VCV002423442.4 - ClinVar

NC_000004.11:g.(?_102001669)_(103806607_?)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.

(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

NC_000004.11:g.(?_102001669)_(103806607_?)del

Variation ID: 2423442 Accession: VCV002423442.4

Type and length

Deletion, 1,804,939 bp

Location

Cytogenetic: 4q24 4: 102001669-103806607 (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	Feb 13, 2023	Jun 9, 2024	Jun 13, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NC_000004.11:g.(?_102001669)_(103806607_?)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.
BANK1		-	-	GRCh38 GRCh37	69	95
CISD2		-	-	GRCh38 GRCh37	4	78
MANBA		-	-	GRCh38 GRCh37	710	789
NFKB1		-	-	GRCh38 GRCh37	695	738
PPP3CA		-	-	GRCh38 GRCh37	435	464
SLC39A8		-	-	GRCh38 GRCh37	116	214
SLC9B1		-	-	GRCh38 GRCh37	32	89
UBE2D3		-	-	GRCh38 GRCh37	-	18

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	Pathogenic (1)	criteria provided, single submitter	Jun 13, 2022	RCV003105379.5

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 (Jun 13, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003794408.3 First in ClinVar: Feb 13, 2023 Last updated: Jun 09, 2024	Publications: PubMed (4) PubMed: 28942967‚ 29432562‚ 30455226‚ 30951195 Comment: For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PPP3CA-related conditions. … (more) For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PPP3CA-related conditions. This variant is a gross deletion of the genomic region encompassing exon(s) 1-8 of the PPP3CA gene, which includes the initiator codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PPP3CA are known to be pathogenic (PMID: 28942967, 29432562, 30455226, 30951195). (less)

Comment:

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PPP3CA-related conditions. This variant is a gross deletion of the genomic region encompassing exon(s) 1-8 of the PPP3CA gene, which includes the initiator codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PPP3CA are known to be pathogenic (PMID: 28942967, 29432562, 30455226, 30951195).

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
The Epilepsy Genetics Initiative: Systematic reanalysis of diagnostic exomes increases yield.	Epilepsy Genetics Initiative	Epilepsia	2019	PMID: 30951195
Early-onset infant epileptic encephalopathy associated with a de novo PPP3CA gene mutation.	Qian Y	Cold Spring Harbor molecular case studies	2018	PMID: 30455226
Loss-of-function and gain-of-function mutations in PPP3CA cause two distinct disorders.	Mizuguchi T	Human molecular genetics	2018	PMID: 29432562
De Novo Mutations in PPP3CA Cause Severe Neurodevelopmental Disease with Seizures.	Myers CT	American journal of human genetics	2017	PMID: 28942967

Text-mined citations for this variant ...

Record last updated Sep 30, 2024

ClinVar Genomic variation as it relates to human health

NC_000004.11:g.(?_102001669)_(103806607_?)del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...