STOML2
stomatin like 2, the group of Stomatin family
Basic information
Region (hg38): 9:35099776-35103195
Links
Phenotypes
GenCC
Source:
No genCC data.
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 STOML2 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 | 15 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 0 | 0 |
Variants in STOML2
This is a list of pathogenic ClinVar variants found in the STOML2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-35100042-A-G | not specified | Uncertain significance (Nov 20, 2024) | ||
| 9-35100621-C-T | not specified | Uncertain significance (Jun 14, 2023) | ||
| 9-35100960-C-T | not specified | Uncertain significance (Oct 16, 2023) | ||
| 9-35100997-C-T | not specified | Uncertain significance (Feb 07, 2025) | ||
| 9-35101258-G-A | not specified | Uncertain significance (Jan 20, 2023) | ||
| 9-35101267-G-A | not specified | Uncertain significance (Sep 23, 2023) | ||
| 9-35101485-G-A | not specified | Uncertain significance (Apr 08, 2024) | ||
| 9-35101735-T-C | not specified | Uncertain significance (May 03, 2023) | ||
| 9-35101793-C-T | not specified | Uncertain significance (Jun 24, 2022) | ||
| 9-35102135-T-A | not specified | Uncertain significance (Oct 03, 2023) | ||
| 9-35102145-C-T | not specified | Uncertain significance (Feb 06, 2023) | ||
| 9-35102717-C-T | not specified | Uncertain significance (Dec 03, 2024) | ||
| 9-35102762-G-C | not specified | Uncertain significance (Jul 05, 2024) | ||
| 9-35102768-C-T | not specified | Uncertain significance (Aug 10, 2021) | ||
| 9-35102799-C-G | not specified | Uncertain significance (May 20, 2024) | ||
| 9-35103069-G-A | not specified | Uncertain significance (Jan 19, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STOML2 | protein_coding | protein_coding | ENST00000356493 | 10 | 3267 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00241 | 0.995 | 125730 | 0 | 18 | 125748 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.55 | 148 | 211 | 0.701 | 0.0000127 | 2266 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000119 | 0.000119 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000617 | 0.0000615 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000196 | 0.000196 |
| Other | 0.000163 | 0.000163 |
dbNSFP
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
- loftool
- rvis_EVS
- -0.47
- rvis_percentile_EVS
- 23.04
Haploinsufficiency Scores
- pHI
- 0.877
- hipred
- Y
- hipred_score
- 0.615
- ghis
- 0.673
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.954
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Stoml2
- Phenotype
Gene ontology
- Biological process
- mitochondrial calcium ion transmembrane transport;cellular calcium ion homeostasis;mitochondrion organization;lipid localization;positive regulation of mitochondrial membrane potential;interleukin-2 production;mitochondrial protein processing;CD4-positive, alpha-beta T cell activation;mitochondrial ATP synthesis coupled proton transport;T cell receptor signaling pathway;protein complex oligomerization;positive regulation of mitochondrial DNA replication;positive regulation of cardiolipin metabolic process;stress-induced mitochondrial fusion
- Cellular component
- immunological synapse;mitochondrial inner membrane;mitochondrial intermembrane space;cytoskeleton;COP9 signalosome;actin cytoskeleton;extrinsic component of plasma membrane;T cell receptor complex;membrane raft
- Molecular function
- signaling receptor binding;protein binding;GTPase binding;cardiolipin binding