STRAP
serine/threonine kinase receptor associated protein, the group of SMN complex|WD repeat domain containing
Basic information
Region (hg38): 12:15882387-15903478
Links
Phenotypes
GenCC
Source:
No genCC data.
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 STRAP 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 | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 0 | 0 |
Variants in STRAP
This is a list of pathogenic ClinVar variants found in the STRAP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-15882714-A-G | not specified | Uncertain significance (Nov 08, 2024) | ||
| 12-15882739-C-G | not specified | Uncertain significance (Dec 01, 2022) | ||
| 12-15882774-A-G | not specified | Uncertain significance (Jun 26, 2023) | ||
| 12-15882775-G-A | not specified | Uncertain significance (Oct 08, 2024) | ||
| 12-15882777-G-C | not specified | Uncertain significance (Feb 25, 2025) | ||
| 12-15882811-C-G | not specified | Uncertain significance (May 18, 2022) | ||
| 12-15889932-G-A | not specified | Uncertain significance (Dec 28, 2023) | ||
| 12-15890639-C-T | not specified | Uncertain significance (Mar 14, 2024) | ||
| 12-15894089-C-T | not specified | Uncertain significance (Feb 02, 2022) | ||
| 12-15894102-T-G | not specified | Uncertain significance (Mar 26, 2024) | ||
| 12-15894132-C-A | not specified | Uncertain significance (Dec 23, 2024) | ||
| 12-15895375-A-G | not specified | Uncertain significance (Nov 10, 2022) | ||
| 12-15895376-C-G | not specified | Uncertain significance (Jun 12, 2023) | ||
| 12-15895432-A-G | not specified | Uncertain significance (Feb 22, 2025) | ||
| 12-15895490-C-T | not specified | Uncertain significance (Jan 24, 2025) | ||
| 12-15902918-A-C | not specified | Uncertain significance (May 13, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STRAP | protein_coding | protein_coding | ENST00000419869 | 10 | 21088 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.901 | 0.0986 | 125741 | 0 | 6 | 125747 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.08 | 106 | 186 | 0.571 | 0.00000881 | 2285 |
| Missense in Polyphen | 31 | 71.322 | 0.43465 | 828 | ||
| Synonymous | 1.05 | 54 | 64.7 | 0.834 | 0.00000314 | 653 |
| Loss of Function | 3.60 | 3 | 20.7 | 0.145 | 0.00000111 | 245 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000359 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: The SMN complex plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. STRAP plays a role in the cellular distribution of the SMN complex. Negatively regulates TGF-beta signaling but positively regulates the PDPK1 kinase activity by enhancing its autophosphorylation and by significantly reducing the association of PDPK1 with 14-3-3 protein. {ECO:0000269|PubMed:16251192, ECO:0000269|PubMed:18984161}.;
- Pathway
- RNA transport - Homo sapiens (human);TGF-beta Signaling Pathway;EMT transition in Colorectal Cancer;Signal Transduction;TGF_beta_Receptor;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Downregulation of TGF-beta receptor signaling;TGF-beta receptor signaling activates SMADs;TGF-beta receptor signaling
(Consensus)
Recessive Scores
- pRec
- 0.125
Intolerance Scores
- loftool
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.64
Haploinsufficiency Scores
- pHI
- 0.190
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.632
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Strap
- 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); 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); 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); neoplasm; embryo phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;spliceosomal snRNP assembly;negative regulation of epithelial cell migration;negative regulation of epithelial to mesenchymal transition;maintenance of gastrointestinal epithelium;negative regulation of transforming growth factor beta receptor signaling pathway;negative regulation of epithelial cell proliferation;negative regulation of pathway-restricted SMAD protein phosphorylation
- Cellular component
- nucleoplasm;cytoplasm;cytosol;SMN complex;SMN-Sm protein complex
- Molecular function
- RNA binding;signaling receptor binding;protein binding