STX2
Basic information
Region (hg38): 12:130789600-130839254
Previous symbols: [ "STX2B", "STX2C", "STX2A", "EPIM" ]
Links
Phenotypes
GenCC
Source:
- spermatogenic failure (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (34 variants)
- not_provided (3 variants)
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. These statistics are base on transcript: NM_000194356.4. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 34 | 35 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 34 | 0 | 1 |
GnomAD
Source:
| 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:
- 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