NM_001032221.6(STXBP1):c.767T>C (p.Leu256Pro) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 30, 2017
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:: RCV000444312.1

Allele description [Variation Report for NM_001032221.6(STXBP1):c.767T>C (p.Leu256Pro)]

NM_001032221.6(STXBP1):c.767T>C (p.Leu256Pro)

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.767T>C (p.Leu256Pro)

HGVS:

NC_000009.12:g.127666269T>C
NG_016623.1:g.59063T>C
NM_001032221.6:c.767T>CMANE SELECT
NM_001374306.2:c.758T>C
NM_001374307.2:c.725T>C
NM_001374308.2:c.725T>C
NM_001374309.2:c.725T>C
NM_001374310.2:c.725T>C
NM_001374311.2:c.725T>C
NM_001374312.2:c.725T>C
NM_001374313.2:c.767T>C
NM_001374314.1:c.767T>C
NM_001374315.2:c.767T>C
NM_003165.6:c.767T>C
NP_001027392.1:p.Leu256Pro
NP_001361235.1:p.Leu253Pro
NP_001361236.1:p.Leu242Pro
NP_001361237.1:p.Leu242Pro
NP_001361238.1:p.Leu242Pro
NP_001361239.1:p.Leu242Pro
NP_001361240.1:p.Leu242Pro
NP_001361241.1:p.Leu242Pro
NP_001361242.1:p.Leu256Pro
NP_001361243.1:p.Leu256Pro
NP_001361244.1:p.Leu256Pro
NP_003156.1:p.Leu256Pro
NC_000009.11:g.130428548T>C
NM_003165.3:c.767T>C

Protein change:

L242P

Links:

dbSNP: rs1057524834

NCBI 1000 Genomes Browser:

rs1057524834

Molecular consequence:

NM_001032221.6:c.767T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374306.2:c.758T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374307.2:c.725T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374308.2:c.725T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374309.2:c.725T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374310.2:c.725T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374311.2:c.725T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374312.2:c.725T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374313.2:c.767T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374314.1:c.767T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374315.2:c.767T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003165.6:c.767T>C - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000536577	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Jan 30, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000536577

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Jan 30, 2017)

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, SCV000536577.4

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

Description

The L256P variant in the STXBP1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The L256P variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The L256P variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. The L256P variant is a strong candidate for a pathogenic variant.

#	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: Sep 17, 2022

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