GRCh37/hg19 4q13.2-13.3(chr4:69146217-75500577)x1 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 19, 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:: RCV003485422.1

Allele description [Variation Report for GRCh37/hg19 4q13.2-13.3(chr4:69146217-75500577)x1]

GRCh37/hg19 4q13.2-13.3(chr4:69146217-75500577)x1

Genes:

ADAMTS3:ADAM metallopeptidase with thrombospondin type 1 motif 3 [Gene - OMIM - HGNC]
CXCL1:C-X-C motif chemokine ligand 1 [Gene - OMIM - HGNC]
CXCL2:C-X-C motif chemokine ligand 2 [Gene - OMIM - HGNC]
CXCL3:C-X-C motif chemokine ligand 3 [Gene - OMIM - HGNC]
CXCL5:C-X-C motif chemokine ligand 5 [Gene - OMIM - HGNC]
CXCL6:C-X-C motif chemokine ligand 6 [Gene - OMIM - HGNC]
CXCL8:C-X-C motif chemokine ligand 8 [Gene - OMIM - HGNC]
GRSF1:G-rich RNA sequence binding factor 1 [Gene - OMIM - HGNC]
GC:GC vitamin D binding protein [Gene - OMIM - HGNC]
MOB1B:MOB kinase activator 1B [Gene - OMIM - HGNC]
RUFY3:RUN and FYVE domain containing 3 [Gene - OMIM - HGNC]
RASSF6:Ras association domain family member 6 [Gene - OMIM - HGNC]
UGT2A1:UDP glucuronosyltransferase family 2 member A1 complex locus [Gene - OMIM - HGNC]
UGT2A2:UDP glucuronosyltransferase family 2 member A2 [Gene - OMIM - HGNC]
UGT2A3:UDP glucuronosyltransferase family 2 member A3 [Gene - OMIM - HGNC]
UGT2B10:UDP glucuronosyltransferase family 2 member B10 [Gene - OMIM - HGNC]
UGT2B11:UDP glucuronosyltransferase family 2 member B11 [Gene - OMIM - HGNC]
UGT2B15:UDP glucuronosyltransferase family 2 member B15 [Gene - OMIM - HGNC]
UGT2B17:UDP glucuronosyltransferase family 2 member B17 [Gene - OMIM - HGNC]
UGT2B28:UDP glucuronosyltransferase family 2 member B28 [Gene - OMIM - HGNC]
UGT2B4:UDP glucuronosyltransferase family 2 member B4 [Gene - OMIM - HGNC]
UGT2B7:UDP glucuronosyltransferase family 2 member B7 [Gene - OMIM - HGNC]
UTP3:UTP3 small subunit processome component [Gene - OMIM - HGNC]
YTHDC1:YTH N6-methyladenosine RNA binding protein C1 [Gene - OMIM - HGNC]
AFM:afamin [Gene - OMIM - HGNC]
ALB:albumin [Gene - OMIM - HGNC]
AFP:alpha fetoprotein [Gene - OMIM - HGNC]
AMBN:ameloblastin [Gene - OMIM - HGNC]
AMTN:amelotin [Gene - OMIM - HGNC]
AREG:amphiregulin [Gene - OMIM - HGNC]
ANKRD17:ankyrin repeat domain 17 [Gene - OMIM - HGNC]
CABS1:calcium binding protein, spermatid associated 1 [Gene - OMIM - HGNC]
CSN1S1:casein alpha s1 [Gene - OMIM - HGNC]
CSN2:casein beta [Gene - OMIM - HGNC]
CSN3:casein kappa [Gene - OMIM - HGNC]
COX18:cytochrome c oxidase assembly factor COX18 [Gene - OMIM - HGNC]
DCK:deoxycytidine kinase [Gene - OMIM - HGNC]
ENAM:enamelin [Gene - OMIM - HGNC]
EREG:epiregulin [Gene - OMIM - HGNC]
EPGN:epithelial mitogen [Gene - OMIM - HGNC]
FDCSP:follicular dendritic cell secreted protein [Gene - OMIM - HGNC]
HTN1:histatin 1 [Gene - OMIM - HGNC]
HTN3:histatin 3 [Gene - OMIM - HGNC]
JCHAIN:joining chain of multimeric IgA and IgM [Gene - OMIM - HGNC]
MTHFD2L:methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2 like [Gene - OMIM - HGNC]
MUC7:mucin 7, secreted [Gene - OMIM - HGNC]
NPFFR2:neuropeptide FF receptor 2 [Gene - OMIM - HGNC]
ODAM:odontogenic, ameloblast associated [Gene - OMIM - HGNC]
OPRPN:opiorphin prepropeptide [Gene - OMIM - HGNC]
PF4V1:platelet factor 4 variant 1 [Gene - OMIM - HGNC]
PF4:platelet factor 4 [Gene - OMIM - HGNC]
PPBP:pro-platelet basic protein [Gene - OMIM - HGNC]
PRR27:proline rich 27 [Gene - HGNC]
SLC4A4:solute carrier family 4 member 4 [Gene - OMIM - HGNC]
STATH:statherin [Gene - OMIM - HGNC]
SMR3A:submaxillary gland androgen regulated protein 3A [Gene - OMIM - HGNC]
SMR3B:submaxillary gland androgen regulated protein 3B [Gene - OMIM - HGNC]
SULT1B1:sulfotransferase family 1B member 1 [Gene - OMIM - HGNC]
SULT1E1:sulfotransferase family 1E member 1 [Gene - OMIM - HGNC]
TMPRSS11E:transmembrane serine protease 11E [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

4q13.2-13.3

Genomic location:

Chr4: 69146217 - 75500577 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 4q13.2-13.3(chr4:69146217-75500577)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
SCV004231348	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Jan 19, 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

SCV004231348

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Jan 19, 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, SCV004231348.1

#	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 numerous protein-coding genes. Deletions of 4q13.3 have been identified in individuals with various phenotypes (Chopra 2021, Maldziene 2020). Heterozygous loss-of-function variants of ANKRD are associated with autosomal dominant Chopra-Amiel-Gordon syndrome (OMIM 619504). Additionally, heterozygous variants of ENAM are associated with autosomal dominant amelogenesis imperfecta type IB (OMIM 104500). Further, 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: Chopra et al., Am J Hum Genet. 2021 Jun 3;108(6):1138-1150. PMID: 33909992 Maldziene et al., BMC Med Genomics. 2020 Apr 16;13(1):63. PMID: 32299451

#	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