STX2

syntaxin 2, the group of Syntaxins

Basic information

Region (hg38): 12:130789600-130839254

Previous symbols: [ "STX2B", "STX2C", "STX2A", "EPIM" ]

Links

ENSG00000111450 ∙ NCBI:2054 ∙ OMIM:132350 ∙ HGNC:3403 ∙ Uniprot:P32856 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the STX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STX2 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			11		1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	11	0	2

Variants in STX2

This is a list of pathogenic ClinVar variants found in the STX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-130796051-C-T		not specified	Uncertain significance (Nov 23, 2024)
12-130798539-T-C		not specified	Uncertain significance (May 04, 2022)
12-130798560-T-C		not specified	Uncertain significance (May 30, 2022)
12-130798635-C-T		not specified	Uncertain significance (Feb 16, 2023)
12-130801176-T-C		not specified	Uncertain significance (Aug 20, 2023)
12-130801253-T-C		not specified	Uncertain significance (Nov 14, 2024)
12-130801287-T-C		not specified	Uncertain significance (Jan 10, 2022)
12-130801294-G-A			Benign (Jun 18, 2018)
12-130801468-C-T		not specified	Uncertain significance (Jul 09, 2024)
12-130807018-G-A		not specified	Uncertain significance (Oct 25, 2024)
12-130808647-C-T		not specified	Uncertain significance (Oct 12, 2024)
12-130808665-C-T		not specified	Uncertain significance (May 04, 2022)
12-130808702-T-C			Benign (Dec 31, 2019)
12-130812971-C-T		not specified	Uncertain significance (Feb 17, 2022)
12-130812987-T-C		not specified	Uncertain significance (Mar 13, 2023)
12-130821680-A-G			Benign (Apr 05, 2018)
12-130821697-G-A		not specified	Uncertain significance (Feb 07, 2023)
12-130827218-T-C		not specified	Uncertain significance (Oct 02, 2023)
12-130827231-C-T		not specified	Uncertain significance (Jan 10, 2023)
12-130827246-C-G		not specified	Uncertain significance (Mar 20, 2024)
12-130839089-C-T		not specified	Uncertain significance (Dec 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STX2	protein_coding	protein_coding	ENST00000392373	10	49667

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.11e-7	0.703	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.108	160	164	0.976	0.00000928	1913
Missense in Polyphen		52	54.525	0.95369		650
Synonymous	0.173	52	53.6	0.970	0.00000313	505
Loss of Function	1.22	13	18.7	0.695	0.00000114	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000303	0.000300
Ashkenazi Jewish	0.00	0.00
East Asian	0.000280	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000152	0.000149
Middle Eastern	0.000280	0.000272
South Asian	0.000137	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for epithelial morphogenesis. May mediate Ca(2+)-regulation of exocytosis acrosomal reaction in sperm.
• Pathway: Synaptic vesicle cycle - Homo sapiens (human);SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Synaptic Vesicle Pathway;Splicing factor NOVA regulated synaptic proteins (Consensus)

Recessive Scores

• pRec: 0.234

Intolerance Scores

• loftool: 0.941
• rvis_EVS: 0.57
• rvis_percentile_EVS: 82.08

Haploinsufficiency Scores

• pHI: 0.155
• hipred: Y
• hipred_score: 0.565
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.784

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stx2
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; immune system phenotype; digestive/alimentary phenotype; reproductive system phenotype; liver/biliary system phenotype

Gene ontology

• Biological process: intracellular protein transport;exocytosis;vesicle fusion;signal transduction;acrosome reaction;ectoderm development;animal organ morphogenesis;cell differentiation;synaptic vesicle fusion to presynaptic active zone membrane;response to hydroperoxide;vesicle docking;protein complex oligomerization;cornified envelope assembly
• Cellular component: extracellular space;plasma membrane;synaptic vesicle;endomembrane system;integral component of membrane;basolateral plasma membrane;lamellipodium;SNARE complex;presynaptic membrane;intracellular membrane-bounded organelle;presynaptic active zone membrane
• Molecular function: SNARE binding;SNAP receptor activity;protein binding;protein dimerization activity;calcium-dependent protein binding