STOM
Basic information
Region (hg38): 9:121338987-121370304
Previous symbols: [ "EPB7", "EPB72" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (22 variants)
- not_provided (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the STOM gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004099.6. 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 | 23 | 23 | ||||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 24 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STOM | protein_coding | protein_coding | ENST00000286713 | 7 | 31177 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000270 | 0.783 | 125723 | 0 | 25 | 125748 | 0.0000994 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.67 | 107 | 168 | 0.637 | 0.00000919 | 1865 |
| Missense in Polyphen | 25 | 67.8 | 0.36873 | 727 | ||
| Synonymous | 1.19 | 50 | 61.9 | 0.808 | 0.00000358 | 591 |
| Loss of Function | 1.19 | 9 | 13.8 | 0.654 | 6.69e-7 | 161 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000186 | 0.000185 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000669 | 0.0000653 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Regulates ion channel activity and transmembrane ion transport. Regulates ASIC2 and ASIC3 channel activity.;
- Pathway
- Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Neutrophil degranulation;Stimuli-sensing channels;Ion channel transport;Innate Immune System;Immune System;Transport of small molecules
(Consensus)
Recessive Scores
- pRec
- 0.148
Intolerance Scores
- loftool
- 0.440
- rvis_EVS
- 0.28
- rvis_percentile_EVS
- 71.08
Haploinsufficiency Scores
- pHI
- 0.400
- hipred
- Y
- hipred_score
- 0.528
- ghis
- 0.471
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.980
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Stom
- Phenotype
Gene ontology
- Biological process
- neutrophil degranulation;positive regulation by host of viral genome replication;protein homooligomerization;positive regulation of protein targeting to membrane;regulation of acid-sensing ion channel activity
- Cellular component
- extracellular space;mitochondrion;endoplasmic reticulum;cytoskeleton;plasma membrane;integral component of plasma membrane;membrane;vesicle;azurophil granule membrane;specific granule membrane;melanosome;membrane raft;perinuclear region of cytoplasm;extracellular exosome;tertiary granule membrane;blood microparticle
- Molecular function
- protein binding;protein homodimerization activity;RNA polymerase binding