SEPTIN5
Basic information
Region (hg38): 22:19714502-19724224
Previous symbols: [ "PNUTL1", "SEPT5" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (8 variants)
- Inborn genetic diseases (6 variants)
- Abnormal bleeding (1 variants)
- Macrothrombocytopenia (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEPTIN5 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 | 6 | |||||
| missense | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 1 | 1 | ||||
| non coding ? | 2 | |||||
| Total | 0 | 0 | 4 | 8 | 1 |
Variants in SEPTIN5
This is a list of pathogenic ClinVar variants found in the SEPTIN5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SEPTIN5 | protein_coding | protein_coding | ENST00000455784 | 12 | 10309 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.927 | 0.0733 | 125521 | 0 | 7 | 125528 | 0.0000279 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.63 | 128 | 243 | 0.526 | 0.0000157 | 2459 |
| Missense in Polyphen | 58 | 120.16 | 0.48268 | 1137 | ||
| Synonymous | -0.749 | 111 | 101 | 1.09 | 0.00000727 | 664 |
| Loss of Function | 3.70 | 3 | 21.6 | 0.139 | 0.00000106 | 245 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000290 | 0.0000290 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000266 | 0.0000264 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Filament-forming cytoskeletal GTPase (By similarity). May play a role in cytokinesis (Potential). May play a role in platelet secretion (By similarity). {ECO:0000250, ECO:0000305}.;
- Pathway
- Parkinson,s disease - Homo sapiens (human);Parkin-Ubiquitin Proteasomal System pathway;Parkinsons Disease Pathway
(Consensus)
Recessive Scores
- pRec
- 0.278
Intolerance Scores
- loftool
- 0.413
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.07
Haploinsufficiency Scores
- pHI
- 0.284
- hipred
- Y
- hipred_score
- 0.882
- ghis
- 0.630
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.998
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sept5
- Phenotype
- homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; immune system phenotype;
Gene ontology
- Biological process
- synaptic vesicle targeting;regulation of exocytosis;cytoskeleton-dependent cytokinesis;regulation of synaptic vesicle exocytosis
- Cellular component
- plasma membrane;septin ring;synaptic vesicle;microtubule cytoskeleton;septin complex
- Molecular function
- GTPase activity;structural molecule activity;protein binding;GTP binding;protein-containing complex scaffold activity