VCV000503586.2 - ClinVar

GRCh37/hg19 13q22.1-31.3(chr13:74459395-93481294)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

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh37/hg19 13q22.1-31.3(chr13:74459395-93481294)x1

Variation ID: 503586 Accession: VCV000503586.2

Type and length

copy number loss, 19,021,900 bp

Location

Cytogenetic: 13q22.1-31.3 13: 74459395-93481294 (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	Apr 2, 2018	Dec 11, 2022	Sep 26, 2017

HGVS

Nucleotide	Protein	Molecular consequence
NC_000013.10:g.(?_74459395)_(93481294_?)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

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.
EDNRB		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	92	384
GPC5		No evidence available	No evidence available	GRCh38 GRCh37	79	166
ACOD1		-	-	GRCh38 GRCh37	5	75
CLN5		-	-	GRCh38 GRCh37	598	798
COMMD6		-	-	GRCh38 GRCh37	2	70
FBXL3		-	-	GRCh38 GRCh37	24	96
KCTD12		-	-	GRCh38 GRCh37	20	90
KLF12		-	-	GRCh38 GRCh37	18	91
LINC00402	-	-	-	GRCh38 GRCh37	-	66
LMO7		-	-	GRCh38 GRCh37	133	210

There are 23 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	Sep 26, 2017	RCV000598789.2

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.
Pathogenic (Sep 26, 2017)	criteria provided, single submitter (Clinical Cytogenomics Laboratory Policy on CNV Interpretation) Method: clinical testing	See Cases Affected status: yes Allele origin: unknown	Clinical Genomics Laboratory, Laboratory for Precision Diagnostics, University of Washington Accession: SCV000709772.3 First in ClinVar: Apr 02, 2018 Last updated: Dec 11, 2022	Publications: PubMed (8) PubMed: 21892160‚ 25391829‚ 26360630‚ 19363806‚ 25118007‚ 26365529‚ 10528251‚ 19764031 Comment: Patient also had 4p15.32p15.31(16,834,640_17,818,885)x3 Number of individuals with the variant: 1 Clinical Features: Developmental delay (present) , Dysmorphic facial features (present) , Failure to thrive (present) , Clitoromegaly (present) Age: 0-9 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
13q31.1 microdeletion: A prenatal case report with macrocephaly and macroglossia.	Poreau B	European journal of medical genetics	2015	PMID: 26365529
Expanding the phenotype of feingold syndrome-2.	Grote LE	American journal of medical genetics. Part A	2015	PMID: 26360630
A fourth case of Feingold syndrome type 2: psychiatric presentation and management.	Ganjavi H	BMJ case reports	2014	PMID: 25391829
Familial co-segregation of Coffin-Lowry syndrome inherited from the mother and autosomal dominant Waardenburg type IV syndrome due to deletion of EDNRB inherited from the father.	Loupe J	European journal of medical genetics	2014	PMID: 25118007
Germline deletion of the miR-17∼92 cluster causes skeletal and growth defects in humans.	de Pontual L	Nature genetics	2011	PMID: 21892160
Clinical variability of Waardenburg-Shah syndrome in patients with proximal 13q deletion syndrome including the endothelin-B receptor locus.	Tüysüz B	American journal of medical genetics. Part A	2009	PMID: 19764031
Phenotype and 244k array-CGH characterization of chromosome 13q deletions: an update of the phenotypic map of 13q21.1-qter.	Kirchhoff M	American journal of medical genetics. Part A	2009	PMID: 19363806
Novel nonsense mutation of the endothelin-B receptor gene in a family with Waardenburg-Hirschsprung disease.	Syrris P	American journal of medical genetics	1999	PMID: 10528251

Text-mined citations for this variant ...

Record last updated Sep 01, 2024

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 13q22.1-31.3(chr13:74459395-93481294)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...