STX18

syntaxin 18, the group of Syntaxins

Basic information

Region (hg38): 4:4415742-4542346

Links

ENSG00000168818 ∙ NCBI:53407 ∙ OMIM:606046 ∙ HGNC:15942 ∙ Uniprot:Q9P2W9 ∙ 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 STX18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX18 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	26	1	0

Variants in STX18

This is a list of pathogenic ClinVar variants found in the STX18 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-4417350-C-T		not specified	Uncertain significance (Aug 13, 2021)
4-4417416-C-T		not specified	Uncertain significance (Oct 19, 2021)
4-4420051-C-G		not specified	Uncertain significance (Nov 09, 2024)
4-4420051-C-T		not specified	Uncertain significance (Nov 25, 2024)
4-4420121-T-G		not specified	Uncertain significance (Dec 18, 2023)
4-4420881-T-A		not specified	Uncertain significance (Oct 21, 2024)
4-4420918-C-G		not specified	Uncertain significance (Jan 20, 2023)
4-4423523-G-T		not specified	Uncertain significance (Oct 11, 2024)
4-4423577-C-G		not specified	Uncertain significance (Nov 09, 2024)
4-4425177-A-T		not specified	Uncertain significance (Oct 08, 2024)
4-4425196-A-C		not specified	Uncertain significance (Aug 10, 2021)
4-4425203-C-T		not specified	Uncertain significance (Oct 14, 2023)
4-4425215-T-A		not specified	Uncertain significance (Oct 17, 2023)
4-4425222-A-G		not specified	Uncertain significance (Dec 27, 2023)
4-4434787-G-C		not specified	Uncertain significance (Aug 09, 2021)
4-4434855-T-A		not specified	Uncertain significance (Oct 06, 2021)
4-4438399-C-T		not specified	Likely benign (Feb 28, 2023)
4-4438406-C-T		not specified	Uncertain significance (Nov 07, 2024)
4-4438420-T-C		not specified	Uncertain significance (Dec 20, 2023)
4-4438459-G-C		not specified	Uncertain significance (Sep 29, 2022)
4-4457222-G-C		not specified	Uncertain significance (May 28, 2024)
4-4457234-G-C		not specified	Uncertain significance (Apr 13, 2022)
4-4457444-A-T		not specified	Uncertain significance (Feb 01, 2023)
4-4457453-C-G		not specified	Uncertain significance (Apr 15, 2024)
4-4457482-G-T		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STX18	protein_coding	protein_coding	ENST00000306200	11	126605

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.49e-7	0.911	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.698	158	185	0.855	0.00000956	2203
Missense in Polyphen		30	33.464	0.89649		430
Synonymous	-0.771	78	69.8	1.12	0.00000402	606
Loss of Function	1.72	14	22.9	0.612	0.00000134	247

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000366	0.000362
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000163	0.000158
Middle Eastern	0.000326	0.000326
South Asian	0.000271	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Syntaxin that may be involved in targeting and fusion of Golgi-derived retrograde transport vesicles with the ER. {ECO:0000269|PubMed:15029241}.
• Pathway: Phagosome - Homo sapiens (human);SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Vesicle-mediated transport;Membrane Trafficking;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.161

Intolerance Scores

• loftool: 0.786
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.153
• hipred: Y
• hipred_score: 0.602
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.878

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stx18
• Phenotype: embryo 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); homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: intracellular protein transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;membrane fusion;endoplasmic reticulum membrane organization;positive regulation of organelle assembly;positive regulation of ER to Golgi vesicle-mediated transport;regulation of Golgi organization
• Cellular component: Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;SNARE complex
• Molecular function: SNAP receptor activity;protein binding;protein domain specific binding