STOM
protein-codingstomatin, the group of Stomatin family
Gene summary
This gene encodes a member of a highly conserved family of integral membrane proteins. The encoded protein localizes to the cell membrane of red blood cells and other cell types, where it may regulate ion channels and transporters. Loss of localization of the encoded protein is associated with hereditary stomatocytosis, a form of hemolytic anemia. There is a pseudogene for this gene on chromosome 6. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]
- EPB7
- EPB72
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~31.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to STOM variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004099.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 29 | 29 | ||||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 34 | 0 | 0 | 34 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004090.4 | 7 | MANE Select | |
| Ensembl | ENSP00000286713.2 | 7 | MANE Select | |
| RefSeq | NP_001257455.1 | 7 | Standard | |
| RefSeq | NP_001257456.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glucocorticoid Receptor Pathway
- Nuclear Receptors Meta-Pathway
- Neutrophil degranulation
- Stimuli-sensing channels
- Ion channel transport
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
Molecular Function
- protein binding
- protein homodimerization activity
- RNA polymerase binding
Cellular Component
- extracellular space
- mitochondrion
- endoplasmic reticulum
- cytoskeleton
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000286713
- Coding exons
- 7
- Length
- 31177
- Individuals with no LoFs
- 125723
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 25
- Defined
- 125748
- p
- 0.0000994
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.67 | 107 | 168 | 0.637 | 0.00000919 | 1865 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00019 | 0.00018 | rare |
| South Asian | 0.000067 | 0.000065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulates ion channel activity and transmembrane ion transport. Regulates ASIC2 and ASIC3 channel activity.;
Recessive Scores
- pRec
- 0.148
Intolerance Scores
- LoFtool
- 0.440
- RVIS EVS
- 0.28
- RVIS percentile EVS
- 71.08
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.980
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |