VCV002579288.1 - ClinVar

GRCh38/hg38 20q13.33(chr20:62632017-63794804)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

GRCh38/hg38 20q13.33(chr20:62632017-63794804)x1

Variation ID: 2579288 Accession: VCV002579288.1

Type and length

copy number loss, 1,162,788 bp

Location

Cytogenetic: 20q13.33 20: 62632017-63794804 (GRCh38) [ 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	Sep 16, 2023	Sep 16, 2023	Aug 24, 2023

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.
KCNQ2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh38 GRCh37	2167	2299
EEF1A2		No evidence available	No evidence available	GRCh38 GRCh37	511	672
ARFGAP1		-	-	GRCh38 GRCh37	47	119
ARFRP1		-	-	GRCh38 GRCh37	20	76
BHLHE23		-	-	GRCh38 GRCh37	9	61
BIRC7		-	-	GRCh38 GRCh37	31	98
CHRNA4		-	-	GRCh38 GRCh37	892	1162
COL20A1		-	-	GRCh38 GRCh37	156	228
COL9A3		-	-	GRCh38 GRCh37	1278	1488
DIDO1		-	-	GRCh38 GRCh37	124	175

There are 157 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh38).

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.
Neurodevelopmental disorder	Pathogenic (1)	criteria provided, single submitter	Aug 24, 2023	RCV003327727.2

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 (Aug 24, 2023)	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019) Method: research	Neurodevelopmental disorder (Autosomal dominant inheritance) Affected status: yes Allele origin: de novo	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard Accession: SCV004034255.1 First in ClinVar: Sep 16, 2023 Last updated: Sep 16, 2023	Publications: PubMed (2) PubMed: 31690835‚ 24098143 Comment: A confirmed de novo heterozygous deletion of 20q13.3 encompassing 33 genes (https://genescout.omim.org/) was identified by exome sequencing and confirmed by qPCR in one individual with … (more) A confirmed de novo heterozygous deletion of 20q13.3 encompassing 33 genes (https://genescout.omim.org/) was identified by exome sequencing and confirmed by qPCR in one individual with chromosome 20q13.3 microdeletion syndrome ([GRCh38] chr20:62632017_63794804x1)(PMID: 24098143). These breakpoints have been estimated by qPCR and therefore may not reflect the true breakpoints. The patient phenotype is nonspecific, but is consistent with cases described in the literature and/or published databases with overlapping variants. There is complete overlap with the KCNQ2 gene which is known to be haploinsufficient and has been assessed by the ClinGen Dosage Sensitivity Working Group (https://search.clinicalgenome.org/kb/gene-dosage). In summary, the 20q13.3 deletion meets criteria to be classified as pathogenic. The ACMG/ClinGen evidence codes and points used in this curation are as follows: 1: 0 points, 2: 1.00 points, 3: 0.45 points, 4-5: 0.15 points; Total: 1.6 points; Riggs 2020 (PMID: 31690835) (less)

Comment:

A confirmed de novo heterozygous deletion of 20q13.3 encompassing 33 genes (https://genescout.omim.org/) was identified by exome sequencing and confirmed by qPCR in one individual with chromosome 20q13.3 microdeletion syndrome ([GRCh38] chr20:62632017_63794804x1)(PMID: 24098143). These breakpoints have been estimated by qPCR and therefore may not reflect the true breakpoints. The patient phenotype is nonspecific, but is consistent with cases described in the literature and/or published databases with overlapping variants. There is complete overlap with the KCNQ2 gene which is known to be haploinsufficient and has been assessed by the ClinGen Dosage Sensitivity Working Group (https://search.clinicalgenome.org/kb/gene-dosage). In summary, the 20q13.3 deletion meets criteria to be classified as pathogenic. The ACMG/ClinGen evidence codes and points used in this curation are as follows: 1: 0 points, 2: 1.00 points, 3: 0.45 points, 4-5: 0.15 points; Total: 1.6 points; Riggs 2020 (PMID: 31690835)

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

Title	Author	Journal	Year	Link
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	Genetics in medicine : official journal of the American College of Medical Genetics	2020	PMID: 31690835
Both rare and de novo copy number variants are prevalent in agenesis of the corpus callosum but not in cerebellar hypoplasia or polymicrogyria.	Sajan SA	PLoS genetics	2013	PMID: 24098143

Text-mined citations for this variant ...

Record last updated Sep 01, 2024

ClinVar Genomic variation as it relates to human health

GRCh38/hg38 20q13.33(chr20:62632017-63794804)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...