VCV001679109.3 - ClinVar

NCBI36/hg18 2p25.3(chr2:20341-2288046)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.

not provided

no classification provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NCBI36/hg18 2p25.3(chr2:20341-2288046)x1

Variation ID: 1679109 Accession: VCV001679109.3

Type and length

copy number loss, 2,267,706 bp

Location

Cytogenetic: 2p25.3 2: 20341-2288046 (NCBI36) [ 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	Apr 29, 2022	Jun 17, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NC_000002.10:g.(?_20341)_(2288046_?)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

Genes

No affected genes found.

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.
Chromosome 2p25.3 deletion syndrome Intellectual disability, autosomal dominant 39	not provided (1)	no classification provided	-	RCV002226422.3

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.
not provided (-)	no classification provided Method: phenotyping only	Chromosome 2p25.3 deletion syndrome Intellectual disability, autosomal dominant 39 Explanation for multiple conditions: Uncertain. The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. Affected status: yes Allele origin: de novo	GenomeConnect - Brain Gene Registry Accession: SCV002505376.3 First in ClinVar: Apr 29, 2022 Last updated: Jun 17, 2024	Comment: Variant interpreted as Pathogenic and reported on 04-18-2014 by Lab or GTR ID 320353. Assertions are reported exactly as they appear on the patient provided … (more) Variant interpreted as Pathogenic and reported on 04-18-2014 by Lab or GTR ID 320353. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator John Constantino MD PhD from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/. (less) Clinical Features: Abnormality of the amniotic fluid (present) , Decreased fetal movement (present) , Abnormal delivery (present) , Pregnancy history (present) , Obesity (present) , Abnormality of … (more) Abnormality of the amniotic fluid (present) , Decreased fetal movement (present) , Abnormal delivery (present) , Pregnancy history (present) , Obesity (present) , Abnormality of eye movement (present) , Myopia (present) , Cognitive impairment (present) , Abnormality of coordination (present) , Generalized hypotonia (present) , EEG abnormality (present) , Autistic behavior (present) , Motor stereotypies (present) , Anxiety (present) , Depression (present) , Compulsive behaviors (present) , Short attention span (present) , Hyperhidrosis (present) , Abnormal curvature of the vertebral column (present) , Abnormal muscle physiology (present) , Abnormality of the bladder (present) (less) Indication for testing: Diagnostic Age: 10-19 years Sex: female Testing laboratory: Diagnostic Medical Genetics, Mount Sinai Hospital, Sinai Health System Date variant was reported to submitter: 2014-04-18 Testing laboratory interpretation: Pathogenic

Comment:

Variant interpreted as Pathogenic and reported on 04-18-2014 by Lab or GTR ID 320353. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator John Constantino MD PhD from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.

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

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Jun 17, 2024

ClinVar Genomic variation as it relates to human health

NCBI36/hg18 2p25.3(chr2:20341-2288046)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...