GRCh37/hg19 2q21.3-23.3(chr2:136473383-152727396) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 15, 2021
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:: RCV001352659.1

Allele description [Variation Report for GRCh37/hg19 2q21.3-23.3(chr2:136473383-152727396)]

GRCh37/hg19 2q21.3-23.3(chr2:136473383-152727396)

Genes:

ARL5A:ARF like GTPase 5A [Gene - OMIM - HGNC]
CXCR4:C-X-C motif chemokine receptor 4 [Gene - OMIM - HGNC]
LRP1B:LDL receptor related protein 1B [Gene - OMIM - HGNC]
LYPD6:LY6/PLAUR domain containing 6 [Gene - OMIM - HGNC]
LYPD6B:LY6/PLAUR domain containing 6B [Gene - HGNC]
NMI:N-myc and STAT interactor [Gene - OMIM - HGNC]
R3HDM1:R3H domain containing 1 [Gene - OMIM - HGNC]
RBM43:RNA binding motif protein 43 [Gene - HGNC]
ARHGAP15:Rho GTPase activating protein 15 [Gene - OMIM - HGNC]
RND3:Rho family GTPase 3 [Gene - OMIM - HGNC]
TNFAIP6:TNF alpha induced protein 6 [Gene - OMIM - HGNC]
UBXN4:UBX domain protein 4 [Gene - OMIM - HGNC]
ACVR2A:activin A receptor type 2A [Gene - OMIM - HGNC]
DARS1:aspartyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
CACNB4:calcium voltage-gated channel auxiliary subunit beta 4 [Gene - OMIM - HGNC]
EPC2:enhancer of polycomb homolog 2 [Gene - OMIM - HGNC]
GTDC1:glycosyltransferase like domain containing 1 [Gene - OMIM - HGNC]
HNMT:histamine N-methyltransferase [Gene - OMIM - HGNC]
KYNU:kynureninase [Gene - OMIM - HGNC]
LCT:lactase [Gene - OMIM - HGNC]
MMADHC:metabolism of cobalamin associated D [Gene - OMIM - HGNC]
MBD5:methyl-CpG binding domain protein 5 [Gene - OMIM - HGNC]
MCM6:minichromosome maintenance complex component 6 [Gene - OMIM - HGNC]
NEB:nebulin [Gene - OMIM - HGNC]
NXPH2:neurexophilin 2 [Gene - OMIM - HGNC]
ORC4:origin recognition complex subunit 4 [Gene - OMIM - HGNC]
RIF1:replication timing regulatory factor 1 [Gene - OMIM - HGNC]
SPOPL:speckle type BTB/POZ protein like [Gene - HGNC]
THSD7B:thrombospondin type 1 domain containing 7B [Gene - HGNC]
ZEB2:zinc finger E-box binding homeobox 2 [Gene - OMIM - HGNC]

Variant type:

copy number gain

Cytogenetic location:

2q21.3-23.3

Genomic location:

Chr2: 136473383 - 152727396 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 2q21.3-23.3(chr2:136473383-152727396)

Condition(s)

Name:: Global developmental delay (DD)
Identifiers:: MedGen: C0557874; Human Phenotype Ontology: HP:0001263

Name:: Short stature
Identifiers:: MedGen: C0349588; Human Phenotype Ontology: HP:0004322

Name:: Strabismus
Identifiers:: MONDO: MONDO:0003432; MedGen: C0038379; Human Phenotype Ontology: HP:0000486

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Mouse T15 class I MHC gene (exon 5)
Mouse T15 class I MHC gene (exon 5)
gi|54230|emb|X16220.1|

Nucleotide
CPLX1 complexin 1 [Homo sapiens]
CPLX1 complexin 1 [Homo sapiens]
Gene ID:10815

Gene
Homo sapiens long intergenic non-protein coding RNA 239 (LINC00239), long non-co...
Homo sapiens long intergenic non-protein coding RNA 239 (LINC00239), long non-coding RNA
gi|223278361|ref|NR_026774.1|

Nucleotide
SAMN33343903 (1)
SRA
PREDICTED: Tursiops truncatus chromodomain helicase DNA binding protein 3 (CHD3)...
PREDICTED: Tursiops truncatus chromodomain helicase DNA binding protein 3 (CHD3), transcript variant X16, mRNA
gi|1835220574|ref|XM_033848655.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001547227	Medical Genetics Laboratory, CHRU Nancy	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Mar 15, 2021)	de novo	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

SCV001547227

Medical Genetics Laboratory, CHRU Nancy

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Mar 15, 2021)

de novo

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	de novo	yes	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 Medical Genetics Laboratory, CHRU Nancy, SCV001547227.1

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

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

Last Updated: Oct 8, 2024

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