VCV000565290.1 - ClinVar

Single allele

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

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

Single allele

Variation ID: 565290 Accession: VCV000565290.1

Type and length

Deletion, 9,844,949 bp

Location

Cytogenetic: 13q14.2-21.1 13: 48225451-58070399 (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	Oct 3, 2018	Oct 3, 2018

HGVS

Nucleotide	Protein	Molecular consequence
NC_000013.10:g.48225451_58070399del

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.
RB1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	3632	3793
ALG11		-	-	GRCh38 GRCh37	79	285
ARL11		-	-	GRCh38 GRCh37	17	86
ATP7B		-	-	GRCh38 GRCh37	2918	3062
CAB39L		-	-	GRCh38 GRCh37	22	87
CCDC70	-	-	-	GRCh38 GRCh37	-	91
CDADC1		-	-	GRCh38 GRCh37	19	81
CKAP2		-	-	GRCh38 GRCh37	52	116
CNMD		-	-	GRCh38 GRCh37	24	92
CYSLTR2		-	-	GRCh38 GRCh37	35	95

There are 42 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.
Intellectual disability	Likely pathogenic (1)	no assertion criteria provided	-	RCV000684766.2

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 (-)	no assertion criteria provided Method: research	Intellectual disability Affected status: yes Allele origin: de novo	Prof. Thelma's Laboratory, Department of Genetics, University of Delhi South Campus Accession: SCV000681417.1 First in ClinVar: Oct 03, 2018 Last updated: Oct 03, 2018	Comment: The de novo deletion at 13q14.2-q21.1 is observed in two siblings with mid Intellectual disability. Other clinical features observed include large face, Large ears, short … (more) The de novo deletion at 13q14.2-q21.1 is observed in two siblings with mid Intellectual disability. Other clinical features observed include large face, Large ears, short philtrum, congenital cataract, disproportionate body (LS>US), body skeletal development poor, thinness in rib cage, short stature, impaired cognition, IQ is low, unclear speech, hyperactivity, depression, joint hyperlaxicity/hypotonia, arachnodactyly (spider fingers), prognathism, teeth and gum problems. The deleted region encompasses functionally relevant genes and therefore the haploinsufficiency of the respective genes may contribute to disease phenotype. (less) Observation 1: Age: 30-39 years Sex: male Geographic origin: India Observation 2: Age: 30-39 years Sex: male Geographic origin: India

Comment:

The de novo deletion at 13q14.2-q21.1 is observed in two siblings with mid Intellectual disability. Other clinical features observed include large face, Large ears, short philtrum, congenital cataract, disproportionate body (LS>US), body skeletal development poor, thinness in rib cage, short stature, impaired cognition, IQ is low, unclear speech, hyperactivity, depression, joint hyperlaxicity/hypotonia, arachnodactyly (spider fingers), prognathism, teeth and gum problems. The deleted region encompasses functionally relevant genes and therefore the haploinsufficiency of the respective genes may contribute to disease phenotype.

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 Oct 15, 2023

ClinVar Genomic variation as it relates to human health

Single allele

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...