TMEM115
Basic information
Region (hg38): 3:50354749-50359521
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 TMEM115 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 | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
Variants in TMEM115
This is a list of pathogenic ClinVar variants found in the TMEM115 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-50355353-G-A | not specified | Uncertain significance (Feb 28, 2024) | ||
| 3-50355356-G-A | not specified | Uncertain significance (May 31, 2023) | ||
| 3-50355381-T-A | not specified | Uncertain significance (Apr 25, 2022) | ||
| 3-50355416-G-A | not specified | Uncertain significance (Aug 16, 2022) | ||
| 3-50358223-C-T | not specified | Uncertain significance (Apr 08, 2024) | ||
| 3-50358329-G-C | not specified | Uncertain significance (Dec 09, 2023) | ||
| 3-50358340-A-C | not specified | Uncertain significance (Oct 27, 2022) | ||
| 3-50358396-G-C | not specified | Uncertain significance (Dec 28, 2022) | ||
| 3-50358468-A-G | not specified | Uncertain significance (Apr 12, 2022) | ||
| 3-50358522-C-T | not specified | Uncertain significance (Jun 01, 2023) | ||
| 3-50358568-C-T | not specified | Uncertain significance (May 30, 2022) | ||
| 3-50358598-A-G | not specified | Uncertain significance (May 05, 2023) | ||
| 3-50358837-G-A | not specified | Uncertain significance (Mar 13, 2023) | ||
| 3-50358981-G-A | not specified | Uncertain significance (Aug 14, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TMEM115 | protein_coding | protein_coding | ENST00000266025 | 2 | 4862 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.795 | 0.204 | 125254 | 0 | 1 | 125255 | 0.00000399 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.48 | 150 | 211 | 0.713 | 0.0000130 | 2218 |
| Missense in Polyphen | 55 | 81.716 | 0.67306 | 877 | ||
| Synonymous | -0.924 | 110 | 98.3 | 1.12 | 0.00000615 | 814 |
| Loss of Function | 2.57 | 1 | 9.59 | 0.104 | 5.83e-7 | 92 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May play a role in retrograde transport of proteins from the Golgi to the endoplasmic reticulum. May indirectly play a role in protein glycosylation in the Golgi. {ECO:0000269|PubMed:24806965}.;
- Pathway
- Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-mediated anterograde transport;ER to Golgi Anterograde Transport
(Consensus)
Recessive Scores
- pRec
- 0.126
Intolerance Scores
- loftool
- 0.0373
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.58
Haploinsufficiency Scores
- pHI
- 0.299
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.577
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.524
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tmem115
- Phenotype
- homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- protein glycosylation;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;negative regulation of cell population proliferation;protein transport
- Cellular component
- Golgi membrane;nucleus;Golgi apparatus;integral component of membrane;Golgi transport complex;Golgi cisterna membrane
- Molecular function
- molecular_function;protein binding;identical protein binding