TMED10
transmembrane p24 trafficking protein 10, the group of Transmembrane p24 trafficking proteins
Basic information
Region (hg38): 14:75131469-75176612
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 TMED10 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 | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 6 | 0 | 1 |
Variants in TMED10
This is a list of pathogenic ClinVar variants found in the TMED10 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-75134952-A-G | not specified | Uncertain significance (Jan 24, 2024) | ||
| 14-75134976-C-G | not specified | Uncertain significance (Mar 13, 2023) | ||
| 14-75135008-T-TA | Benign (Jul 06, 2018) | |||
| 14-75135034-A-G | Benign (Feb 26, 2021) | |||
| 14-75135817-T-C | not specified | Uncertain significance (Nov 06, 2023) | ||
| 14-75147726-T-C | not specified | Uncertain significance (Jun 21, 2021) | ||
| 14-75152058-A-G | not specified | Uncertain significance (May 31, 2022) | ||
| 14-75176381-C-T | not specified | Uncertain significance (Dec 07, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TMED10 | protein_coding | protein_coding | ENST00000303575 | 5 | 45162 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.860 | 0.139 | 125720 | 0 | 22 | 125742 | 0.0000875 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.14 | 59 | 127 | 0.466 | 0.00000666 | 1424 |
| Missense in Polyphen | 10 | 43.861 | 0.228 | 599 | ||
| Synonymous | -0.0118 | 49 | 48.9 | 1.00 | 0.00000236 | 442 |
| Loss of Function | 2.77 | 1 | 10.8 | 0.0924 | 6.26e-7 | 124 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000911 | 0.0000908 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000110 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000132 | 0.000132 |
| Middle Eastern | 0.000110 | 0.000109 |
| South Asian | 0.0000984 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in vesicular protein trafficking. Mainly functions in the early secretory pathway. Thought to act as cargo receptor at the lumenal side for incorporation of secretory cargo molecules into transport vesicles and to be involved in vesicle coat formation at the cytoplasmic side. In COPII vesicle-mediated anterograde transport involved in the transport of GPI-anchored proteins and proposed to act together with TMED2 as their cargo receptor; the function specifically implies SEC24C and SEC24D of the COPII vesicle coat and lipid raft-like microdomains of the ER. Recognizes GPI anchors structural remodeled in the ER by PGAP1 and MPPE1 (By similarity). In COPI vesicle-mediated retrograde transport involved in the biogenesis of COPI vesicles and vesicle coat recruitment. On Golgi membranes, acts as primary receptor for ARF1-GDP which is involved in COPI-vesicle formation. Increases coatomer-dependent GTPase-activating activity of ARFGAP2. Involved in trafficking of G protein-coupled receptors (GPCRs). Regulates F2LR1, OPRM1 and P2RY4 exocytic trafficking from the Golgi to the plasma membrane thus contributing to receptor resensitization. Involved in trafficking of amyloid beta A4 protein and soluble APP-beta release (independent of modulation of gamma-secretase activity). As part of the presenilin-dependent gamma-secretase complex regulates gamma-cleavages of the amyloid beta A4 protein to yield amyloid-beta 40 (Abeta40). Involved in organization of the Golgi apparatus. {ECO:0000250, ECO:0000269|PubMed:10052452, ECO:0000269|PubMed:11726511, ECO:0000269|PubMed:16641999, ECO:0000269|PubMed:17288597, ECO:0000269|PubMed:19296914, ECO:0000269|PubMed:20427317, ECO:0000269|PubMed:21219331}.;
- Pathway
- miR-targeted genes in adipocytes - TarBase;miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;mRNA Processing;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Cargo concentration in the ER;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;COPI-mediated anterograde transport;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Recessive Scores
- pRec
- 0.157
Intolerance Scores
- loftool
- 0.342
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.25
Haploinsufficiency Scores
- pHI
- 0.619
- hipred
- Y
- hipred_score
- 0.739
- ghis
- 0.524
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.990
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tmed10
- Phenotype
- cellular phenotype; endocrine/exocrine gland 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); reproductive system phenotype;
Gene ontology
- Biological process
- kidney development;intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;Golgi organization;vesicle cargo loading;COPI-coated vesicle budding;response to alkaloid;regulated exocytosis;vesicle targeting, to, from or within Golgi;COPI coating of Golgi vesicle;COPII vesicle coating;protein complex oligomerization;regulation of amyloid-beta formation
- Cellular component
- Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;cis-Golgi network;plasma membrane;ER to Golgi transport vesicle membrane;integral component of membrane;transport vesicle;COPII-coated ER to Golgi transport vesicle;COPI-coated vesicle;trans-Golgi network transport vesicle;secretory granule membrane;endoplasmic reticulum-Golgi intermediate compartment membrane;melanosome;zymogen granule membrane;gamma-secretase complex
- Molecular function
- protein binding;syntaxin binding;protein-containing complex binding