VCV000548966.2 - ClinVar

GRCh37/hg19 20p11.22-11.21(chr20:21680345-24383453)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 20p11.22-11.21(chr20:21680345-24383453)x1

Variation ID: 548966 Accession: VCV000548966.2

Type and length

copy number loss, 2,703,109 bp

Location

Cytogenetic: 20p11.22-11.21 20: 21680345-24383453 (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	Jul 21, 2018	Dec 11, 2022	Oct 5, 2017

HGVS

Nucleotide	Protein	Molecular consequence
NC_000020.10:g.(?_21680345)_(24383453_?)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.
CD93		-	-	GRCh38 GRCh37	61	83
CST1		-	-	GRCh38 GRCh37	25	48
CST11		-	-	GRCh38 GRCh37	-	35
CST2		-	-	GRCh38 GRCh37	26	50
CST3		-	-	GRCh38 GRCh37	21	64
CST4		-	-	GRCh38 GRCh37	25	47
CST5		-	-	GRCh38 GRCh37	18	40
CST8		-	-	GRCh38 GRCh37	12	36
CST9		-	-	GRCh38 GRCh37	16	39
CST9L		-	-	GRCh38 GRCh37	7	31

There are 9 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh37).

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	Likely pathogenic (1)	criteria provided, single submitter	Oct 5, 2017	RCV000663385.2

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.
Likely pathogenic (Oct 05, 2017)	criteria provided, single submitter (Clinical Cytogenomics Laboratory Policy on CNV Interpretation) Method: clinical testing	See Cases Affected status: yes Allele origin: de novo	Clinical Genomics Laboratory, Laboratory for Precision Diagnostics, University of Washington Accession: SCV000786671.2 First in ClinVar: Jul 21, 2018 Last updated: Dec 11, 2022	Publications: PubMed (7) PubMed: 28255477‚ 21204230‚ 15930903‚ 9268100‚ 23657910‚ 25765999‚ 12774041 Number of individuals with the variant: 1 Clinical Features: Heterotaxy (present) , Ventriculomegaly (present) , Ventricular septal defect (present) , Pyriform aperture stenosis (present) , Thrombocytopenia (present) , Hypoglycemia (present) , Biliary atresia (present) … (more) Heterotaxy (present) , Ventriculomegaly (present) , Ventricular septal defect (present) , Pyriform aperture stenosis (present) , Thrombocytopenia (present) , Hypoglycemia (present) , Biliary atresia (present) , Bicuspid aortic valve (present) , Atrial septal defect (present) , Coarctation of aorta (present) (less) Age: 0-9 years Sex: female Tissue: Umbilical cord 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
A Newborn with Panhypopituitarism and Seizures.	Kale T	Case reports in genetics	2017	PMID: 28255477
Heterozygous deletion of FOXA2 segregates with disease in a family with heterotaxy, panhypopituitarism, and biliary atresia.	Tsai EA	Human mutation	2015	PMID: 25765999
Delineation of a region responsible for panhypopituitarism in 20p11.2.	Dayem-Quere M	American journal of medical genetics. Part A	2013	PMID: 23657910
20p11 deletion in a female child with panhypopituitarism, cleft lip and palate, dysmorphic facial features, global developmental delay and seizure disorder.	Williams PG	American journal of medical genetics. Part A	2011	PMID: 21204230
A deletion of proximal 20p inherited from a normal mosaic carrier mother in a newborn with panhypopituitarism and craniofacial dysmorphism.	Garcia-Heras J	Clinical dysmorphology	2005	PMID: 15930903
Mutations in PAX1 may be associated with Klippel-Feil syndrome.	McGaughran JM	European journal of human genetics : EJHG	2003	PMID: 12774041
Intersitial deletion of 20p: new candidate region for Hirschsprung disease and autism?	Michaelis RC	American journal of medical genetics	1997	PMID: 9268100

Text-mined citations for this variant ...

Record last updated Dec 11, 2022

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 20p11.22-11.21(chr20:21680345-24383453)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...