STAM
signal transducing adaptor molecule, the group of ESCRT-0
Basic information
Region (hg38): 10:17644151-17716824
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (71 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the STAM gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003473.4. 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 | 2 | |||||
| missense | 69 | 70 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 69 | 2 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STAM | protein_coding | protein_coding | ENST00000377524 | 14 | 71790 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.850 | 0.150 | 125735 | 0 | 12 | 125747 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.294 | 279 | 293 | 0.952 | 0.0000147 | 3563 |
| Missense in Polyphen | 42 | 68.279 | 0.61513 | 879 | ||
| Synonymous | -0.270 | 109 | 105 | 1.03 | 0.00000618 | 1005 |
| Loss of Function | 4.05 | 5 | 28.2 | 0.177 | 0.00000128 | 350 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000579 | 0.0000579 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000618 | 0.0000615 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000656 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in intracellular signal transduction mediated by cytokines and growth factors. Upon IL-2 and GM-CSL stimulation, it plays a role in signaling leading to DNA synthesis and MYC induction. May also play a role in T-cell development. Involved in down-regulation of receptor tyrosine kinase via multivesicular body (MVBs) when complexed with HGS (ESCRT-0 complex). The ESCRT-0 complex binds ubiquitin and acts as sorting machinery that recognizes ubiquitinated receptors and transfers them to further sequential lysosomal sorting/trafficking processes.;
- Pathway
- Jak-STAT signaling pathway - Homo sapiens (human);Endocytosis - Homo sapiens (human);JAK-STAT-Ncore;Vitamin D Receptor Pathway;VEGFA-VEGFR2 Signaling Pathway;EGF-EGFR Signaling Pathway;Disease;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Endosomal Sorting Complex Required For Transport (ESCRT);Metabolism of proteins;Infectious disease;Metalloprotease DUBs;EGFR downregulation;Signaling by EGFR;Clathrin-mediated endocytosis;EGFR1;Deubiquitination;IL2-mediated signaling events;Cargo recognition for clathrin-mediated endocytosis;IL4;IL-7;Negative regulation of MET activity;Signaling by MET;Signaling by Receptor Tyrosine Kinases;InlB-mediated entry of Listeria monocytogenes into host cell;Listeria monocytogenes entry into host cells
(Consensus)
Recessive Scores
- pRec
- 0.165
Intolerance Scores
- loftool
- 0.398
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.65
Haploinsufficiency Scores
- pHI
- 0.306
- hipred
- Y
- hipred_score
- 0.819
- ghis
- 0.591
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.987
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Stam
- 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); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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); reproductive system phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- intracellular protein transport;signal transduction;positive regulation of signal transduction;endosomal transport;macroautophagy;protein deubiquitination;multivesicular body assembly;negative regulation of epidermal growth factor receptor signaling pathway;membrane organization;positive regulation of exosomal secretion;regulation of extracellular exosome assembly
- Cellular component
- cytosol;early endosome membrane;ESCRT-0 complex
- Molecular function
- SH3/SH2 adaptor activity;protein binding;ubiquitin-like protein ligase binding