VCV001373812.4 - ClinVar

NC_000020.10:g.(?_389402)_(746418_?)del

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.

(2)

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

NC_000020.10:g.(?_389402)_(746418_?)del

Variation ID: 1373812 Accession: VCV001373812.4

Type and length

Deletion, 357,017 bp

Location

Cytogenetic: 20p13 20: 389402-746418 (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	Mar 28, 2022	Nov 11, 2023	Jan 5, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NC_000020.10:g.(?_389402)_(746418_?)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.
CSNK2A1		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	188	264
RBCK1		-	-	GRCh38 GRCh37	480	558
SCRT2	-	-	-	GRCh38 GRCh37	25	94
SLC52A3		-	-	GRCh38 GRCh37	443	507
SRXN1		-	-	GRCh38 GRCh37	5	79
TBC1D20		-	-	GRCh38 GRCh37	129	225
TCF15		-	-	GRCh38 GRCh37	18	90

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.
not provided	no classifications from unflagged records (1)	no classifications from unflagged records	-	RCV001877503.7
Brown-Vialetto-van Laere syndrome 1	Pathogenic (1)	criteria provided, single submitter	Jan 5, 2022	RCV001900457.5

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 (Jan 05, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Brown-Vialetto-van Laere syndrome 1 Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV002243830.3 First in ClinVar: Mar 28, 2022 Last updated: Nov 11, 2023	Publications: PubMed (3) PubMed: 20206331‚ 22824638‚ 25462087 Comment: A gross deletion of the genomic region encompassing the full coding sequence of the SLC52A3 gene has been identified. Loss-of-function variants in SLC52A3 are known … (more) A gross deletion of the genomic region encompassing the full coding sequence of the SLC52A3 gene has been identified. Loss-of-function variants in SLC52A3 are known to be pathogenic (PMID: 20206331, 22824638, 25462087). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with SLC52A3-related conditions. For these reasons, this variant has been classified as Pathogenic. (less)
Pathogenic (Jul 06, 2022)	Flagged submission flagged submission (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV002140163 appears to (...more) Source: NCBI	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV002140163.3 First in ClinVar: Mar 28, 2022 Last updated: Nov 11, 2023	Publications: PubMed (1) PubMed: 24239381 Comment: A gross deletion of the genomic region encompassing the full coding sequence of the TBC1D20 gene has been identified. Loss-of-function variants in TBC1D20 are known … (more) A gross deletion of the genomic region encompassing the full coding sequence of the TBC1D20 gene has been identified. Loss-of-function variants in TBC1D20 are known to be pathogenic (PMID: 24239381). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with TBC1D20-related conditions. For these reasons, this variant has been classified as Pathogenic. (less)
Flagged submissions do not contribute to the aggregate classification or review status for the variant. Learn more

Comment:

A gross deletion of the genomic region encompassing the full coding sequence of the SLC52A3 gene has been identified. Loss-of-function variants in SLC52A3 are known to be pathogenic (PMID: 20206331, 22824638, 25462087). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with SLC52A3-related conditions. For these reasons, this variant has been classified as Pathogenic.

Comment:

A gross deletion of the genomic region encompassing the full coding sequence of the TBC1D20 gene has been identified. Loss-of-function variants in TBC1D20 are known to be pathogenic (PMID: 24239381). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with TBC1D20-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Title	Author	Journal	Year	Link
Adult onset Brown-Vialetto-Van Laere syndrome with opsoclonus and a novel heterozygous mutation: a case report.	Cosgrove J	Clinical neurology and neurosurgery	2015	PMID: 25462087
Loss-of-function mutations in TBC1D20 cause cataracts and male infertility in blind sterile mice and Warburg micro syndrome in humans.	Liegel RP	American journal of human genetics	2013	PMID: 24239381
Brown-Vialetto-van Laere and Fazio-Londe overlap syndromes: a clinical, biochemical and genetic study.	Ciccolella M	Neuromuscular disorders : NMD	2012	PMID: 22824638
Brown-Vialetto-Van Laere syndrome, a ponto-bulbar palsy with deafness, is caused by mutations in c20orf54.	Green P	American journal of human genetics	2010	PMID: 20206331

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NC_000020.10:g.(?_389402)_(746418_?)del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...