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GRCh37/hg19 2q23.3-24.1(chr2:154852961-159126250)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 1, 2021
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001827793.1

Allele description [Variation Report for GRCh37/hg19 2q23.3-24.1(chr2:154852961-159126250)x1]

GRCh37/hg19 2q23.3-24.1(chr2:154852961-159126250)x1

Genes:
  • ACVR1:activin A receptor type 1 [Gene - OMIM - HGNC]
  • ACVR1C:activin A receptor type 1C [Gene - OMIM - HGNC]
  • CCDC148:coiled-coil domain containing 148 [Gene - HGNC]
  • CYTIP:cytohesin 1 interacting protein [Gene - OMIM - HGNC]
  • ERMN:ermin [Gene - OMIM - HGNC]
  • GPD2:glycerol-3-phosphate dehydrogenase 2 [Gene - OMIM - HGNC]
  • NR4A2:nuclear receptor subfamily 4 group A member 2 [Gene - OMIM - HGNC]
  • GALNT13:polypeptide N-acetylgalactosaminyltransferase 13 [Gene - OMIM - HGNC]
  • GALNT5:polypeptide N-acetylgalactosaminyltransferase 5 [Gene - OMIM - HGNC]
  • KCNJ3:potassium inwardly rectifying channel subfamily J member 3 [Gene - OMIM - HGNC]
  • UPP2:uridine phosphorylase 2 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
2q23.3-24.1
Genomic location:
Chr2: 154852961 - 159126250 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 2q23.3-24.1(chr2:154852961-159126250)x1
HGVS:
NC_000002.11:g.(?_154852961)_(159126250_?)del

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002096343Quest Diagnostics Nichols Institute San Juan Capistrano
no assertion criteria provided
Pathogenic
(Apr 1, 2021) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002096343.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The copy number loss of 2q23.3q24.1 involves multiple protein-coding genes, including NR4A2 (OMIM 601828), and is expected to cause phenotypic and/or developmental abnormalities. De novo hemizygous deletions involving NR4A2 have been identified in multiple individuals with neurodevelopmental disorders, including language impairment, developmental delay, intellectual disability and/or autism spectrum disorder (Levy et al., Clin Genet. 2018 Aug;94(2):264-268. PMID: 29770430; Leppa et al., Am J Hum Genet. 2016 Sep 1;99(3):540-554. PMID: 27569545).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 14, 2023