VCV000006517.2 - ClinVar

NG_042866.2:g.(460061_462693)_(532018_533659)del

Germline

Classification

no assertion criteria provided. Learn more about how ClinVar calculates review status.

risk factor

This classification is based on the single submission received

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.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NG_042866.2:g.(460061_462693)_(532018_533659)del

Variation ID: 6517 Accession: VCV000006517.2

Type and length

Deletion, -

Location

Cytogenetic: 11q13.3-q13.4 -

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 4, 2013	Oct 8, 2024	Jun 1, 2010

HGVS

Nucleotide	Protein	Molecular consequence
NC_000011.8:g.(70148322_70149963)_(70219288_70221920)del
NG_042866.2:g.(460061_462693)_(532018_533659)del

Protein change

Other names

69-KB DEL

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

OMIM: 603290.0002

Comment on variant

NCBI staff provided HGVS expressions for OMIM allelic variant 603290.0002 based on the supplementary materials to the paper by Berkel et al., 2010 (PubMed). The legend to figure S1 stated: "Genomic sequence position is according to the UCSC Human Genome Browser assembly March 2006...The breakpoints of SK0217-003 were further narrowed down by qPCR and reside within 1642 bp (position 70,149,963 - 70,148,322) at the centromeric and within 2633 bp (position 70,221,920 – 70,219,288) at the telomeric end resulting in a deletion of about 69 kb"

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.
SHANK2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	424	438

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.
Autism, susceptibility to, 17	risk factor (1)	no assertion criteria provided	Jun 1, 2010	RCV000006890.3

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.
risk factor (Jun 01, 2010) C Contributing to aggregate classification	no assertion criteria provided Method: literature only	AUTISM, SUSCEPTIBILITY TO, 17 Affected status: not provided Allele origin: germline	OMIM Accession: SCV000027086.2 First in ClinVar: Apr 04, 2013 Last updated: Oct 08, 2024	Publications: PubMed (1) PubMed: 20473310 Comment on evidence: In a patient with autism (613436), Berkel et al. (2010) identified a de novo heterozygous 69-kb deletion in the SHANK2 gene, resulting in the deletion … (more) In a patient with autism (613436), Berkel et al. (2010) identified a de novo heterozygous 69-kb deletion in the SHANK2 gene, resulting in the deletion of exon 6 and 7 followed by a frameshift. The patient also had mental retardation, with an IQ of 67. (less)

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
Mutations in the SHANK2 synaptic scaffolding gene in autism spectrum disorder and mental retardation.	Berkel S	Nature genetics	2010	PMID: 20473310

Text-mined citations for this variant ...

Record last updated Oct 08, 2024

ClinVar Genomic variation as it relates to human health

NG_042866.2:g.(460061_462693)_(532018_533659)del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...