NC_000023.10:g.(?_47460607)_(47464667_?)del AND Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 23, 2018
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV004580283.2

Allele description [Variation Report for NC_000023.10:g.(?_47460607)_(47464667_?)del]

NC_000023.10:g.(?_47460607)_(47464667_?)del

Gene:: SYN1:synapsin I [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: Xp11.23
Genomic location:: ChrX: 47460607 - 47464667 (on Assembly GRCh37)
Preferred name:: NC_000023.10:g.(?_47460607)_(47464667_?)del
HGVS:: NC_000023.10:g.(?_47460607)_(47464667_?)del
This HGVS expression did not pass validation

Condition(s)

Name:: Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
Synonyms:: Epilepsy, X-linked, with variable learning disabilities and behavior disorders; X-linked epilepsy-learning disabilities-behavior disorders syndrome
Identifiers:: MONDO: MONDO:0010339; MedGen: C5774177; Orphanet: 85294; OMIM: 300491

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005064286	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Nov 23, 2018)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 14985377, 21441247, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005064286

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Nov 23, 2018)

unknown

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Identification of a mutation in synapsin I, a synaptic vesicle protein, in a family with epilepsy.

Garcia CC, Blair HJ, Seager M, Coulthard A, Tennant S, Buddles M, Curtis A, Goodship JA.

J Med Genet. 2004 Mar;41(3):183-6.

PubMed [citation]

PMID:: 14985377
PMCID:: PMC1735688

SYN1 loss-of-function mutations in autism and partial epilepsy cause impaired synaptic function.

Fassio A, Patry L, Congia S, Onofri F, Piton A, Gauthier J, Pozzi D, Messa M, Defranchi E, Fadda M, Corradi A, Baldelli P, Lapointe L, St-Onge J, Meloche C, Mottron L, Valtorta F, Khoa Nguyen D, Rouleau GA, Benfenati F, Cossette P.

Hum Mol Genet. 2011 Jun 15;20(12):2297-307. doi: 10.1093/hmg/ddr122. Epub 2011 Mar 25.

PubMed [citation]

PMID:: 21441247

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005064286.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Loss-of-function variants in SYN1 are known to be pathogenic (PMID: 14985377, 21441247). This variant has not been reported in the literature in individuals with SYN1-related conditions. This variant is a deletion of the genomic region encompassing exon 5 and part of exon 4 (c.639_774+3770del) of the SYN1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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