STX6

syntaxin 6, the group of Syntaxins

Basic information

Region (hg38): 1:180972712-181023121

Links

ENSG00000135823 ∙ NCBI:10228 ∙ OMIM:603944 ∙ HGNC:11441 ∙ Uniprot:O43752 ∙ 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 STX6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX6 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						0
missense			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in STX6

This is a list of pathogenic ClinVar variants found in the STX6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-180976605-G-C		not specified	Uncertain significance (Dec 01, 2022)
1-180984727-C-T		not specified	Uncertain significance (Jul 15, 2024)
1-180984728-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-180984737-T-C		not specified	Uncertain significance (Apr 28, 2023)
1-180984737-T-G		not specified	Uncertain significance (Dec 06, 2024)
1-180984739-C-T		not specified	Uncertain significance (Nov 10, 2024)
1-180984770-T-C		not specified	Uncertain significance (Aug 02, 2023)
1-180984771-A-G		not specified	Likely benign (Dec 23, 2024)
1-180988269-C-T		not specified	Uncertain significance (Jun 09, 2022)
1-180988276-A-T		not specified	Uncertain significance (Apr 09, 2024)
1-180988294-C-T		not specified	Uncertain significance (Aug 19, 2024)
1-180988340-G-C		not specified	Uncertain significance (Feb 03, 2022)
1-180990010-T-A		not specified	Uncertain significance (Jun 06, 2023)
1-180990028-T-C		not specified	Uncertain significance (Oct 20, 2021)
1-180990045-A-G		not specified	Uncertain significance (Jul 22, 2024)
1-180990061-C-G		not specified	Uncertain significance (Nov 25, 2024)
1-180990103-G-T		not specified	Uncertain significance (Mar 19, 2024)
1-180993370-T-C		not specified	Uncertain significance (Feb 05, 2024)
1-180993404-T-C		not specified	Likely benign (Jan 03, 2024)
1-180993413-G-C		not specified	Uncertain significance (May 31, 2022)
1-180993414-A-T		not specified	Uncertain significance (Jan 20, 2025)
1-181002620-G-A		not specified	Uncertain significance (May 31, 2023)
1-181002625-C-A		not specified	Uncertain significance (Aug 14, 2024)
1-181005395-G-T		not specified	Uncertain significance (Dec 04, 2024)
1-181022666-A-G		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STX6	protein_coding	protein_coding	ENST00000258301	8	50187

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0103	0.981	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.434	129	144	0.898	0.00000786	1682
Missense in Polyphen		42	46.885	0.89582		595
Synonymous	0.0288	50	50.3	0.995	0.00000263	463
Loss of Function	2.29	6	15.8	0.379	7.61e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000118	0.000118
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000979	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000987	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in intracellular vesicle trafficking.
• Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Vesicle-mediated transport;Membrane Trafficking;Intra-Golgi traffic;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.170

Intolerance Scores

• loftool: 0.226
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.113
• hipred: Y
• hipred_score: 0.765
• ghis: 0.619

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.934

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stx6

Gene ontology

• Biological process: intracellular protein transport;vesicle fusion;endosome organization;synaptic vesicle to endosome fusion;endocytic recycling;regulation of protein localization;retrograde transport, endosome to Golgi;Golgi vesicle transport;vesicle docking;Golgi ribbon formation;regulation of cellular protein localization
• Cellular component: Golgi membrane;nucleoplasm;early endosome;Golgi apparatus;trans-Golgi network;cytosol;plasma membrane;synaptic vesicle;endomembrane system;integral component of membrane;clathrin-coated vesicle;integral component of synaptic vesicle membrane;SNARE complex;trans-Golgi network membrane;phagocytic vesicle;perinuclear region of cytoplasm
• Molecular function: SNARE binding;SNAP receptor activity;protein binding;syntaxin binding