STX1A

syntaxin 1A, the group of Syntaxins

Basic information

Region (hg38): 7:73699205-73719672

Previous symbols: [ "STX1" ]

Links

ENSG00000106089 ∙ NCBI:6804 ∙ OMIM:186590 ∙ HGNC:11433 ∙ Uniprot:Q16623 ∙ 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 STX1A gene.

• not provided (4 variants)
• Intellectual disability;Seizure (3 variants)
• Intellectual disability;Autism (3 variants)
• Inborn genetic diseases (2 variants)
• Neurodevelopmental abnormality (1 variants)
• Seizure;Intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX1A 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				1		1
missense		3	4			7
nonsense						0
start loss						0
frameshift						0
inframe indel		2				2
splice donor/acceptor (+/-2bp)	1					1
splice region				1		1
non coding				1		1
Total	1	5	4	2	0

Variants in STX1A

This is a list of pathogenic ClinVar variants found in the STX1A region.

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

Position	Type	Phenotype	Significance	ClinVar
7-73700443-G-A		STX1A-related disorder	Likely benign (May 28, 2019)
7-73700490-T-C			Likely benign (Jul 21, 2018)
7-73700734-C-T			Uncertain significance (Mar 01, 2023)
7-73700794-TCTA-T		Intellectual disability;Autism	Likely pathogenic (Apr 22, 2022)
7-73702674-G-A			Likely benign (Apr 01, 2023)
7-73702846-T-C		Intellectual disability;Seizure	Likely pathogenic (Apr 22, 2022)
7-73702852-TCCA-T		Intellectual disability;Autism	Likely pathogenic (Apr 22, 2022)
7-73702969-G-C		Intellectual disability;Seizure	Likely pathogenic (Apr 22, 2022)
7-73702979-T-C		Inborn genetic diseases	Uncertain significance (Feb 10, 2022)
7-73704179-G-C		Neurodevelopmental abnormality • Seizure;Intellectual disability	Likely pathogenic (Apr 22, 2022)
7-73704365-C-T			Likely benign (Aug 13, 2018)
7-73704407-G-A		STX1A-related disorder	Likely benign (Jan 27, 2020)
7-73704424-C-T		Intellectual disability;Autism	Pathogenic (Apr 22, 2022)
7-73705197-A-C		Intellectual disability;Seizure	Uncertain significance (Apr 22, 2022)
7-73708629-C-T			Likely benign (Feb 01, 2024)
7-73708647-G-A		STX1A-related disorder	Benign (Dec 09, 2019)
7-73709038-C-A		STX1A-related disorder	Likely benign (Aug 13, 2019)
7-73719606-C-T		Inborn genetic diseases	Uncertain significance (Jan 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STX1A	protein_coding	protein_coding	ENST00000222812	10	20467

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.979	0.0215	125719	0	3	125722	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.40	98	191	0.512	0.0000123	1930
Missense in Polyphen		23	67.253	0.34199		621
Synonymous	0.950	66	76.6	0.862	0.00000555	507
Loss of Function	3.50	1	16.2	0.0618	8.35e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
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: Plays a role in hormone and neurotransmitter exocytosis (By similarity). Potentially involved in docking of synaptic vesicles at presynaptic active zones. May mediate Ca(2+)- regulation of exocytosis acrosomal reaction in sperm. {ECO:0000250|UniProtKB:P32851}.
• Disease: DISEASE: Note=STX1A is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. {ECO:0000305|PubMed:9311751}.
• Pathway: Synaptic vesicle cycle - Homo sapiens (human);SNARE interactions in vesicular transport - Homo sapiens (human);Amphetamine addiction - Homo sapiens (human);Insulin secretion - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Serotonin Transporter Activity;Synaptic Vesicle Pathway;Monoamine Transport;Developmental Biology;Disease;Other interleukin signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;Effects of Botulinum toxin;Toxicity of botulinum toxin type C (BoNT/C);Uptake and actions of bacterial toxins;Neurotoxicity of clostridium toxins;Infectious disease;Immune System;Neuronal System;Glutamate Neurotransmitter Release Cycle;Dopamine Neurotransmitter Release Cycle;Acetylcholine Neurotransmitter Release Cycle;GABA synthesis, release, reuptake and degradation;Neurotransmitter release cycle;Neurexins and neuroligins;Transmission across Chemical Synapses;Protein-protein interactions at synapses;Serotonin Neurotransmitter Release Cycle;Norepinephrine Neurotransmitter Release Cycle;LGI-ADAM interactions (Consensus)

Recessive Scores

• pRec: 0.438

Intolerance Scores

• loftool: 0.298
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.479
• hipred: Y
• hipred_score: 0.853
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.722

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stx1a
• Phenotype: embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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); normal 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); growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: positive regulation of neurotransmitter secretion;intracellular protein transport;exocytosis;vesicle fusion;response to gravity;positive regulation of norepinephrine secretion;regulation of synaptic vesicle priming;synaptic vesicle docking;cytokine-mediated signaling pathway;synaptic vesicle fusion to presynaptic active zone membrane;secretion by cell;positive regulation of catecholamine secretion;SNARE complex assembly;positive regulation of calcium ion-dependent exocytosis;vesicle docking;regulation of insulin secretion;protein localization to membrane;positive regulation of excitatory postsynaptic potential
• Cellular component: extracellular region;cytosol;plasma membrane;synaptic vesicle;voltage-gated potassium channel complex;endomembrane system;postsynaptic density;integral component of membrane;cell junction;secretory granule;integral component of synaptic vesicle membrane;axon;SNARE complex;nuclear membrane;actomyosin;presynaptic membrane;neuron projection;presynaptic active zone membrane;synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex;synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex;synaptobrevin 2-SNAP-25-syntaxin-1a complex;glutamatergic synapse;integral component of presynaptic membrane
• Molecular function: SNARE binding;SNAP receptor activity;protein binding;calcium channel inhibitor activity;chloride channel inhibitor activity;kinase binding;protein domain specific binding;protein binding, bridging;myosin head/neck binding;ATP-dependent protein binding;ion channel binding;protein heterodimerization activity;protein N-terminus binding;calcium-dependent protein binding