VCV002427222.8 - ClinVar

NC_000023.10:g.(?_46466387)_(47489243_?)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_000023.10:g.(?_46466387)_(47489243_?)del

Variation ID: 2427222 Accession: VCV002427222.8

Type and length

Deletion, 1,022,857 bp

Location

Cytogenetic: Xp11.23 X: 46466387-47489243 (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	Aug 23, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NC_000023.10:g.(?_46466387)_(47489243_?)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.
RP2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	357	568
SYN1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	505	681
ZNF41		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	78	232
ARAF		-	-	GRCh38 GRCh37	36	187
CDK16		-	-	GRCh38 GRCh37	47	200
CFP		-	-	GRCh38 GRCh37	173	321
INE1		-	-	GRCh38 GRCh37	-	156
JADE3		-	-	GRCh38 GRCh37	32	190
LINC01560	-	-	-	GRCh38 GRCh37	1	155
NDUFB11		-	-	GRCh38 GRCh37	68	226

There are 7 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.
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders	Pathogenic (1)	criteria provided, single submitter	Aug 23, 2022	RCV003123056.4

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 (Aug 23, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003796289.3 First in ClinVar: Feb 13, 2023 Last updated: Jun 09, 2024	Publications: PubMed (2) PubMed: 14985377‚ 21441247 Comment: For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with SYN1-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 SYN1-related conditions. A gross deletion of the genomic region encompassing the full coding sequence of the SYN1 gene has been identified. Loss-of-function variants in SYN1 are known to be pathogenic (PMID: 14985377, 21441247). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. (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 SYN1-related conditions. A gross deletion of the genomic region encompassing the full coding sequence of the SYN1 gene has been identified. Loss-of-function variants in SYN1 are known to be pathogenic (PMID: 14985377, 21441247). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes.

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
SYN1 loss-of-function mutations in autism and partial epilepsy cause impaired synaptic function.	Fassio A	Human molecular genetics	2011	PMID: 21441247
Identification of a mutation in synapsin I, a synaptic vesicle protein, in a family with epilepsy.	Garcia CC	Journal of medical genetics	2004	PMID: 14985377

Text-mined citations for this variant ...

Record last updated Sep 30, 2024

ClinVar Genomic variation as it relates to human health

NC_000023.10:g.(?_46466387)_(47489243_?)del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...