STX8

syntaxin 8, the group of Syntaxins

Basic information

Region (hg38): 17:9250471-9576591

Links

ENSG00000170310 ∙ NCBI:9482 ∙ OMIM:604203 ∙ HGNC:11443 ∙ Uniprot:Q9UNK0 ∙ 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 STX8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX8 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	14	1	1

Variants in STX8

This is a list of pathogenic ClinVar variants found in the STX8 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-9250601-C-G		not specified	Uncertain significance (Nov 22, 2022)
17-9250630-A-G		not specified	Uncertain significance (Mar 06, 2023)
17-9378599-T-C		not specified	Uncertain significance (Jan 23, 2023)
17-9491909-C-T		not specified	Uncertain significance (Aug 28, 2023)
17-9505039-T-G		not specified	Uncertain significance (May 30, 2024)
17-9505052-T-G		Malignant tumor of prostate	Uncertain significance (-)
17-9505058-T-A		not specified	Uncertain significance (Apr 07, 2023)
17-9505091-G-A		not specified	Uncertain significance (May 27, 2022)
17-9505113-G-A		not specified	Uncertain significance (Feb 14, 2023)
17-9557525-T-C		not specified	Uncertain significance (Apr 12, 2022)
17-9568370-C-T			Uncertain significance (Aug 15, 2023)
17-9568379-C-T		not specified	Likely benign (Aug 21, 2023)
17-9568388-C-G		not specified	Uncertain significance (Mar 02, 2023)
17-9568399-T-C		not specified	Uncertain significance (Sep 26, 2023)
17-9568408-C-T		not specified	Uncertain significance (Jun 10, 2022)
17-9568435-T-C		not specified	Uncertain significance (Mar 02, 2023)
17-9575802-G-A		not specified	Uncertain significance (Aug 16, 2022)
17-9575803-T-C			Benign (Mar 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STX8	protein_coding	protein_coding	ENST00000306357	8	326121

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.32e-8	0.362	125708	0	39	125747	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.544	148	131	1.13	0.00000692	1542
Missense in Polyphen		53	47.128	1.1246		578
Synonymous	0.896	38	45.7	0.831	0.00000247	436
Loss of Function	0.772	14	17.5	0.801	0.00000108	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000382	0.000381
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.0000544	0.0000544
South Asian	0.000265	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Vesicle trafficking protein that functions in the early secretory pathway, possibly by mediating retrograde transport from cis-Golgi membranes to the ER.
• Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics (Consensus)

Recessive Scores

• pRec: 0.201

Intolerance Scores

• loftool: 0.374
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.78

Haploinsufficiency Scores

• pHI: 0.133
• hipred: Y
• hipred_score: 0.728
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.502

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stx8
• Phenotype: skeleton phenotype; normal phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: intracellular protein transport;vesicle fusion;endosome to lysosome transport;early endosome to late endosome transport;vesicle docking;cellular response to interferon-gamma;regulation of protein localization to plasma membrane
• Cellular component: lysosomal membrane;endosome;early endosome;late endosome;endoplasmic reticulum;trans-Golgi network;cytosol;integral component of plasma membrane;endomembrane system;integral component of membrane;SNARE complex;late endosome membrane;vesicle;phagocytic vesicle;perinuclear region of cytoplasm;recycling endosome
• Molecular function: SNARE binding;SNAP receptor activity;protein binding;chloride channel inhibitor activity;syntaxin binding;ubiquitin protein ligase binding