VCV002580893.1 - ClinVar

GRCh37/hg19 3p26.2-25.3(chr3:3691505-9917651)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

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh37/hg19 3p26.2-25.3(chr3:3691505-9917651)x1

Variation ID: 2580893 Accession: VCV002580893.1

Type and length

copy number loss, -

Location

Cytogenetic: 3p26.2-25.3 3: 3669542-9937745 (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	Sep 30, 2023	Sep 30, 2023	Sep 27, 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.
BRPF1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	380	442
SETD5		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	1105	1175
ITPR1		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	1760	1967
ARL8B		-	-	GRCh38 GRCh37	3	93
ARPC4		-	-	GRCh38 GRCh37	1	71
ARPC4-TTLL3	-	-	-	GRCh38 GRCh37	-	175
BHLHE40		-	-	GRCh38 GRCh37	30	120
CAMK1		-	-	GRCh38 GRCh37	-	92
CAV3		-	-	GRCh38 GRCh37	102	452
CIDEC		-	-	GRCh38 GRCh37	50	116

There are 21 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.
3p- syndrome	Pathogenic (1)	no assertion criteria provided	Sep 27, 2023	RCV003330127.1

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 (Sep 27, 2023)	no assertion criteria provided Method: clinical testing	3p- syndrome (Autosomal dominant inheritance) Affected status: yes Allele origin: de novo	Medicover Genetics GmbH, Medicover Humangenetik Berlin-Lichtenberg MVZ Accession: SCV004036167.1 First in ClinVar: Sep 30, 2023 Last updated: Sep 30, 2023	Publications: PubMed (3) PubMed: 33643973‚ 11977162‚ 19760623 Clinical Features: Hypotonia (present) , Strabismus (present) , Abnormality of the face (present) , Glandular hypospadias (present) , Low-set ears (present) , Retrognathia (present) , Abnormality of … (more) Hypotonia (present) , Strabismus (present) , Abnormality of the face (present) , Glandular hypospadias (present) , Low-set ears (present) , Retrognathia (present) , Abnormality of the nose (present) , Frontal bossing (present) , Synophrys (present) , Abnormal digit morphology (present) (less) Zygosity: Single Heterozygote Age: 0-9 years Sex: male

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
Case Report: A Case Report and Literature Review of 3p Deletion Syndrome.	Fu J	Frontiers in pediatrics	2021	PMID: 33643973
Microarray based analysis of 3p25-p26 deletions (3p- syndrome).	Shuib S	American journal of medical genetics. Part A	2009	PMID: 19760623
Molecular cytogenetic characterization of a subtle interstitial del(3)(p25.3p26.2) in a patient with deletion 3p syndrome.	Cargile CB	American journal of medical genetics	2002	PMID: 11977162

Text-mined citations for this variant ...

Record last updated Dec 02, 2023

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 3p26.2-25.3(chr3:3691505-9917651)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...