VCV000559575.1 - ClinVar

GRCh37/hg19 9p24.3-11.2(chr9:204193-44259464)x4

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 9p24.3-11.2(chr9:204193-44259464)x4

Variation ID: 559575 Accession: VCV000559575.1

Type and length

copy number gain, 44,055,272 bp

Location

Cytogenetic: 9p24.3-11.2 9: 204193-44259464 (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 17, 2018	Aug 17, 2018	Dec 19, 2016

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.
CDKN2A		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	1284	1437
DMRT1		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	82	305
ELAVL2		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	24	99
MTAP		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	166	253
PAX5		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	198	311
DMRT2		No evidence available	No evidence available	GRCh38 GRCh37	156	348
FREM1		No evidence available	No evidence available	GRCh38 GRCh37	1193	1361
KANK1		No evidence available	No evidence available	GRCh38 GRCh37	840	1185
SMARCA2		No evidence available	No evidence available	GRCh38 GRCh37	1226	1402
ACER2		-	-	GRCh38 GRCh37	24	121

There are 193 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.
Syndromic hydrocephalus due to diffuse villous hyperplasia of choroid plexus	Likely pathogenic (1)	criteria provided, single submitter	Dec 19, 2016	RCV000677299.1

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 (Dec 19, 2016)	criteria provided, single submitter (Furey et al. (Cold Spring Harb Mol Case Stud. 2018 Jun 12)) Method: clinical testing	Syndromic hydrocephalus due to diffuse villous hyperplasia of choroid plexus Bilateral hyperplasia of choroid (more...) Affected status: yes Allele origin: unknown	Kahle Lab, Yale University Accession: SCV000803381.1 First in ClinVar: Aug 17, 2018 Last updated: Aug 17, 2018 Comment: Microarray result: arr [hg19] 9p24.3-p11.2 (204,193-44,259,464)x4, 15q13.2-q13.3 (30,943,903-32,510,863)x1 (Triplication of chr 9p and deletion of 15q13.3)	Publications: PubMed (3) PubMed: 20433267‚ 16523225‚ 15007227 Comment: Apart from one report of monosomy 1p36, all other genetic reports of hydrocephalus in patients with diffuse villous hyperplasia of choroid plexus have identified gain … (more) Apart from one report of monosomy 1p36, all other genetic reports of hydrocephalus in patients with diffuse villous hyperplasia of choroid plexus have identified gain of chromosome 9p, making this chromosome aberration highly likely to be pathogenic and associated with the disease. Interestingly, gain of chromosome 9p has been well described as associated with several cases of choroid plexus papilloma and choroid plexus carcinoma. (less) Number of individuals with the variant: 1 Clinical Features: Hydrocephalus (present) , Sensorineural hearing loss (present) , Global developmental delay (present) , Facial dysmorphism (present) Secondary finding: no Testing laboratory: Yale Center for Genome Analysis Date variant was reported to submitter: 2016-11-01 Testing laboratory interpretation: not provided

Comment:

Apart from one report of monosomy 1p36, all other genetic reports of hydrocephalus in patients with diffuse villous hyperplasia of choroid plexus have identified gain of chromosome 9p, making this chromosome aberration highly likely to be pathogenic and associated with the disease. Interestingly, gain of chromosome 9p has been well described as associated with several cases of choroid plexus papilloma and choroid plexus carcinoma.

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
9p24 triplication in syndromic hydrocephalus with diffuse villous hyperplasia of the choroid plexus.	Furey C	Cold Spring Harbor molecular case studies	2018	PMID: 29895553
Diffuse villous hyperplasia of the choroid plexus and its surgical management.	Cataltepe O	Journal of neurosurgery. Pediatrics	2010	PMID: 20433267
Diffuse villous hyperplasia of choroid plexus.	Iplikcioglu AC	Acta neurochirurgica	2006	PMID: 16523225
Hydrocephalus due to diffuse villous hyperplasia of the choroid plexus. Case report and review of the literature.	Fujimoto Y	Pediatric neurosurgery	2004	PMID: 15007227

Text-mined citations for this variant ...

Record last updated Sep 01, 2024

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 9p24.3-11.2(chr9:204193-44259464)x4

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...