NM_001032221.6(STXBP1):c.294del (p.Lys98fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 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:: RCV001008763.1

Allele description [Variation Report for NM_001032221.6(STXBP1):c.294del (p.Lys98fs)]

NM_001032221.6(STXBP1):c.294del (p.Lys98fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

9q34.11

Genomic location:

Preferred name:

NM_001032221.6(STXBP1):c.294del (p.Lys98fs)

HGVS:

NC_000009.12:g.127660077del
NG_016623.1:g.52871del
NM_001032221.6:c.294delMANE SELECT
NM_001374306.2:c.294del
NM_001374307.2:c.252del
NM_001374308.2:c.252del
NM_001374309.2:c.252del
NM_001374310.2:c.252del
NM_001374311.2:c.252del
NM_001374312.2:c.252del
NM_001374313.2:c.294del
NM_001374314.1:c.294del
NM_001374315.2:c.294del
NM_003165.6:c.294del
NP_001027392.1:p.Lys98fs
NP_001361235.1:p.Lys98fs
NP_001361236.1:p.Lys84fs
NP_001361237.1:p.Lys84fs
NP_001361238.1:p.Lys84fs
NP_001361239.1:p.Lys84fs
NP_001361240.1:p.Lys84fs
NP_001361241.1:p.Lys84fs
NP_001361242.1:p.Lys98fs
NP_001361243.1:p.Lys98fs
NP_001361244.1:p.Lys98fs
NP_003156.1:p.Lys98fs
NC_000009.11:g.130422356del
NM_003165.3:c.294delA

Protein change:

K84fs

Links:

dbSNP: rs1588306826

NCBI 1000 Genomes Browser:

rs1588306826

Molecular consequence:

NM_001032221.6:c.294del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374306.2:c.294del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374307.2:c.252del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374308.2:c.252del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374309.2:c.252del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374310.2:c.252del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374311.2:c.252del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374312.2:c.252del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374313.2:c.294del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374314.1:c.294del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374315.2:c.294del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003165.6:c.294del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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SRX5126835 (1)
SRA
MSO1 Mso1p [Saccharomyces cerevisiae S288C]
MSO1 Mso1p [Saccharomyces cerevisiae S288C]
Gene ID:855785

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001168551	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Aug 13, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001168551

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Aug 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, SCV001168551.1

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

Description

The c.294delA pathogenic variant in the STXBP1 gene causes a frameshift starting with codon Lysine 98, changes this amino acid to an Asparagine residue and creates a premature Stop codon at position 22 of the new reading frame, denoted p.Lys98AsnfsX22. This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.294delA variant is not observed in large population cohorts (Lek et al., 2016). Although this pathogenic variant has not been previously reported to our knowledge, its presence is consistent with the diagnosis of an STXBP1-related disorder in this individual.

#	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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