TMED4
Basic information
Region (hg38): 7:44576392-44582287
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 TMED4 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 TMED4
This is a list of pathogenic ClinVar variants found in the TMED4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
7-44579520-G-A | not specified | Uncertain significance (Jun 18, 2021) | ||
7-44579616-G-A | not specified | Uncertain significance (Feb 12, 2024) | ||
7-44581128-C-T | not specified | Uncertain significance (Mar 11, 2022) | ||
7-44581457-C-T | not specified | Uncertain significance (Jul 25, 2023) | ||
7-44581466-A-C | not specified | Uncertain significance (Apr 07, 2022) | ||
7-44581775-G-A | not specified | Uncertain significance (Mar 06, 2023) | ||
7-44582104-C-G | not specified | Uncertain significance (Feb 02, 2022) | ||
7-44582121-C-G | not specified | Uncertain significance (Aug 09, 2021) | ||
7-44582190-G-A | not specified | Uncertain significance (Jan 29, 2024) | ||
7-44582194-C-A | not specified | Uncertain significance (Jun 06, 2022) | ||
7-44582194-C-G | not specified | Likely benign (Nov 12, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TMED4 | protein_coding | protein_coding | ENST00000457408 | 5 | 4394 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.243 | 0.751 | 125734 | 0 | 13 | 125747 | 0.0000517 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.738 | 117 | 142 | 0.826 | 0.00000813 | 1482 |
Missense in Polyphen | 23 | 40.191 | 0.57226 | 395 | ||
Synonymous | 0.321 | 53 | 56.1 | 0.945 | 0.00000311 | 442 |
Loss of Function | 2.37 | 3 | 11.8 | 0.255 | 5.91e-7 | 113 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000904 | 0.0000904 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000880 | 0.0000879 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in vesicular protein trafficking, mainly in the early secretory pathway. targeting. Involved in the maintenance of the Golgi apparatus. Appears to play a role in the biosynthesis of secreted cargo including processing. Involved in endoplasmic reticulum stress response. May play a role in the regulation of heat-shock response and apoptosis (By similarity). {ECO:0000250}.;
Intolerance Scores
- loftool
- rvis_EVS
- -0.19
- rvis_percentile_EVS
- 39.68
Haploinsufficiency Scores
- pHI
- 0.282
- hipred
- Y
- hipred_score
- 0.528
- ghis
- 0.594
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.227
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tmed4
- Phenotype
Gene ontology
- Biological process
- intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;positive regulation of I-kappaB kinase/NF-kappaB signaling
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;integral component of membrane;COPII-coated ER to Golgi transport vesicle
- Molecular function