STOML3
protein-codingstomatin like 3, the group of Stomatin family
Gene summary
Predicted to enable ion channel inhibitor activity. Predicted to act upstream of or within signal transduction. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~24.9 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 STOML3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_145286.3. 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 | 0 | |||||
| missense | 61 | 1 | 62 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 1 | 62 | 1 | 0 | 64 |
Highest pathogenic variant AF is 0.0011941649
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_660329.1 | 7 | MANE Select | |
| Ensembl | ENSP00000368952.4 | 7 | MANE Select | |
| RefSeq | NP_001137505.1 | 7 | Standard | |
| Ensembl | ENSP00000401989.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Stimuli-sensing channels
- Ion channel transport
- Transport of small molecules
Biological Process
- signal transduction
- biological_process
- ion transmembrane transport
Molecular Function
- molecular_function
Cellular Component
- cellular_component
- plasma membrane
- cilium
- integral component of membrane
- membrane raft
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000379631
- Coding exons
- 7
- Length
- 25142
- Individuals with no LoFs
- 125476
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 271
- Defined
- 125748
- p
- 0.00108
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.372 | 185 | 171 | 1.08 | 0.00000985 | 1860 |
| Missense (PolyPhen) | 80 | 79.902 | 1.0012 | 837 | ||
| Synonymous | 1.06 | 56 | 67.0 | 0.835 | 0.00000376 | 609 |
| Loss of Function | -0.735 | 19 | 15.8 | 1.20 | 9.42e-7 | 163 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.0013 | 0.0013 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00023 | 0.00023 | rare |
| European (Non-Finnish) | 0.0017 | 0.0017 | notable |
| South Asian | 0.00062 | 0.00059 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Required for the function of many mechanoreceptors. Modulate mechanotransduction channels and acid-sensing ion channels (ASIC) proteins. Potentiates PIEZO1 and PIEZO2 function by increasing their sensitivity to mechanical stimulations. {ECO:0000250|UniProtKB:Q6PE84}.;
Recessive Scores
- pRec
- 0.127
Intolerance Scores
- LoFtool
- 0.218
- RVIS EVS
- 0.46
- RVIS percentile EVS
- 78.59
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |