VCV001209857.2 - ClinVar

GRCh37/hg19 13q12.2-12.3(chr13:28669064-31367407)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.

Likely pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh37/hg19 13q12.2-12.3(chr13:28669064-31367407)x1

Variation ID: 1209857 Accession: VCV001209857.2

Type and length

copy number loss, 2,698,344 bp

Location

Cytogenetic: 13q12.2-12.3 13: 28669064-31367407 (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	Aug 27, 2021	Aug 27, 2021	Jan 11, 2021

HGVS

Nucleotide	Protein	Molecular consequence
NC_000013.10:g.(?_28669064)_(31367407_?)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.
ALOX5AP		-	-	GRCh38 GRCh37	10	56
FLT1		-	-	GRCh38 GRCh37	85	134
FLT3		-	-	GRCh38 GRCh37	212	254
HMGB1		-	-	GRCh38 GRCh37	20	64
KATNAL1		-	-	GRCh38 GRCh37	22	60
LINC00427	-	-	-	GRCh38 GRCh37	-	40
MTUS2		-	-	GRCh38 GRCh37	33	83
PAN3		-	-	GRCh38 GRCh37	33	78
POMP		-	-	GRCh38 GRCh37	109	149
SLC46A3		-	-	GRCh38 GRCh37	29	68

There are 3 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh37).

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.
13q12.2q12.3 deletion	Likely pathogenic (1)	no assertion criteria provided	Jan 11, 2021	RCV001579311.2

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 (Jan 11, 2021)	no assertion criteria provided Method: clinical testing	13q12.2q12.3 deletion Affected status: yes Allele origin: unknown	Medicover Genetics GmbH, Medicover Humangenetik Berlin-Lichtenberg MVZ Accession: SCV001805854.1 First in ClinVar: Aug 27, 2021 Last updated: Aug 27, 2021	Publications: PubMed (4) PubMed: 24664804‚ 31690835‚ 33023587‚ 25506442 Clinical Features: Abnormal heart morphology (present) , Patchy alopecia (present) , Delayed speech and language development (present) , Global developmental delay (present) , Motor delay (present) , … (more) Abnormal heart morphology (present) , Patchy alopecia (present) , Delayed speech and language development (present) , Global developmental delay (present) , Motor delay (present) , Short stature (present) , Microcephaly (present) , Abnormal facial shape (present) (less) Age: 0-9 years Sex: female

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 novel phenotype of 13q12.3 microdeletion characterized by epilepsy in an Asian child: a case report.	Wang M	BMC medical genomics	2020	PMID: 33023587
Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).	Riggs ER	Genetics in medicine : official journal of the American College of Medical Genetics	2020	PMID: 31690835
A new case of 13q12.2q13.1 microdeletion syndrome contributes to phenotype delineation.	Mandrile G	Case reports in genetics	2014	PMID: 25506442
A newly recognized 13q12.3 microdeletion syndrome characterized by intellectual disability, microcephaly, and eczema/atopic dermatitis encompassing the HMGB1 and KATNAL1 genes.	Bartholdi D	American journal of medical genetics. Part A	2014	PMID: 24664804

Text-mined citations for this variant ...

Record last updated Oct 15, 2023

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 13q12.2-12.3(chr13:28669064-31367407)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...