STX3

syntaxin 3, the group of Syntaxins

Basic information

Region (hg38): 11:59713455-59805882

Previous symbols: [ "STX3A" ]

Links

ENSG00000166900 ∙ NCBI:6809 ∙ OMIM:600876 ∙ HGNC:11438 ∙ Uniprot:Q13277 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• microvillus inclusion disease (Supportive), mode of inheritance: AR
• microvillus inclusion disease (Moderate), mode of inheritance: AR
• retinal dystrophy and microvillus inclusion disease (Strong), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the STX3 gene.

• not provided (143 variants)
• Inborn genetic diseases (15 variants)
• Retinal dystrophy and microvillus inclusion disease (1 variants)
• Diarrhea 12, with microvillus atrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX3 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				32	2	34
missense			62	3	3	68
nonsense	2					2
start loss						0
frameshift	2					2
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region			2	7	3	12
non coding			6	24	2	32
Total	4	1	68	59	7

Highest pathogenic variant AF is 0.0000460

Variants in STX3

This is a list of pathogenic ClinVar variants found in the STX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-59713473-T-C		not specified	Likely benign (Jan 26, 2023)
11-59713496-A-G			Benign (Feb 24, 2021)
11-59713559-G-A		not specified	Uncertain significance (Aug 10, 2023)
11-59713608-A-T		not specified	Uncertain significance (Oct 10, 2023)
11-59713688-T-A		not specified	Uncertain significance (Dec 14, 2023)
11-59713697-T-C		not specified	Uncertain significance (Feb 22, 2023)
11-59713703-A-G		not specified	Uncertain significance (Jun 28, 2022)
11-59713788-C-T		not specified	Uncertain significance (Dec 11, 2023)
11-59713803-G-A		not specified	Uncertain significance (Aug 08, 2022)
11-59755615-C-T			Uncertain significance (Jul 15, 2022)
11-59755617-T-C			Likely benign (Jun 30, 2022)
11-59755629-G-A			Likely benign (Aug 25, 2022)
11-59755634-C-T			Uncertain significance (Apr 11, 2022)
11-59755636-G-T			Likely pathogenic (Dec 11, 2023)
11-59755645-G-A			Likely benign (Apr 27, 2023)
11-59755647-C-A			Likely benign (Nov 10, 2023)
11-59755647-C-G			Likely benign (Dec 22, 2022)
11-59755647-C-T			Benign (Jan 21, 2024)
11-59755648-G-T			Likely benign (Feb 10, 2023)
11-59755652-G-A			Likely benign (Mar 02, 2022)
11-59755653-CGGGGTGCTGCCAGGA-C			Likely benign (Dec 11, 2022)
11-59773213-G-A			Likely benign (Jan 09, 2024)
11-59773214-C-G		Inborn genetic diseases	Uncertain significance (Nov 08, 2022)
11-59773216-G-C			Uncertain significance (Jun 27, 2022)
11-59773224-A-G			Likely benign (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STX3	protein_coding	protein_coding	ENST00000337979	10	92426

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0413	0.958	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0100	172	172	1.00	0.00000994	1922
Missense in Polyphen		64	73.143	0.87499		769
Synonymous	-0.0709	66	65.3	1.01	0.00000411	521
Loss of Function	2.85	6	19.6	0.306	0.00000120	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000731	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potentially involved in docking of synaptic vesicles at presynaptic active zones.
• Pathway: Synaptic vesicle cycle - Homo sapiens (human);SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Synaptic Vesicle Pathway;Other interleukin signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;Immune System (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• loftool: 0.429
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.15

Haploinsufficiency Scores

• pHI: 0.131
• hipred: Y
• hipred_score: 0.762
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.917

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stx3
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; 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: intracellular protein transport;exocytosis;vesicle fusion;positive regulation of cell population proliferation;synaptic vesicle docking;cytokine-mediated signaling pathway;neuron projection development;synaptic vesicle fusion to presynaptic active zone membrane;positive regulation of cell adhesion;vesicle docking;positive regulation of chemotaxis;long-term synaptic potentiation;exocytic insertion of neurotransmitter receptor to postsynaptic membrane;positive regulation of protein localization to plasma membrane;positive regulation of protein localization to cell surface
• Cellular component: vacuole;plasma membrane;cell-cell junction;synaptic vesicle;endomembrane system;integral component of membrane;apical plasma membrane;lamellipodium;dendrite;growth cone;SNARE complex;melanosome;specific granule;azurophil granule;zymogen granule membrane;presynaptic membrane;neuron projection;presynaptic active zone membrane;extracellular exosome;Schaffer collateral - CA1 synapse;postsynapse;glutamatergic synapse
• Molecular function: SNARE binding;SNAP receptor activity;protein binding;arachidonic acid binding