STX1B

syntaxin 1B, the group of Syntaxins

Basic information

Region (hg38): 16:30989255-31010638

Previous symbols: [ "STX1B1", "STX1B2" ]

Links

ENSG00000099365 ∙ NCBI:112755 ∙ OMIM:601485 ∙ HGNC:18539 ∙ Uniprot:P61266 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• generalized epilepsy with febrile seizures plus (Supportive), mode of inheritance: AD
• generalized epilepsy with febrile seizures plus (Definitive), mode of inheritance: AD
• generalized epilepsy with febrile seizures plus, type 9 (Strong), mode of inheritance: AD
• generalized epilepsy with febrile seizures plus, type 9 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Generalized epilepsy with febrile seizures plus, type 9	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	11591834; 18479394; 25362483
As with many disorders involving seizure risk, optimal control is beneficial, and genetic diagnosis may be beneficial related to medication selection

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the STX1B gene.

• Generalized epilepsy with febrile seizures plus, type 9 (256 variants)
• not provided (82 variants)
• Inborn genetic diseases (25 variants)
• Neurodevelopmental disorder (2 variants)
• - (2 variants)
• Neonatal hemochromatosis (2 variants)
• Epileptic encephalopathy (1 variants)
• not specified (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX1B 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			3	48	4	55
missense		6	91	2		99
nonsense	3	4				7
start loss			2			2
frameshift	8	3	2			13
inframe indel		2	3			5
splice donor/acceptor (+/-2bp)	4	14				18
splice region			16	18	4	38
non coding			4	47	15	66
Total	15	29	105	97	19

Variants in STX1B

This is a list of pathogenic ClinVar variants found in the STX1B region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30989353-A-AG		Neonatal hemochromatosis	Uncertain significance (Mar 23, 2023)
16-30989573-T-C		Neonatal hemochromatosis	Likely benign (Mar 23, 2023)
16-30992550-G-A			Likely benign (Aug 07, 2018)
16-30992641-CG-C			Benign (Aug 15, 2019)
16-30992641-C-CG			Benign (Aug 08, 2019)
16-30992641-C-CGG			Benign (Aug 20, 2019)
16-30992647-G-A			Likely benign (Jul 17, 2018)
16-30992649-G-GGC			Likely benign (Aug 25, 2018)
16-30992693-G-GGGGGTGGAGGA			Benign (Jul 09, 2018)
16-30992811-T-TG			Likely benign (Oct 11, 2018)
16-30992812-G-C		Generalized epilepsy with febrile seizures plus, type 9	Uncertain significance (Oct 16, 2018)
16-30992817-G-T		Generalized epilepsy with febrile seizures plus, type 9	Uncertain significance (Apr 11, 2018)
16-30992823-A-G			Uncertain significance (Jun 01, 2021)
16-30992824-C-T		Generalized epilepsy with febrile seizures plus, type 9	Likely benign (Jul 16, 2020)
16-30992826-A-G		Generalized epilepsy with febrile seizures plus, type 9	Likely benign (Nov 23, 2022)
16-30992827-G-A		Generalized epilepsy with febrile seizures plus, type 9	Benign (Aug 14, 2023)
16-30992827-G-T		Generalized epilepsy with febrile seizures plus, type 9	Likely benign (May 25, 2023)
16-30992833-C-T		Generalized epilepsy with febrile seizures plus, type 9	Likely benign (Jul 19, 2023)
16-30992834-G-A		Generalized epilepsy with febrile seizures plus, type 9	Uncertain significance (Feb 06, 2022)
16-30992835-TC-T		Generalized epilepsy with febrile seizures plus, type 9	Uncertain significance (Aug 29, 2019)
16-30992835-T-TC		Generalized epilepsy with febrile seizures plus, type 9	Likely pathogenic (Sep 07, 2022)
16-30992836-C-T		Generalized epilepsy with febrile seizures plus, type 9 • Inborn genetic diseases	Likely benign (Jan 19, 2024)
16-30992838-C-T		Generalized epilepsy with febrile seizures plus, type 9	Uncertain significance (Apr 23, 2023)
16-30992839-C-G		Generalized epilepsy with febrile seizures plus, type 9	Likely benign (Dec 08, 2023)
16-30992840-C-A		Generalized epilepsy with febrile seizures plus, type 9	Uncertain significance (Feb 18, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STX1B	protein_coding	protein_coding	ENST00000215095	10	21373

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.988	0.0123	125744	0	2	125746	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.94	68	179	0.381	0.0000102	1914
Missense in Polyphen		9	50.258	0.17908		493
Synonymous	0.303	69	72.3	0.955	0.00000458	519
Loss of Function	3.68	1	17.7	0.0566	9.04e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potentially involved in docking of synaptic vesicles at presynaptic active zones. May mediate Ca(2+)-regulation of exocytosis acrosomal reaction in sperm (By similarity). {ECO:0000250}.
• Disease: DISEASE: Generalized epilepsy with febrile seizures plus 9 (GEFSP9) [MIM:616172]: An autosomal dominant neurologic disorder characterized by febrile and/or afebrile seizures manifesting in early childhood. Seizure are variable and include generalized tonic-clonic, atonic, myoclonic, complex partial, and absence types. Most patients have remission of seizures later in childhood with no residual neurologic deficits. Rarely, patients may show mild developmental delay or mild intellectual disabilities. {ECO:0000269|PubMed:25362483}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Synaptic vesicle cycle - Homo sapiens (human);SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Synaptic Vesicle Pathway;Developmental Biology;Disease;Toxicity of botulinum toxin type C (BoNT/C);Uptake and actions of bacterial toxins;Neurotoxicity of clostridium toxins;Infectious disease;LGI-ADAM interactions (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.0723
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.228
• hipred: Y
• hipred_score: 0.771
• ghis: 0.653

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.757

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stx1b
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: stx1b
• Affected structure: optic tectum
• Phenotype tag: abnormal
• Phenotype quality: decreased process quality

Gene ontology

• Biological process: positive regulation of neurotransmitter secretion;intracellular protein transport;exocytosis;vesicle docking involved in exocytosis;vesicle fusion;regulation of gene expression;regulation of synaptic vesicle priming;negative regulation of neuron projection development;synaptic vesicle docking;synaptic vesicle fusion to presynaptic active zone membrane;vesicle docking;calcium ion-regulated exocytosis of neurotransmitter;regulation of synaptic activity;spontaneous neurotransmitter secretion;exocytic insertion of neurotransmitter receptor to postsynaptic membrane;negative regulation of synaptic vesicle recycling;positive regulation of spontaneous neurotransmitter secretion;negative regulation of macropinocytosis;positive regulation of excitatory postsynaptic potential
• Cellular component: nucleus;microtubule organizing center;spindle;cytosol;plasma membrane;synaptic vesicle;endomembrane system;membrane;integral component of membrane;axon;SNARE complex;neuromuscular junction;presynaptic membrane;presynaptic active zone membrane
• Molecular function: SNARE binding;signaling receptor binding;SNAP receptor activity;protein kinase binding;protein domain specific binding