NM_001032221.6(STXBP1):c.313TTC[1] (p.Phe106del) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 9, 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:: RCV001302286.8

Allele description [Variation Report for NM_001032221.6(STXBP1):c.313TTC[1] (p.Phe106del)]

NM_001032221.6(STXBP1):c.313TTC[1] (p.Phe106del)

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.313TTC[1] (p.Phe106del)

HGVS:

NC_000009.12:g.127660096TTC[1]
NG_016623.1:g.52890TTC[1]
NM_001032221.6:c.313TTC[1]MANE SELECT
NM_001374306.2:c.313TTC[1]
NM_001374307.2:c.271TTC[1]
NM_001374308.2:c.271TTC[1]
NM_001374309.2:c.271TTC[1]
NM_001374310.2:c.271TTC[1]
NM_001374311.2:c.271TTC[1]
NM_001374312.2:c.271TTC[1]
NM_001374313.2:c.313TTC[1]
NM_001374314.1:c.313TTC[1]
NM_001374315.2:c.313TTC[1]
NM_003165.6:c.313TTC[1]
NP_001027392.1:p.Phe106del
NP_001361235.1:p.Phe106del
NP_001361236.1:p.Phe92del
NP_001361237.1:p.Phe92del
NP_001361238.1:p.Phe92del
NP_001361239.1:p.Phe92del
NP_001361240.1:p.Phe92del
NP_001361241.1:p.Phe92del
NP_001361242.1:p.Phe106del
NP_001361243.1:p.Phe106del
NP_001361244.1:p.Phe106del
NP_003156.1:p.Phe106del
NC_000009.11:g.130422373_130422375del
NC_000009.11:g.130422375TTC[1]

Protein change:

F106del

Links:

dbSNP: rs1840975645

NCBI 1000 Genomes Browser:

rs1840975645

Molecular consequence:

NM_001032221.6:c.313TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374306.2:c.313TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374307.2:c.271TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374308.2:c.271TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374309.2:c.271TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374310.2:c.271TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374311.2:c.271TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374312.2:c.271TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374313.2:c.313TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374314.1:c.313TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374315.2:c.313TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_003165.6:c.313TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV001491486	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 9, 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

SCV001491486

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 9, 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001491486.4

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

Description

Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. This variant, c.316_318del, results in the deletion of 1 amino acid(s) of the STXBP1 protein (p.Phe106del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with STXBP1-related conditions.

#	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: Sep 29, 2024

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