STMN3
Basic information
Region (hg38): 20:63639705-63657682
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (19 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the STMN3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015894.4. 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 | 19 | 1 | 20 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 19 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STMN3 | protein_coding | protein_coding | ENST00000370053 | 5 | 13720 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0839 | 0.876 | 125350 | 0 | 4 | 125354 | 0.0000160 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.34 | 65 | 103 | 0.629 | 0.00000570 | 1153 |
| Missense in Polyphen | 19 | 34.411 | 0.55214 | 333 | ||
| Synonymous | -0.141 | 48 | 46.8 | 1.03 | 0.00000277 | 336 |
| Loss of Function | 1.75 | 3 | 8.51 | 0.353 | 3.61e-7 | 112 |
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) | 0.0000591 | 0.0000354 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Exhibits microtubule-destabilizing activity, which is antagonized by STAT3. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- loftool
- 0.109
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.39
Haploinsufficiency Scores
- pHI
- 0.181
- hipred
- N
- hipred_score
- 0.399
- ghis
- 0.638
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.527
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Stmn3
- Phenotype
Gene ontology
- Biological process
- blastocyst hatching;microtubule depolymerization;nervous system development;regulation of microtubule polymerization or depolymerization;cytoplasmic microtubule organization;neuron projection development;negative regulation of Rac protein signal transduction;regulation of GTPase activity;regulation of cytoskeleton organization
- Cellular component
- cytoplasm;Golgi apparatus;growth cone;neuron projection
- Molecular function
- tubulin binding;protein domain specific binding