NM_001032221.6(STXBP1):c.260_261del (p.Leu87fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 13, 2018
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:: RCV001008326.1

Allele description [Variation Report for NM_001032221.6(STXBP1):c.260_261del (p.Leu87fs)]

NM_001032221.6(STXBP1):c.260_261del (p.Leu87fs)

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.260_261del (p.Leu87fs)

HGVS:

NC_000009.12:g.127660039TC[2]
NC_000009.12:g.127660039_127660040TC[2]
NG_016623.1:g.52833TC[2]
NM_001032221.6:c.260_261delMANE SELECT
NM_001374306.2:c.260_261del
NM_001374307.2:c.218_219del
NM_001374308.2:c.218_219del
NM_001374309.2:c.218_219del
NM_001374310.2:c.218_219del
NM_001374311.2:c.218_219del
NM_001374312.2:c.218_219del
NM_001374313.2:c.260_261del
NM_001374314.1:c.260_261del
NM_001374315.2:c.260_261del
NM_003165.6:c.260_261del
NP_001027392.1:p.Leu87fs
NP_001361235.1:p.Leu87fs
NP_001361236.1:p.Leu73fs
NP_001361237.1:p.Leu73fs
NP_001361238.1:p.Leu73fs
NP_001361239.1:p.Leu73fs
NP_001361240.1:p.Leu73fs
NP_001361241.1:p.Leu73fs
NP_001361242.1:p.Leu87fs
NP_001361243.1:p.Leu87fs
NP_001361244.1:p.Leu87fs
NP_003156.1:p.Leu87fs
NC_000009.11:g.130422318TC[2]
NM_003165.3:c.260_261del
NM_003165.3:c.260_261delTC

Protein change:

L73fs

Molecular consequence:

NM_001032221.6:c.260_261del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374306.2:c.260_261del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374307.2:c.218_219del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374308.2:c.218_219del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374309.2:c.218_219del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374310.2:c.218_219del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374311.2:c.218_219del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374312.2:c.218_219del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374313.2:c.260_261del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374314.1:c.260_261del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374315.2:c.260_261del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003165.6:c.260_261del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001168094	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Sep 13, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001168094

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Sep 13, 2018)

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, SCV001168094.1

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

Description

The c.260_261delTC variant in the STXBP1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.260_261delTC variant causes a frameshift starting with codon Leucine 87, changes this amino acid to a Histidine residue, and creates a premature Stop codon at position 3 of the new reading frame, denoted p.Leu87HisfsX3. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.260_261delTC variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.260_261delTC as 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: Mar 16, 2024

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