STX10

syntaxin 10, the group of Syntaxins

Basic information

Region (hg38): 19:13144058-13150383

Links

ENSG00000104915 ∙ NCBI:8677 ∙ OMIM:603765 ∙ HGNC:11428 ∙ Uniprot:O60499 ∙ 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 STX10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX10 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in STX10

This is a list of pathogenic ClinVar variants found in the STX10 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-13144480-C-T		not specified	Uncertain significance (Sep 16, 2021)
19-13144579-C-T		not specified	Uncertain significance (Feb 27, 2024)
19-13144619-C-T		not specified	Uncertain significance (Jul 25, 2023)
19-13144645-A-C		not specified	Uncertain significance (Jun 01, 2023)
19-13144666-A-G		not specified	Uncertain significance (Dec 28, 2022)
19-13144795-G-A		not specified	Uncertain significance (Apr 17, 2023)
19-13144842-A-G		not specified	Uncertain significance (Dec 10, 2024)
19-13145307-T-C		not specified	Uncertain significance (Oct 20, 2024)
19-13145331-G-A		not specified	Uncertain significance (Feb 22, 2023)
19-13145338-C-T		not specified	Uncertain significance (Jul 15, 2021)
19-13145380-G-C		not specified	Uncertain significance (Mar 03, 2025)
19-13145391-A-G		not specified	Uncertain significance (Dec 02, 2022)
19-13149041-C-A		not specified	Uncertain significance (Jun 11, 2024)
19-13149058-C-T		not specified	Likely benign (Dec 07, 2021)
19-13149061-C-T		not specified	Uncertain significance (Jul 02, 2024)
19-13149091-C-T		not specified	Uncertain significance (Sep 03, 2024)
19-13149501-G-T		not specified	Uncertain significance (Jan 16, 2025)
19-13149540-C-T		not specified	Uncertain significance (Mar 18, 2024)
19-13149734-T-C		not specified	Uncertain significance (Jul 15, 2021)
19-13149759-C-G		not specified	Uncertain significance (Dec 20, 2024)
19-13149762-G-C		not specified	Uncertain significance (Oct 25, 2023)
19-13149781-C-T		not specified	Uncertain significance (Feb 16, 2023)
19-13149800-A-G		not specified	Uncertain significance (Sep 28, 2022)
19-13149815-G-A		not specified	Uncertain significance (Oct 08, 2024)
19-13150170-A-C		not specified	Uncertain significance (Jun 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STX10	protein_coding	protein_coding	ENST00000587230	8	6326

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.31e-9	0.106	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00708	159	159	1.00	0.00000916	1620
Missense in Polyphen		41	35.368	1.1592		432
Synonymous	0.143	64	65.5	0.978	0.00000410	472
Loss of Function	0.141	14	14.6	0.960	6.72e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00103	0.00102
Ashkenazi Jewish	0.000104	0.0000992
East Asian	0.000925	0.000925
Finnish	0.00	0.00
European (Non-Finnish)	0.000170	0.000167
Middle Eastern	0.000925	0.000925
South Asian	0.000131	0.000131
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: SNARE involved in vesicular transport from the late endosomes to the trans-Golgi network. {ECO:0000269|PubMed:18195106}.
• Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Vesicle-mediated transport;Membrane Trafficking;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.327
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.215
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.852

Gene Damage Prediction

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

Gene ontology

• Biological process: intracellular protein transport;vesicle fusion;regulation of protein localization;early endosome to Golgi transport;retrograde transport, endosome to Golgi;vesicle docking
• Cellular component: trans-Golgi network;cytosol;synaptic vesicle;endomembrane system;integral component of membrane;integral component of synaptic vesicle membrane;SNARE complex;vesicle;trans-Golgi network membrane;perinuclear region of cytoplasm
• Molecular function: SNARE binding;SNAP receptor activity;protein binding;syntaxin binding