STOML2
protein-codingstomatin like 2, the group of Stomatin family
Gene summary
Enables GTPase binding activity; T cell receptor binding activity; and cardiolipin binding activity. Involved in intracellular calcium ion homeostasis; mitochondrion organization; and protein complex oligomerization. Acts upstream of or within T cell receptor signaling pathway. Located in several cellular components, including immunological synapse; membrane raft; and mitochondrial envelope. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.4 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 STOML2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_013442.3. 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 | 1 | 1 | ||||
| missense | 36 | 36 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 41 | 0 | 0 | 41 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_038470.1 | 10 | MANE Select | |
| Ensembl | ENSP00000348886.5 | 10 | MANE Select | |
| RefSeq | NP_001273960.1 | 9 | Standard | |
| RefSeq | NP_001273961.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- mitochondrial calcium ion transmembrane transport
- cellular calcium ion homeostasis
- mitochondrion organization
- lipid localization
- positive regulation of mitochondrial membrane potential
Molecular Function
- signaling receptor binding
- protein binding
- GTPase binding
- cardiolipin binding
Cellular Component
- immunological synapse
- mitochondrial inner membrane
- mitochondrial intermembrane space
- cytoskeleton
- COP9 signalosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000356493
- Coding exons
- 10
- Length
- 3267
- Individuals with no LoFs
- 125730
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 18
- Defined
- 125748
- p
- 0.0000716
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.55 | 148 | 211 | 0.701 | 0.0000127 | 2266 |
| Missense (PolyPhen) | 55 | 91.734 | 0.59956 | 1012 | ||
| Synonymous | -0.481 | 90 | 84.4 | 1.07 | 0.00000491 | 768 |
| Loss of Function | 2.59 | 8 | 20.7 | 0.386 | 0.00000115 | 213 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000062 | 0.000062 | rare |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Mitochondrial protein that probably regulates the biogenesis and the activity of mitochondria. Stimulates cardiolipin biosynthesis, binds cardiolipin-enriched membranes where it recruits and stabilizes some proteins including prohibitin and may therefore act in the organization of functional microdomains in mitochondrial membranes. Through regulation of the mitochondrial function may play a role into several biological processes including cell migration, cell proliferation, T-cell activation, calcium homeostasis and cellular response to stress. May play a role in calcium homeostasis through negative regulation of calcium efflux from mitochondria. Required for mitochondrial hyperfusion a pro-survival cellular response to stress which results in increased ATP production by mitochondria. May also regulate the organization of functional domains at the plasma membrane and play a role in T-cell activation through association with the T-cell receptor signaling complex and its regulation. {ECO:0000269|PubMed:17121834, ECO:0000269|PubMed:18641330, ECO:0000269|PubMed:19597348, ECO:0000269|PubMed:19944461, ECO:0000269|PubMed:21746876, ECO:0000269|PubMed:22623988}.;
Recessive Scores
- pRec
- 0.150
Intolerance Scores
- RVIS EVS
- -0.47
- RVIS percentile EVS
- 23.04
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.954
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |