STXBP3

syntaxin binding protein 3

Basic information

Region (hg38): 1:108746674-108809523

Links

ENSG00000116266 ∙ NCBI:6814 ∙ OMIM:608339 ∙ HGNC:11446 ∙ Uniprot:O00186 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	32	2		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		2	1			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)
1-108756714-G-A		Immune dysregulation, autoimmunity, and autoinflammation	Uncertain significance (Jun 19, 2024)
1-108758547-C-T		not specified	Uncertain significance (Nov 09, 2024)
1-108758556-A-G		not specified	Uncertain significance (Jan 03, 2024)
1-108760035-A-G		not specified	Uncertain significance (Feb 11, 2022)
1-108760075-A-G		not specified	Uncertain significance (Sep 16, 2021)
1-108772668-T-C		Immune dysregulation, autoimmunity, and autoinflammation	Uncertain significance (Jun 19, 2024)
1-108772669-A-T		not specified	Uncertain significance (Dec 03, 2024)
1-108772743-A-G		not specified	Likely benign (Dec 09, 2024)
1-108772761-G-A		not specified	Likely benign (Mar 22, 2021)
1-108772766-G-T		not specified	Uncertain significance (May 16, 2023)
1-108772798-A-G		not specified	Uncertain significance (Jan 21, 2025)
1-108772803-G-A		not specified	Uncertain significance (Mar 15, 2024)
1-108776347-A-G		not specified	Uncertain significance (Jan 30, 2024)
1-108776361-G-A			Likely pathogenic (Apr 04, 2024)
1-108779299-C-T		not specified	Uncertain significance (May 25, 2023)
1-108779363-T-G		not specified	Uncertain significance (Sep 08, 2024)
1-108782433-A-G		not specified	Uncertain significance (Apr 07, 2023)
1-108782656-C-T		not specified	Uncertain significance (Jul 25, 2023)
1-108793627-T-G		not specified	Uncertain significance (Feb 27, 2024)
1-108793631-G-A		not specified	Uncertain significance (Jan 02, 2024)
1-108793636-C-A		not specified	Uncertain significance (Apr 26, 2024)
1-108793643-CTAAGG-C		STXBP3-related disorders	Likely pathogenic (Nov 20, 2024)
1-108793648-G-A		See cases	Uncertain significance (Nov 24, 2022)
1-108793649-T-G			Likely pathogenic (Oct 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STXBP3	protein_coding	protein_coding	ENST00000370008	19	62853

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000516	1.00	125719	0	23	125742	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.76	216	302	0.714	0.0000149	3908
Missense in Polyphen		61	116.65	0.52291		1482
Synonymous	1.18	86	101	0.851	0.00000496	1037
Loss of Function	3.49	14	36.9	0.380	0.00000196	469

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000314	0.000308
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000892	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.000100	0.0000980
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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