STXBP3

syntaxin binding protein 3

Basic information

Region (hg38): 1:108746674-108809523

Links

ENSG00000116266NCBI:6814OMIM:608339HGNC:11446Uniprot:O00186AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the STXBP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STXBP3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
0
missense
1
clinvar
32
clinvar
2
clinvar
35
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
2
clinvar
1
clinvar
3
splice region
0
non coding
0
Total 0 3 33 2 0

Variants in STXBP3

This is a list of pathogenic ClinVar variants found in the STXBP3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
1-108746772-G-C not specified Uncertain significance (Mar 09, 2025)3802773
1-108756714-G-A Immune dysregulation, autoimmunity, and autoinflammation Uncertain significance (Jun 19, 2024)3252047
1-108758547-C-T not specified Uncertain significance (Nov 09, 2024)3451010
1-108758556-A-G not specified Uncertain significance (Jan 03, 2024)3171793
1-108760035-A-G not specified Uncertain significance (Feb 11, 2022)2383536
1-108760075-A-G not specified Uncertain significance (Sep 16, 2021)2384731
1-108772668-T-C Immune dysregulation, autoimmunity, and autoinflammation Uncertain significance (Jun 19, 2024)3252048
1-108772669-A-T not specified Uncertain significance (Dec 03, 2024)3171794
1-108772743-A-G not specified Likely benign (Dec 09, 2024)3451013
1-108772761-G-A not specified Likely benign (Mar 22, 2021)1301694
1-108772766-G-T not specified Uncertain significance (May 16, 2023)2546799
1-108772798-A-G not specified Uncertain significance (Jan 21, 2025)2371606
1-108772803-G-A not specified Uncertain significance (Mar 15, 2024)3323481
1-108776347-A-G not specified Uncertain significance (Jan 30, 2024)3171795
1-108776361-G-A Likely pathogenic (Apr 04, 2024)3068187
1-108779299-C-T not specified Uncertain significance (May 25, 2023)2551955
1-108779363-T-G not specified Uncertain significance (Sep 08, 2024)3451011
1-108782433-A-G not specified Uncertain significance (Apr 07, 2023)2554253
1-108782656-C-T not specified Uncertain significance (Jul 25, 2023)2591708
1-108793627-T-G not specified Uncertain significance (Feb 27, 2024)3171788
1-108793631-G-A not specified Uncertain significance (Jan 02, 2024)3171789
1-108793636-C-A not specified Uncertain significance (Apr 26, 2024)3323480
1-108793643-CTAAGG-C STXBP3-related disorders Likely pathogenic (Nov 20, 2024)3378407
1-108793648-G-A See cases Uncertain significance (Nov 24, 2022)2431650
1-108793649-T-G Likely pathogenic (Oct 01, 2022)1879089

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
STXBP3protein_codingprotein_codingENST00000370008 1962853
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00005161.001257190231257420.0000915
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.762163020.7140.00001493908
Missense in Polyphen61116.650.522911482
Synonymous1.18861010.8510.000004961037
Loss of Function3.491436.90.3800.00000196469

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003140.000308
Ashkenazi Jewish0.00009950.0000992
East Asian0.00005440.0000544
Finnish0.00009240.0000924
European (Non-Finnish)0.00008920.0000879
Middle Eastern0.00005440.0000544
South Asian0.0001000.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Together with STX4 and VAMP2, may play a role in insulin-dependent movement of GLUT4 and in docking/fusion of intracellular GLUT4-containing vesicles with the cell surface in adipocytes. {ECO:0000250}.;
Pathway
Insulin Signaling;Disinhibition of SNARE formation;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

pRec
0.146

Intolerance Scores

loftool
0.606
rvis_EVS
-0.51
rvis_percentile_EVS
21.41

Haploinsufficiency Scores

pHI
0.303
hipred
Y
hipred_score
0.522
ghis
0.629

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
K
gene_indispensability_pred
E
gene_indispensability_score
0.810

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Stxbp3
Phenotype
homeostasis/metabolism phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype;

Zebrafish Information Network

Gene name
stxbp3
Affected structure
otolith
Phenotype tag
abnormal
Phenotype quality
decreased size

Gene ontology

Biological process
cellular glucose homeostasis;vesicle docking involved in exocytosis;brain development;protein to membrane docking;insulin secretion;response to insulin;neutrophil degranulation;negative regulation of calcium ion-dependent exocytosis;negative regulation of glucose import;protein heterooligomerization;platelet aggregation;cellular response to interferon-gamma
Cellular component
cytosol;plasma membrane;basolateral plasma membrane;apical plasma membrane;platelet alpha granule;specific granule;phagocytic vesicle;extracellular exosome;tertiary granule;presynapse
Molecular function
protein binding;syntaxin-1 binding;syntaxin binding