VCV001807710.1 - ClinVar

GRCh37/hg19 2q24.1(chr2:156996368-157372032)x1

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Likely pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh37/hg19 2q24.1(chr2:156996368-157372032)x1

Variation ID: 1807710 Accession: VCV001807710.1

Type and length

copy number loss, -

Location

Cytogenetic: 2q24.1 2: 156996368-157372032 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Dec 31, 2022	Dec 31, 2022	Jul 1, 2021

HGVS

Protein change

Other names

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
NR4A2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	153	189
GPD2		-	-	GRCh38 GRCh37	56	82

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Likely pathogenic (1)	criteria provided, single submitter	Jul 1, 2021	RCV002472516.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely pathogenic (Jul 01, 2021)	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019) Method: clinical testing	not provided Affected status: unknown Allele origin: unknown	Quest Diagnostics Nichols Institute San Juan Capistrano Accession: SCV002772384.1 First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022	Comment: The copy number loss of 2q24.1 involves a full copy of NR4A2 (OMIM 601828) and multiple exons of the 5-prime portion of GPD2 (OMIM 138430; … (more) The copy number loss of 2q24.1 involves a full copy of NR4A2 (OMIM 601828) and multiple exons of the 5-prime portion of GPD2 (OMIM 138430; NM_001083112.3). Although NR4A2 is not currently associated with an OMIM phenotype, de novo hemizygous deletions and heterozygous loss-of-function sequence variants of NR4A2 have been reported in individuals with mild to moderate intellectual disability, language impairment, and behavioral abnormalities. Other phenotypes may include epilepsy and early adult-onset dystonia (Singh, et al., Genetics in Medicine (2020) 22:1413?1417. PMID: 32366965; Wirth et al., Mov Disord. 2020 May;35(5):880-885. PMID: 31922365; Ramos, et al., Clin Case Rep. 2019 Jul 11;7(8):1582-1584. PMID:31428396; Levy et al., Clin Genet. 2018 Aug;94(2):264-268. PMID: 29770430; Reuter et al., Am J Med Genet A. 2017 Aug;173(8):2231-2234. PMID: 28544326; Leppa et al., Am J Hum Genet. 2016 Sep 1;99(3):540-554. PMID: 27569545). Additionally, heterozygous sequence variants of NR4A2 have been identified in individuals with other neuropsychiatric phenotypes, such as schizophrenia and Parkinson's disease (Chen et al. Am J Med Genet. 2001 Dec 8;105(8):753-7. PMID: 11803525; Buervenich et al., Am J Med Genet. 2000 Dec 4;96(6):808-13. PMID: 11121187; Le et al., Nat Genet. 2003 Jan;33(1):85-9. PMID: 12496759; Sleiman et al., Neurosci Lett. 2009 Jun 26;457(2):75-9. PMID: 19429166; Liu et al., Eur J Neurol. 2013 Mar;20(3):584-7. PMID: 22827504; Grimes et al., Mov Disord. 2006 Jul;21(7):906-9. PMID: 16532445). Further, heterozygous missense variants of GPD2 are associated with autosomal dominant susceptibility to type 2 diabetes mellitus (OMIM 125853) and a de novo intronic variant predicted to disrupt splicing was identified in an individual with autism spectrum disorder (Satterstrom et al., Cell. 2020 Feb 6;180(3):568-584.e23. PMID: 31981491). There are no overlapping copy number losses of this region in the general populations of the Database of Genomic Variants (DGV). Thus, this copy number variant (CNVs) is interpreted as likely pathogenic. (less)

Comment:

The copy number loss of 2q24.1 involves a full copy of NR4A2 (OMIM 601828) and multiple exons of the 5-prime portion of GPD2 (OMIM 138430; NM_001083112.3). Although NR4A2 is not currently associated with an OMIM phenotype, de novo hemizygous deletions and heterozygous loss-of-function sequence variants of NR4A2 have been reported in individuals with mild to moderate intellectual disability, language impairment, and behavioral abnormalities. Other phenotypes may include epilepsy and early adult-onset dystonia (Singh, et al., Genetics in Medicine (2020) 22:1413?1417. PMID: 32366965; Wirth et al., Mov Disord. 2020 May;35(5):880-885. PMID: 31922365; Ramos, et al., Clin Case Rep. 2019 Jul 11;7(8):1582-1584. PMID:31428396; Levy et al., Clin Genet. 2018 Aug;94(2):264-268. PMID: 29770430; Reuter et al., Am J Med Genet A. 2017 Aug;173(8):2231-2234. PMID: 28544326; Leppa et al., Am J Hum Genet. 2016 Sep 1;99(3):540-554. PMID: 27569545). Additionally, heterozygous sequence variants of NR4A2 have been identified in individuals with other neuropsychiatric phenotypes, such as schizophrenia and Parkinson's disease (Chen et al. Am J Med Genet. 2001 Dec 8;105(8):753-7. PMID: 11803525; Buervenich et al., Am J Med Genet. 2000 Dec 4;96(6):808-13. PMID: 11121187; Le et al., Nat Genet. 2003 Jan;33(1):85-9. PMID: 12496759; Sleiman et al., Neurosci Lett. 2009 Jun 26;457(2):75-9. PMID: 19429166; Liu et al., Eur J Neurol. 2013 Mar;20(3):584-7. PMID: 22827504; Grimes et al., Mov Disord. 2006 Jul;21(7):906-9. PMID: 16532445). Further, heterozygous missense variants of GPD2 are associated with autosomal dominant susceptibility to type 2 diabetes mellitus (OMIM 125853) and a de novo intronic variant predicted to disrupt splicing was identified in an individual with autism spectrum disorder (Satterstrom et al., Cell. 2020 Feb 6;180(3):568-584.e23. PMID: 31981491). There are no overlapping copy number losses of this region in the general populations of the Database of Genomic Variants (DGV). Thus, this copy number variant (CNVs) is interpreted as likely pathogenic.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Dec 31, 2022

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 2q24.1(chr2:156996368-157372032)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...