VCV000929370.1 - ClinVar

GRCh37/hg19 20p13(chr20:63244-813880)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 20p13(chr20:63244-813880)x1

Variation ID: 929370 Accession: VCV000929370.1

Type and length

copy number loss, 750,637 bp

Location

Cytogenetic: 20p13 20: 63244-813880 (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	Jun 26, 2020	Jun 26, 2020	Oct 14, 2019

HGVS

Nucleotide	Protein	Molecular consequence
NC_000020.10:g.(?_63244)_(813880_?)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.
CSNK2A1		Some evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	190	266
C20orf96	-	-	-	GRCh38 GRCh37	5	67
DEFB125	-	-	-	GRCh38 GRCh37	16	67
DEFB126		-	-	GRCh38 GRCh37	9	68
DEFB127	-	-	-	GRCh38 GRCh37	7	66
DEFB128	-	-	-	GRCh38 GRCh37	8	67
DEFB129	-	-	-	GRCh38 GRCh37	14	73
DEFB132	-	-	-	GRCh38 GRCh37	11	72
NRSN2		-	-	GRCh38 GRCh37	24	88
RBCK1		-	-	GRCh38 GRCh37	480	558

There are 8 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	Oct 14, 2019	RCV001194569.1

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.
Pathogenic (Oct 14, 2019)	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: SCV001364212.1 First in ClinVar: Jun 26, 2020 Last updated: Jun 26, 2020	Publications: PubMed (5) PubMed: 29619237‚ 29240241‚ 30655572‚ 27048600‚ 29383814 Number of individuals with the variant: 1 Clinical Features: Developmental delay (present) Age: 0-9 years Sex: male 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
Identification of de novo CSNK2A1 and CSNK2B variants in cases of global developmental delay with seizures.	Nakashima M	Journal of human genetics	2019	PMID: 30655572
Refining the clinical phenotype of Okur-Chung neurodevelopmental syndrome.	Akahira-Azuma M	Human genome variation	2018	PMID: 29619237
Extending the phenotype associated with the CSNK2A1-related Okur-Chung syndrome-A clinical study of 11 individuals.	Owen CI	American journal of medical genetics. Part A	2018	PMID: 29383814
Okur-Chung neurodevelopmental syndrome: Eight additional cases with implications on phenotype and genotype expansion.	Chiu ATG	Clinical genetics	2018	PMID: 29240241
De novo mutations in CSNK2A1 are associated with neurodevelopmental abnormalities and dysmorphic features.	Okur V	Human genetics	2016	PMID: 27048600

Text-mined citations for this variant ...

Record last updated Mar 26, 2023

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 20p13(chr20:63244-813880)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...