NM_001032221.6(STXBP1):c.1672delinsAACGGAAAGTGGGAGGTGGGAGG (p.Gln558fs) AND Developmental and epileptic encephalopathy, 4

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 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:: RCV002255243.1

Allele description [Variation Report for NM_001032221.6(STXBP1):c.1672delinsAACGGAAAGTGGGAGGTGGGAGG (p.Gln558fs)]

NM_001032221.6(STXBP1):c.1672delinsAACGGAAAGTGGGAGGTGGGAGG (p.Gln558fs)

Gene:

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

Variant type:

Indel

Cytogenetic location:

9q34.11

Genomic location:

Preferred name:

NM_001032221.6(STXBP1):c.1672delinsAACGGAAAGTGGGAGGTGGGAGG (p.Gln558fs)

HGVS:

NC_000009.12:g.127682530delinsAACGGAAAGTGGGAGGTGGGAGG
NG_016623.1:g.75324delinsAACGGAAAGTGGGAGGTGGGAGG
NM_001032221.6:c.1672delinsAACGGAAAGTGGGAGGTGGGAGGMANE SELECT
NM_001374306.2:c.1663delinsAACGGAAAGTGGGAGGTGGGAGG
NM_001374307.2:c.1630delinsAACGGAAAGTGGGAGGTGGGAGG
NM_001374308.2:c.1630delinsAACGGAAAGTGGGAGGTGGGAGG
NM_001374309.2:c.1630delinsAACGGAAAGTGGGAGGTGGGAGG
NM_001374310.2:c.1630delinsAACGGAAAGTGGGAGGTGGGAGG
NM_001374311.2:c.1630delinsAACGGAAAGTGGGAGGTGGGAGG
NM_001374312.2:c.1630delinsAACGGAAAGTGGGAGGTGGGAGG
NM_001374313.2:c.1672delinsAACGGAAAGTGGGAGGTGGGAGG
NM_001374314.1:c.1672delinsAACGGAAAGTGGGAGGTGGGAGG
NM_001374315.2:c.1564delinsAACGGAAAGTGGGAGGTGGGAGG
NM_003165.6:c.1672delinsAACGGAAAGTGGGAGGTGGGAGG
NP_001027392.1:p.Gln558fs
NP_001361235.1:p.Gln555fs
NP_001361236.1:p.Gln544fs
NP_001361237.1:p.Gln544fs
NP_001361238.1:p.Gln544fs
NP_001361239.1:p.Gln544fs
NP_001361240.1:p.Gln544fs
NP_001361241.1:p.Gln544fs
NP_001361242.1:p.Gln558fs
NP_001361243.1:p.Gln558fs
NP_001361244.1:p.Gln522fs
NP_003156.1:p.Gln558fs
NC_000009.11:g.130444809delinsAACGGAAAGTGGGAGGTGGGAGG
NM_003165.6:c.1672delCinsAACGGAAAGTGGGAGGTGGGAGG

Protein change:

Q522fs

Links:

dbSNP: rs2131536257

NCBI 1000 Genomes Browser:

rs2131536257

Molecular consequence:

NM_001032221.6:c.1672delinsAACGGAAAGTGGGAGGTGGGAGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374306.2:c.1663delinsAACGGAAAGTGGGAGGTGGGAGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374307.2:c.1630delinsAACGGAAAGTGGGAGGTGGGAGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374308.2:c.1630delinsAACGGAAAGTGGGAGGTGGGAGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374309.2:c.1630delinsAACGGAAAGTGGGAGGTGGGAGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374310.2:c.1630delinsAACGGAAAGTGGGAGGTGGGAGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374311.2:c.1630delinsAACGGAAAGTGGGAGGTGGGAGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374312.2:c.1630delinsAACGGAAAGTGGGAGGTGGGAGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374313.2:c.1672delinsAACGGAAAGTGGGAGGTGGGAGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374314.1:c.1672delinsAACGGAAAGTGGGAGGTGGGAGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374315.2:c.1564delinsAACGGAAAGTGGGAGGTGGGAGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003165.6:c.1672delinsAACGGAAAGTGGGAGGTGGGAGG - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Developmental and epileptic encephalopathy, 4 (DEE4)
Synonyms:: Early infantile epileptic encephalopathy 4; STXBP1-Related Epileptic Encephalopathy
Identifiers:: MONDO: MONDO:0012812; MedGen: C2677326; Orphanet: 1934; Orphanet: 33069; OMIM: 612164

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002526713	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 24, 2022)	de novo	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

SCV002526713

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(May 24, 2022)

de novo

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	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Institute of Human Genetics, University of Leipzig Medical Center, SCV002526713.1

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

Description

This variant was identified as de novo (maternity and paternity confirmed)._x000D_ Criteria applied: PVS1, PS2, PM2_SUP

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

Last Updated: Dec 24, 2023

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