VCV000929388.1 - ClinVar

GRCh37/hg19 3q22.3-26.1(chr3:138145289-162275610)x3

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 3q22.3-26.1(chr3:138145289-162275610)x3

Variation ID: 929388 Accession: VCV000929388.1

Type and length

copy number gain, -

Location

Cytogenetic: 3q22.3-26.1 3: 138145289-162275610 (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	Jun 6, 2019

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.
FOXL2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	238	273
ATR		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	3529	3631
ZIC1		No evidence available	No evidence available	GRCh38 GRCh37	143	162
ZIC4		No evidence available	No evidence available	GRCh38 GRCh37	105	125
AADAC		-	-	GRCh38 GRCh37	-	50
AADACL2	-	-	-	GRCh38 GRCh38 GRCh37	10	41
AGTR1		-	-	GRCh38 GRCh37	129	148
ANKUB1	-	-	-	GRCh38 GRCh37	40	60
ARHGEF26		-	-	GRCh38 GRCh38 GRCh37	71	87
ARL14		-	-	GRCh38 GRCh37	1	38

There are 107 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	Jun 6, 2019	RCV001194586.1

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 (Jun 06, 2019)	criteria provided, single submitter (Clinical Cytogenomics Laboratory Policy on CNV Interpretation) Method: clinical testing	See Cases Affected status: yes Allele origin: paternal	Clinical Genomics Laboratory, Laboratory for Precision Diagnostics, University of Washington Accession: SCV001364232.1 First in ClinVar: Jun 26, 2020 Last updated: Jun 26, 2020	Publications: PubMed (4) PubMed: 8182724‚ 8291525‚ 15551338‚ 23322595 Comment: Father carries balanced inverted insertional translocation ins(17;3)(q23;q26.1q22.3); Patient also has 4q22.3(96,376,995_96,828,109)x1 Number of individuals with the variant: 1 Clinical Features: Developmental delay (present) , Hypotonia (present) , Dysmorphic facial features (present) , Insatiable appetite (present) Age: 20-29 years Sex: female 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
A boy with partial trisomy of chromosome 3q24-q28 from paternal balanced insertion and multiple congenital anomalies.	Zhu H	American journal of medical genetics. Part A	2013	PMID: 23322595
Novel case of dup(3q) syndrome due to a de novo interstitial duplication 3q24-q26.31 with minimal overlap to the dup(3q) critical region.	Meins M	American journal of medical genetics. Part A	2005	PMID: 15551338
Partial trisomy 3q causing mild Cornelia de Lange phenotype.	Holder SE	Journal of medical genetics	1994	PMID: 8182724
Partial duplication of 3q (q25.1-->q26.1) without the Brachmann-de Lange phenotype.	Lopez-Rangel E	American journal of medical genetics	1993	PMID: 8291525

Text-mined citations for this variant ...

Record last updated Apr 25, 2022

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 3q22.3-26.1(chr3:138145289-162275610)x3

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...