TMED9
transmembrane p24 trafficking protein 9, the group of Transmembrane p24 trafficking proteins
Basic information
Region (hg38): 5:177592203-177597242
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 TMED9 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 | 10 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 0 |
Variants in TMED9
This is a list of pathogenic ClinVar variants found in the TMED9 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-177592218-G-C | not specified | Uncertain significance (Jan 26, 2022) | ||
| 5-177592225-A-G | not specified | Uncertain significance (May 11, 2022) | ||
| 5-177592227-C-G | not specified | Uncertain significance (Nov 28, 2023) | ||
| 5-177592239-C-T | not specified | Uncertain significance (Sep 16, 2021) | ||
| 5-177592245-C-T | not specified | Uncertain significance (Jan 03, 2022) | ||
| 5-177592246-G-A | not specified | Uncertain significance (May 15, 2024) | ||
| 5-177592257-G-A | not specified | Uncertain significance (Oct 13, 2023) | ||
| 5-177592260-A-G | not specified | Likely benign (Jan 23, 2024) | ||
| 5-177592281-C-T | not specified | Uncertain significance (Aug 28, 2024) | ||
| 5-177592287-C-T | not specified | Uncertain significance (Feb 05, 2024) | ||
| 5-177592291-T-A | Monoclonal B-Cell Lymphocytosis | Uncertain significance (Dec 15, 2015) | ||
| 5-177592645-G-A | not specified | Uncertain significance (Jul 31, 2024) | ||
| 5-177594157-C-G | not specified | Uncertain significance (Oct 04, 2022) | ||
| 5-177595309-C-G | not specified | Uncertain significance (Nov 18, 2022) | ||
| 5-177595360-G-A | not specified | Uncertain significance (Jun 10, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TMED9 | protein_coding | protein_coding | ENST00000332598 | 5 | 3967 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00595 | 0.975 | 125733 | 0 | 15 | 125748 | 0.0000596 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.929 | 104 | 134 | 0.774 | 0.00000696 | 1500 |
| Missense in Polyphen | 25 | 54.018 | 0.46281 | 646 | ||
| Synonymous | -0.264 | 58 | 55.5 | 1.05 | 0.00000271 | 470 |
| Loss of Function | 2.05 | 6 | 14.4 | 0.417 | 8.73e-7 | 131 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000578 | 0.0000578 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.000186 | 0.000185 |
| European (Non-Finnish) | 0.0000637 | 0.0000615 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Appears to be involved in vesicular protein trafficking, mainly in the early secretory pathway. In COPI vesicle-mediated retrograde transport involved in the coatomer recruitment to membranes of the early secretory pathway. Increases coatomer- dependent activity of ARFGAP2. Thought to play a crucial role in the specific retention of p24 complexes in cis-Golgi membranes; specifically contributes to the coupled localization of TMED2 and TMED10 in the cis-Golgi network. May be involved in organization of intracellular membranes, such as of the ER-Golgi intermediate compartment and the Golgi apparatus. Involved in ER localization of PTPN2 isoform PTPB. {ECO:0000269|PubMed:10852829, ECO:0000269|PubMed:14600267, ECO:0000269|PubMed:16595549, ECO:0000269|PubMed:18287528, ECO:0000269|PubMed:19296914}.;
- 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-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;COPI-mediated anterograde transport;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- loftool
- 0.480
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.4
Haploinsufficiency Scores
- pHI
- 0.269
- hipred
- N
- hipred_score
- 0.429
- ghis
- 0.575
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.368
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tmed9
- Phenotype
Gene ontology
- Biological process
- intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;Golgi organization;positive regulation of organelle organization;protein exit from endoplasmic reticulum;early endosome to Golgi transport;COPI coating of Golgi vesicle
- Cellular component
- Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;cytosol;integral component of membrane;transport vesicle;COPII-coated ER to Golgi transport vesicle;trans-Golgi network transport vesicle;endoplasmic reticulum-Golgi intermediate compartment membrane;extracellular exosome
- Molecular function
- protein binding;syntaxin binding