NM_001032221.6(STXBP1):c.863G>T (p.Trp288Leu) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 27, 2020
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:: RCV000686678.5

Allele description [Variation Report for NM_001032221.6(STXBP1):c.863G>T (p.Trp288Leu)]

NM_001032221.6(STXBP1):c.863G>T (p.Trp288Leu)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.11

Genomic location:

Preferred name:

NM_001032221.6(STXBP1):c.863G>T (p.Trp288Leu)

HGVS:

NC_000009.12:g.127668148G>T
NG_016623.1:g.60942G>T
NM_001032221.6:c.863G>TMANE SELECT
NM_001374306.2:c.854G>T
NM_001374307.2:c.821G>T
NM_001374308.2:c.821G>T
NM_001374309.2:c.821G>T
NM_001374310.2:c.821G>T
NM_001374311.2:c.821G>T
NM_001374312.2:c.821G>T
NM_001374313.2:c.863G>T
NM_001374314.1:c.863G>T
NM_001374315.2:c.795-1750G>T
NM_003165.6:c.863G>T
NP_001027392.1:p.Trp288Leu
NP_001361235.1:p.Trp285Leu
NP_001361236.1:p.Trp274Leu
NP_001361237.1:p.Trp274Leu
NP_001361238.1:p.Trp274Leu
NP_001361239.1:p.Trp274Leu
NP_001361240.1:p.Trp274Leu
NP_001361241.1:p.Trp274Leu
NP_001361242.1:p.Trp288Leu
NP_001361243.1:p.Trp288Leu
NP_003156.1:p.Trp288Leu
NC_000009.11:g.130430427G>T
NM_003165.3:c.863G>T

Protein change:

W274L

Links:

dbSNP: rs1564352031

NCBI 1000 Genomes Browser:

rs1564352031

Molecular consequence:

NM_001374315.2:c.795-1750G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001032221.6:c.863G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374306.2:c.854G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374307.2:c.821G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374308.2:c.821G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374309.2:c.821G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374310.2:c.821G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374311.2:c.821G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374312.2:c.821G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374313.2:c.863G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374314.1:c.863G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003165.6:c.863G>T - missense variant - [Sequence Ontology: SO:0001583]

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000814206	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 27, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000814206

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 27, 2020)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000814206.4

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C55"). This variant has not been reported in the literature in individuals with STXBP1-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces tryptophan with leucine at codon 288 of the STXBP1 protein (p.Trp288Leu). The tryptophan residue is highly conserved and there is a small physicochemical difference between tryptophan and leucine. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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

ClinVar

Relating variation to medicine