VCV000252975.2 - ClinVar

GRCh37/hg19 2q31.1-32.3(chr2:177315153-196375520)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.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh37/hg19 2q31.1-32.3(chr2:177315153-196375520)x1

Variation ID: 252975 Accession: VCV000252975.2

Type and length

copy number loss, 19,060,368 bp

Location

Cytogenetic: 2q31.1-32.3 2: 177315153-196375520 (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	Aug 13, 2016	Dec 24, 2022	Jun 7, 2016

HGVS

Nucleotide	Protein	Molecular consequence
NC_000002.11:g.(?_177315153)_(196375520_?)del

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.
COL3A1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh38 GRCh37	3041	3169
NCKAP1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	113	140
TTN		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	11956	31845
STAT1		No evidence available	No evidence available	GRCh38 GRCh37	621	664
AGPS		-	-	GRCh38 GRCh37	660	780
ANKAR		-	-	GRCh38 GRCh37	103	155
ASNSD1		-	-	GRCh38 GRCh37	37	69
C2orf88		-	-	GRCh38 GRCh37	-	108
CALCRL		-	-	GRCh38 GRCh37	1	50
CAVIN2		-	-	GRCh38 GRCh37	32	71

There are 54 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh37) and ClinGen Dosage Sensitivity Map.

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.
See cases	Pathogenic (1)	criteria provided, single submitter	Jun 7, 2016	RCV000239432.2

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.
Pathogenic (Jun 07, 2016)	criteria provided, single submitter (Clinical Cytogenomics Laboratory Policy on CNV Interpretation) Method: clinical testing	See Cases Affected status: yes Allele origin: unknown	Clinical Genomics Laboratory, Laboratory for Precision Diagnostics, University of Washington Accession: SCV000297784.2 First in ClinVar: Aug 13, 2016 Last updated: Dec 24, 2022	Publications: PubMed (5) PubMed: 17352388‚ 18413373‚ 19248183‚ 21637106‚ 24922459 Number of individuals with the variant: 1 Clinical Features: Intellectual disability (present) , Developmental delay (present) , Bilateral clubfoot (present) , Aphasia (present) , Decreased body weight (present) , Autism (present) Age: 0-9 years Sex: female Tissue: Peripheral Blood

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.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Survival is affected by mutation type and molecular mechanism in vascular Ehlers-Danlos syndrome (EDS type IV).	Pepin MG	Genetics in medicine : official journal of the American College of Medical Genetics	2014	PMID: 24922459
COL3A1 haploinsufficiency results in a variety of Ehlers-Danlos syndrome type IV with delayed onset of complications and longer life expectancy.	Leistritz DF	Genetics in medicine : official journal of the American College of Medical Genetics	2011	PMID: 21637106
2q31.2q32.3 deletion syndrome: report of an adult patient.	Prontera P	American journal of medical genetics. Part A	2009	PMID: 19248183
Detection of known and novel genomic rearrangements by array based comparative genomic hybridisation: deletion of ZNF533 and duplication of CHARGE syndrome genes.	Monfort S	Journal of medical genetics	2008	PMID: 18413373
Clinical and molecular characterization of a patient with a 2q31.2-32.3 deletion identified by array-CGH.	Mencarelli MA	American journal of medical genetics. Part A	2007	PMID: 17352388

Text-mined citations for this variant ...

Record last updated Oct 15, 2023

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 2q31.1-32.3(chr2:177315153-196375520)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...