [Gene - OMIM - HGNC]
NDC80:NDC80 kinetochore complex component [Gene - OMIM - HGNC]
ARHGAP28:Rho GTPase activating protein 28 [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]
YES1:YES proto-oncogene 1, Src family tyrosine kinase [Gene - OMIM - HGNC]
ADCYAP1:adenylate cyclase activating polypeptide 1 [Gene - OMIM - HGNC]
CETN1:centrin 1 [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]
LAMA1:laminin subunit alpha 1 [Gene - OMIM - HGNC]
LRRC30:leucine rich repeat containing 30 [Gene - HGNC]
LPIN2:lipin 2 [Gene - OMIM - HGNC]
METTL4:methyltransferase 4, N6-adenosine [Gene - OMIM - HGNC]
MYOM1:myomesin 1 [Gene - OMIM - HGNC]
MYL12A:myosin light chain 12A [Gene - HGNC]
MYL12B:myosin light chain 12B [Gene - OMIM - HGNC]
PTPRM:protein tyrosine phosphatase receptor type M [Gene - OMIM - HGNC]
SMCHD1:structural maintenance of chromosomes flexible hinge domain containing 1 [Gene - OMIM - HGNC]
TYMS:thymidylate synthetase [Gene - OMIM - HGNC]
TMEM200C:transmembrane protein 200C [Gene - HGNC]
USP14:ubiquitin specific peptidase 14 [Gene - OMIM - HGNC]
ZBTB14:zinc finger and BTB domain containing 14 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

18p11.32-11.22

Genomic location:

Chr18: 136227 - 8513569 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 18p11.32-11.22(chr18:136227-8513569)x1

HGVS:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004230244	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Dec 10, 2022)	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

SCV004230244

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Dec 10, 2022)

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, SCV004230244.1

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

Description

The copy number loss of 18p11.32p11.22 involves numerous protein-coding genes. Haploinsufficiency of TGIF1 has been associated with autosomal dominant holoprosencephaly-4 (HPE4; OMIM 142946, Rehm 2015). In addition, there have been reports of patients that have copy number losses that involve 18p11.32p11.31 with variable phenotypes (Chaves 2019, Verrotti 2015). Heterozygous loss-of-function variants of SMCHD1 are associated with facioscapulohumeral muscular dystrophy 2 (OMIM 158901, Lemmers 2015, Balog 2018). There are no similar copy number losses of this region in the general populations of the Database of Genomic Variants. Thus, based on current medical literature and gene content, this copy number variant (CNV) is classified as pathogenic. References: Balog et al., J Med Genet. 2018 Jul;55(7):469-478. PMID: 29563141 Chaves et al., Sci Rep. 2019 Nov 28;9(1):17776. PMID: 31780800, Han et al., Nature. 2013 Nov 7;503(7474):72-7. PMID: 24153177, Lemmers et al., Hum Mutat. 2015 Jul;36(7):679-83. PMID: 25820463, Rehm et al., N Engl J Med. 2015 Jun 4;372(23):2235-42. PMID: 26014595 HGNC:11776, Verrotti et al., Cytogenet Genome Res. 2015;146(2):115-9. PMID: 26278570_x000D__x000D_

#	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

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