NM_001032221.6(STXBP1):c.1689G>A (p.Trp563Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 16, 2021
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:: RCV000427600.3

Allele description [Variation Report for NM_001032221.6(STXBP1):c.1689G>A (p.Trp563Ter)]

NM_001032221.6(STXBP1):c.1689G>A (p.Trp563Ter)

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.1689G>A (p.Trp563Ter)

HGVS:

NC_000009.12:g.127682547G>A
NG_016623.1:g.75341G>A
NM_001032221.6:c.1689G>AMANE SELECT
NM_001374306.2:c.1680G>A
NM_001374307.2:c.1647G>A
NM_001374308.2:c.1647G>A
NM_001374309.2:c.1647G>A
NM_001374310.2:c.1647G>A
NM_001374311.2:c.1647G>A
NM_001374312.2:c.1647G>A
NM_001374313.2:c.1689G>A
NM_001374314.1:c.1689G>A
NM_001374315.2:c.1581G>A
NM_003165.6:c.1689G>A
NP_001027392.1:p.Trp563Ter
NP_001361235.1:p.Trp560Ter
NP_001361236.1:p.Trp549Ter
NP_001361237.1:p.Trp549Ter
NP_001361238.1:p.Trp549Ter
NP_001361239.1:p.Trp549Ter
NP_001361240.1:p.Trp549Ter
NP_001361241.1:p.Trp549Ter
NP_001361242.1:p.Trp563Ter
NP_001361243.1:p.Trp563Ter
NP_001361244.1:p.Trp527Ter
NP_003156.1:p.Trp563Ter
NC_000009.11:g.130444826G>A
NM_003165.3:c.1689G>A

Protein change:

W527*

Links:

dbSNP: rs1057520544

NCBI 1000 Genomes Browser:

rs1057520544

Molecular consequence:

NM_001032221.6:c.1689G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374306.2:c.1680G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374307.2:c.1647G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374308.2:c.1647G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374309.2:c.1647G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374310.2:c.1647G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374311.2:c.1647G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374312.2:c.1647G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374313.2:c.1689G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374314.1:c.1689G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374315.2:c.1581G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_003165.6:c.1689G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000515960	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Dec 16, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000515960

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Dec 16, 2021)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000515960.6

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

Description

Reported previously in a cohort of patients with seizures and/or neurodevelopmental disorders; further clinical information and segregation analysis was not available (Lindy et al., 2018); Nonsense variant in the C-terminus predicted to result in protein truncation, as the last 41 amino acids are lost, and other loss-of-function variants have been reported downstream in the Human Gene Mutation Database (Stenson et al., 2014); Not observed at significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 29655203)

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

Last Updated: Mar 4, 2023

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