STXBP5

syntaxin binding protein 5, the group of WD repeat domain containing

Basic information

Region (hg38): 6:147204180-147391010

Links

ENSG00000164506 ∙ ∙ OMIM:604586 ∙ HGNC:19665 ∙ Uniprot:Q5T5C0 ∙ 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 STXBP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STXBP5 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				10	4	14
missense			49	3	3	55
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				2	1	3
Total	0	0	49	16	8

Variants in STXBP5

This is a list of pathogenic ClinVar variants found in the STXBP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-147204527-G-A		STXBP5-related disorder	Benign (Jan 25, 2023)
6-147204546-A-G		not specified	Uncertain significance (Dec 13, 2023)
6-147205993-A-G		not specified	Uncertain significance (Oct 24, 2023)
6-147206022-G-C		not specified	Uncertain significance (Feb 15, 2023)
6-147235250-C-T		STXBP5-related disorder	Likely benign (Apr 19, 2024)
6-147239221-C-T		not specified	Uncertain significance (Feb 07, 2023)
6-147239239-A-G		not specified	Uncertain significance (Aug 17, 2022)
6-147260720-C-T		STXBP5-related disorder	Likely benign (May 24, 2019)
6-147262345-G-A		not specified	Uncertain significance (Aug 02, 2021)
6-147267078-T-C			Likely benign (Sep 01, 2022)
6-147267084-C-G		not specified	Uncertain significance (Jan 18, 2023)
6-147267146-C-T		STXBP5-related disorder	Likely benign (Jun 24, 2019)
6-147278112-G-A		not specified	Uncertain significance (Nov 10, 2021)
6-147278144-A-G		not specified	Uncertain significance (May 23, 2023)
6-147278153-A-G		STXBP5-related disorder	Likely benign (Jul 16, 2023)
6-147278164-A-G		STXBP5-related disorder	Likely benign (Jun 15, 2021)
6-147311462-A-G		STXBP5-related disorder	Likely benign (Jan 28, 2024)
6-147311523-A-G		STXBP5-related disorder	Uncertain significance (Sep 28, 2022)
6-147313944-C-T		STXBP5-related disorder	Likely benign (Jul 21, 2018)
6-147313972-C-G		STXBP5-related disorder	Likely benign (Feb 01, 2023)
6-147315592-A-G		STXBP5-related disorder	Uncertain significance (Dec 20, 2023)
6-147315617-A-G		STXBP5-related disorder	Benign (May 17, 2018)
6-147315687-C-G		STXBP5-related disorder	Likely benign (Apr 25, 2023)
6-147315734-C-T		not specified	Uncertain significance (Feb 28, 2024)
6-147315744-G-A		STXBP5-related disorder	Likely benign (Aug 13, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STXBP5	protein_coding	protein_coding	ENST00000321680	28	181306

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000441	125734	0	12	125746	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.00	401	609	0.658	0.0000313	7451
Missense in Polyphen		58	128.97	0.44971		1561
Synonymous	0.178	221	224	0.985	0.0000122	2234
Loss of Function	6.41	10	66.3	0.151	0.00000348	821

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000361	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000662	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a regulatory role in calcium-dependent exocytosis and neurotransmitter release. Inhibits membrane fusion between transport vesicles and the plasma membrane. May modulate the assembly of trans-SNARE complexes between transport vesicles and the plasma membrane. Inhibits translocation of GLUT4 from intracellular vesicles to the plasma membrane. Competes with STXBP1 for STX1 binding (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.305
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.98

Haploinsufficiency Scores

• pHI: 0.176
• hipred: Y
• hipred_score: 0.749
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.733

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stxbp5
• 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)

Gene ontology

• Biological process: exocytosis;protein transport;regulation of exocytosis;positive regulation of GTPase activity;positive regulation of exocytosis;synaptic vesicle cycle
• Cellular component: cytoplasm;cytosol;plasma membrane;acetylcholine-gated channel complex;synaptic vesicle;cell junction;cytoplasmic vesicle membrane;SNARE complex;neuromuscular junction;Schaffer collateral - CA1 synapse;extrinsic component of presynaptic membrane;presynaptic cytosol
• Molecular function: GTPase activator activity;syntaxin-1 binding;Rab GTPase binding;syntaxin binding