STX5

syntaxin 5, the group of Syntaxins

Basic information

Region (hg38): 11:62806860-62832051

Previous symbols: [ "STX5A" ]

Links

ENSG00000162236 ∙ NCBI:6811 ∙ OMIM:603189 ∙ HGNC:11440 ∙ Uniprot:Q13190 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital disorder of glycosylation, type IIaa (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital disorder of glycosylation, type IIaa	AR	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	Biochemical; Cardiovascular; Craniofacial; Endocrine; Gastrointestinal; Musculoskeletal; Neurologic; Renal	34711829

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the STX5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX5 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in STX5

This is a list of pathogenic ClinVar variants found in the STX5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62807531-T-C		not specified	Uncertain significance (Nov 17, 2022)
11-62807594-C-T		not specified	Uncertain significance (Dec 05, 2022)
11-62824212-G-C		not specified	Uncertain significance (Aug 17, 2022)
11-62824268-C-T		not specified	Uncertain significance (Nov 21, 2022)
11-62824473-G-A		not specified	Uncertain significance (Jun 07, 2023)
11-62824494-G-A		not specified	Uncertain significance (Dec 12, 2022)
11-62824515-C-T		not specified	Uncertain significance (Sep 14, 2022)
11-62825050-G-A		not specified	Uncertain significance (Mar 29, 2023)
11-62825078-G-A		not specified	Uncertain significance (Oct 26, 2021)
11-62825097-G-C		not specified	Uncertain significance (Aug 04, 2021)
11-62825305-G-A		not specified	Uncertain significance (Mar 06, 2023)
11-62825472-C-A		not specified	Uncertain significance (Aug 02, 2023)
11-62825521-T-C		not specified	Uncertain significance (Mar 14, 2025)
11-62827157-G-T		not specified	Uncertain significance (May 08, 2023)
11-62827201-T-C		not specified	Uncertain significance (Dec 21, 2022)
11-62827383-G-T		not specified	Uncertain significance (Jun 11, 2021)
11-62827601-G-A		not specified	Uncertain significance (Jan 31, 2023)
11-62827609-G-T		not specified	Uncertain significance (Feb 24, 2025)
11-62831023-C-G		not specified	Uncertain significance (Dec 16, 2021)
11-62831024-G-A		not specified	Uncertain significance (Feb 16, 2023)
11-62831035-G-C		not specified	Uncertain significance (Feb 09, 2025)
11-62831115-G-A			Likely benign (Mar 29, 2018)
11-62831128-G-A		not specified	Uncertain significance (Apr 07, 2022)
11-62831188-C-T		not specified	Uncertain significance (Sep 01, 2021)
11-62831205-A-T		not specified	Uncertain significance (Dec 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STX5	protein_coding	protein_coding	ENST00000294179	10	25192

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.843	0.157	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.400	190	206	0.922	0.0000117	2307
Missense in Polyphen		52	63.727	0.81598		786
Synonymous	-0.433	84	79.1	1.06	0.00000437	697
Loss of Function	3.43	3	19.3	0.156	9.10e-7	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates endoplasmic reticulum to Golgi transport. Together with p115/USO1 and GM130/GOLGA2, involved in vesicle tethering and fusion at the cis-Golgi membrane to maintain the stacked and inter-connected structure of the Golgi apparatus. {ECO:0000250|UniProtKB:Q08851}.
• Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Cargo concentration in the ER;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Intra-Golgi traffic;COPI-mediated anterograde transport;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.627
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.358
• hipred: Y
• hipred_score: 0.775
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stx5a

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;vesicle fusion;early endosome to Golgi transport;retrograde transport, endosome to Golgi;positive regulation of protein catabolic process;COPII vesicle coating;vesicle docking;vesicle fusion with Golgi apparatus;Golgi disassembly;regulation of Golgi organization
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;Golgi apparatus;cytosol;endomembrane system;ER to Golgi transport vesicle membrane;integral component of membrane;SNARE complex;vesicle;endoplasmic reticulum-Golgi intermediate compartment membrane
• Molecular function: SNARE binding;SNAP receptor activity;protein binding;cadherin binding;protein N-terminus binding