STMN2
Basic information
Region (hg38): 8:79611116-79666158
Previous symbols: [ "SCGN10" ]
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 STMN2 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 | 2 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 3 | 0 | 0 |
Variants in STMN2
This is a list of pathogenic ClinVar variants found in the STMN2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-79641506-G-A | not specified | Uncertain significance (Mar 19, 2024) | ||
| 8-79641529-G-C | not specified | Uncertain significance (Nov 15, 2021) | ||
| 8-79654923-G-A | not specified | Uncertain significance (Dec 13, 2022) | ||
| 8-79663622-T-C | not specified | Uncertain significance (Mar 02, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STMN2 | protein_coding | protein_coding | ENST00000518111 | 5 | 55362 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.977 | 0.0231 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.69 | 50 | 96.7 | 0.517 | 0.00000517 | 1222 |
| Missense in Polyphen | 13 | 26.246 | 0.49532 | 352 | ||
| Synonymous | -0.482 | 39 | 35.4 | 1.10 | 0.00000189 | 338 |
| Loss of Function | 3.15 | 0 | 11.6 | 0.00 | 6.45e-7 | 138 |
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 | 0.00 | 0.00 |
| 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: Regulator of microtubule stability. When phosphorylated by MAPK8, stabilizes microtubules and consequently controls neurite length in cortical neurons. In the developing brain, negatively regulates the rate of exit from multipolar stage and retards radial migration from the ventricular zone (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.250
Intolerance Scores
- loftool
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.961
- hipred
- Y
- hipred_score
- 0.714
- ghis
- 0.653
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.866
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Stmn2
- Phenotype
Gene ontology
- Biological process
- microtubule depolymerization;negative regulation of microtubule depolymerization;positive regulation of neuron projection development;negative regulation of neuron projection development;regulation of microtubule polymerization or depolymerization;negative regulation of microtubule polymerization;positive regulation of microtubule depolymerization;neuron projection development;regulation of cytoskeleton organization;cellular response to nerve growth factor stimulus
- Cellular component
- cytoplasm;endosome;Golgi apparatus;membrane;lamellipodium;growth cone;neuron projection;neuronal cell body;perinuclear region of cytoplasm
- Molecular function
- protein binding;tubulin binding;calcium-dependent protein binding