STXBP3
Basic information
Region (hg38): 1:108746674-108809523
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 32 | 35 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 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:
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:
- 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