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
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.
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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 1 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 0 |
Variants in STOM
This is a list of pathogenic ClinVar variants found in the STOM region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-121341236-C-T | not specified | Uncertain significance (Mar 23, 2022) | ||
| 9-121341273-T-C | Uncertain significance (Dec 20, 2022) | |||
| 9-121341315-A-T | not specified | Uncertain significance (Oct 05, 2021) | ||
| 9-121341353-A-G | Uncertain significance (Oct 06, 2022) | |||
| 9-121349130-T-A | not specified | Uncertain significance (Feb 28, 2024) | ||
| 9-121349230-C-T | not specified | Uncertain significance (May 23, 2023) | ||
| 9-121349269-C-T | not specified | Uncertain significance (Jan 10, 2023) | ||
| 9-121349293-C-T | not specified | Uncertain significance (May 29, 2024) | ||
| 9-121349314-T-C | not specified | Uncertain significance (Sep 04, 2024) | ||
| 9-121353258-C-T | not specified | Uncertain significance (Oct 01, 2024) | ||
| 9-121356063-A-G | not specified | Uncertain significance (Sep 30, 2024) | ||
| 9-121356111-G-A | not specified | Uncertain significance (Oct 26, 2021) | ||
| 9-121356150-G-A | not specified | Uncertain significance (Nov 08, 2022) | ||
| 9-121370149-C-G | not specified | Uncertain significance (Sep 16, 2021) | ||
| 9-121370186-A-G | Uncertain significance (Jun 23, 2020) |
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