NM_001032221.6(STXBP1):c.323_325+1del AND Early infantile epileptic encephalopathy with suppression bursts

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 24, 2022
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:: RCV001890606.4

Allele description

NM_001032221.6(STXBP1):c.323_325+1del

Gene:

STXBP1:syntaxin binding protein 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

9q34.11

Genomic location:

Preferred name:

NM_001032221.6(STXBP1):c.323_325+1del

HGVS:

NC_000009.12:g.127660102ACTG[1]
NG_016623.1:g.52896ACTG[1]
NM_001032221.6:c.323_325+1delMANE SELECT
NM_001374306.2:c.323_325+1del
NM_001374307.2:c.281_283+1del
NM_001374308.2:c.281_283+1del
NM_001374309.2:c.281_283+1del
NM_001374310.2:c.281_283+1del
NM_001374311.2:c.281_283+1del
NM_001374312.2:c.281_283+1del
NM_001374313.2:c.323_325+1del
NM_001374314.1:c.323_325+1del
NM_001374315.2:c.323_325+1del
NM_003165.6:c.323_325+1del
NC_000009.11:g.130422381ACTG[1]
NC_000009.11:g.130422381_130422384del

Links:

dbSNP: rs2131451053

NCBI 1000 Genomes Browser:

rs2131451053

Molecular consequence:

NM_001032221.6:c.323_325+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374306.2:c.323_325+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374307.2:c.281_283+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374308.2:c.281_283+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374309.2:c.281_283+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374310.2:c.281_283+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374311.2:c.281_283+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374312.2:c.281_283+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374313.2:c.323_325+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374314.1:c.323_325+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001374315.2:c.323_325+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_003165.6:c.323_325+1del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Early infantile epileptic encephalopathy with suppression bursts (EIEE)
Synonyms:: Early infantile epileptic encephalopathy; Ohtahara syndrome; Developmental and epileptic encephalopathy
Identifiers:: MONDO: MONDO:0100062; MedGen: C0393706; Orphanet: 1934; OMIM: PS308350

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002150947	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 24, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 20887364, 26384463, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002150947

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 24, 2022)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

STXBP1 mutations in early infantile epileptic encephalopathy with suppression-burst pattern.

Saitsu H, Kato M, Okada I, Orii KE, Higuchi T, Hoshino H, Kubota M, Arai H, Tagawa T, Kimura S, Sudo A, Miyama S, Takami Y, Watanabe T, Nishimura A, Nishiyama K, Miyake N, Wada T, Osaka H, Kondo N, Hayasaka K, Matsumoto N.

Epilepsia. 2010 Dec;51(12):2397-405. doi: 10.1111/j.1528-1167.2010.02728.x. Epub 2010 Sep 30.

PubMed [citation]

PMID:: 20887364

Loss-of-function mutations of STXBP1 in patients with epileptic encephalopathy.

Yamamoto T, Shimojima K, Yano T, Ueda Y, Takayama R, Ikeda H, Imai K.

Brain Dev. 2016 Mar;38(3):280-4. doi: 10.1016/j.braindev.2015.09.004. Epub 2015 Sep 16.

PubMed [citation]

PMID:: 26384463

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002150947.3

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant is also known as c.323_325+1del. This variant has not been reported in the literature in individuals affected with STXBP1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Asp108Leufs*11) in the STXBP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in STXBP1 are known to be pathogenic (PMID: 20887364, 26384463).

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

Last Updated: Feb 20, 2024

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