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NM_006949.4(STXBP2):c.1621G>A (p.Gly541Ser) AND STXBP2-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 28, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003398562.5

Allele description [Variation Report for NM_006949.4(STXBP2):c.1621G>A (p.Gly541Ser)]

NM_006949.4(STXBP2):c.1621G>A (p.Gly541Ser)

Gene:
STXBP2:syntaxin binding protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_006949.4(STXBP2):c.1621G>A (p.Gly541Ser)
HGVS:
  • NC_000019.10:g.7647436G>A
  • NG_016709.1:g.15332G>A
  • NM_001127396.3:c.1612G>A
  • NM_001272034.2:c.1654G>A
  • NM_006949.4:c.1621G>AMANE SELECT
  • NP_001120868.1:p.Gly538Ser
  • NP_001258963.1:p.Gly552Ser
  • NP_008880.2:p.Gly541Ser
  • LRG_165:g.15332G>A
  • NC_000019.9:g.7712322G>A
  • NM_006949.3:c.1621G>A
  • NR_073560.2:n.1636G>A
Protein change:
G538S; GLY541SER
Links:
OMIM: 601717.0007; dbSNP: rs61736587
NCBI 1000 Genomes Browser:
rs61736587
Molecular consequence:
  • NM_001127396.3:c.1612G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001272034.2:c.1654G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006949.4:c.1621G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_073560.2:n.1636G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
STXBP2-related disorder
Synonyms:
STXBP2-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004119961PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Jun 28, 2024) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004119961.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The STXBP2 c.1621G>A variant is predicted to result in the amino acid substitution p.Gly541Ser. This variant was reported in the homozygous state in a patient with familial hemophagocytic lymphohistiocytosis (FHL) who lacked variants in the PRF1, UNC13D, and STX11 genes (Cetica et al. 2010. PubMed ID: 20798128). It has also been reported along with a second STXBP2 variant in other patients with FHL (Meeths et al. 2010. PubMed ID: 20558610; Rohr et al. 2010. PubMed ID: 20823128). Functional data in Cetica et al. suggest the p.Gly541Ser substitution affects binding of the STXBP2 protein to its effectors. This variant is reported in 0.047% of alleles in individuals of European (Non-Finnish) descent in gnomAD. It has been interpreted as pathogenic by multiple submitters to ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/30219). Taken together, this variant is interpreted as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 13, 2024