STMN1
Basic information
Region (hg38): 1:25884181-25906991
Previous symbols: [ "LAP18", "C1orf215" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the STMN1 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 | 1 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 1 | 0 | 0 |
Variants in STMN1
This is a list of pathogenic ClinVar variants found in the STMN1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-25901558-T-C | not specified | Uncertain significance (Feb 28, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STMN1 | protein_coding | protein_coding | ENST00000426559 | 4 | 22811 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0752 | 0.878 | 125674 | 0 | 2 | 125676 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.61 | 48 | 91.4 | 0.525 | 0.00000489 | 1138 |
| Missense in Polyphen | 5 | 20.789 | 0.24051 | 301 | ||
| Synonymous | 0.785 | 26 | 31.6 | 0.822 | 0.00000153 | 330 |
| Loss of Function | 1.69 | 3 | 8.21 | 0.365 | 5.31e-7 | 92 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000935 | 0.0000924 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the regulation of the microtubule (MT) filament system by destabilizing microtubules. Prevents assembly and promotes disassembly of microtubules. Phosphorylation at Ser- 16 may be required for axon formation during neurogenesis. Involved in the control of the learned and innate fear (By similarity). {ECO:0000250}.;
- Pathway
- MAPK signaling pathway - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Regulation of Microtubule Cytoskeleton;Retinoblastoma (RB) in Cancer;Rac1-Pak1-p38-MMP-2 pathway;MAPK Signaling Pathway;EGF-EGFR Signaling Pathway;stathmin and breast cancer resistance to antimicrotubule agents;Aurora B signaling;Signaling mediated by p38-gamma and p38-delta
(Consensus)
Recessive Scores
- pRec
- 0.389
Intolerance Scores
- loftool
- 0.0707
- rvis_EVS
- 0.28
- rvis_percentile_EVS
- 70.87
Haploinsufficiency Scores
- pHI
- 0.646
- hipred
- Y
- hipred_score
- 0.665
- ghis
- 0.407
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.857
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Stmn1
- Phenotype
- homeostasis/metabolism phenotype; muscle 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); 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); normal phenotype;
Gene ontology
- Biological process
- mitotic cytokinesis;microtubule depolymerization;mitotic spindle organization;signal transduction;axonogenesis;brain development;response to virus;regulation of microtubule polymerization or depolymerization;negative regulation of microtubule polymerization;neuron projection development;negative regulation of Rho protein signal transduction;intracellular signal transduction;hepatocyte growth factor receptor signaling pathway;positive regulation of cellular component movement;regulation of cytoskeleton organization;negative regulation of stress fiber assembly;establishment of skin barrier;negative regulation of thrombin-activated receptor signaling pathway;negative regulation of guanyl-nucleotide exchange factor activity
- Cellular component
- cytoplasm;cytosol;microtubule;membrane;neuron projection;extracellular exosome
- Molecular function
- protein binding;tubulin binding