NM_001032221.6(STXBP1):c.1607_1608del (p.Arg536fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 6, 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:: RCV001008321.1

Allele description [Variation Report for NM_001032221.6(STXBP1):c.1607_1608del (p.Arg536fs)]

NM_001032221.6(STXBP1):c.1607_1608del (p.Arg536fs)

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.1607_1608del (p.Arg536fs)

HGVS:

NC_000009.12:g.127682465_127682466del
NG_016623.1:g.75259_75260del
NM_001032221.6:c.1607_1608delMANE SELECT
NM_001374306.2:c.1598_1599del
NM_001374307.2:c.1565_1566del
NM_001374308.2:c.1565_1566del
NM_001374309.2:c.1565_1566del
NM_001374310.2:c.1565_1566del
NM_001374311.2:c.1565_1566del
NM_001374312.2:c.1565_1566del
NM_001374313.2:c.1607_1608del
NM_001374314.1:c.1607_1608del
NM_001374315.2:c.1499_1500del
NM_003165.6:c.1607_1608del
NP_001027392.1:p.Arg536fs
NP_001361235.1:p.Arg533fs
NP_001361236.1:p.Arg522fs
NP_001361237.1:p.Arg522fs
NP_001361238.1:p.Arg522fs
NP_001361239.1:p.Arg522fs
NP_001361240.1:p.Arg522fs
NP_001361241.1:p.Arg522fs
NP_001361242.1:p.Arg536fs
NP_001361243.1:p.Arg536fs
NP_001361244.1:p.Arg500fs
NP_003156.1:p.Arg536fs
NC_000009.11:g.130444744_130444745del
NM_003165.3:c.1607_1608delGC

Protein change:

R500fs

Links:

dbSNP: rs1588354779

NCBI 1000 Genomes Browser:

rs1588354779

Molecular consequence:

NM_001032221.6:c.1607_1608del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374306.2:c.1598_1599del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374307.2:c.1565_1566del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374308.2:c.1565_1566del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374309.2:c.1565_1566del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374310.2:c.1565_1566del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374311.2:c.1565_1566del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374312.2:c.1565_1566del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374313.2:c.1607_1608del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374314.1:c.1607_1608del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374315.2:c.1499_1500del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003165.6:c.1607_1608del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Mus musculus ubiquitin specific peptidase 32, mRNA (cDNA clone IMAGE:5369173), p...
Mus musculus ubiquitin specific peptidase 32, mRNA (cDNA clone IMAGE:5369173), partial cds
gi|30802103|gb|BC051399.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001168089	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Sep 6, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001168089

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Sep 6, 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, SCV001168089.1

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

Description

The c.1607_1608delGC pathogenic variant in the STXBP1 gene causes a frameshift starting with codon Arginine 536, changes this amino acid to a Proline residue and creates a premature Stop codon at position 13 of the new reading frame, denoted p.Arg536ProfsX13. This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1607_1608delGC 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 a 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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