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.

• not_specified (35 variants)

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. These statistics are base on transcript: NM_000005819.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			33	1		34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	2	0

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