TMED4

transmembrane p24 trafficking protein 4, the group of Transmembrane p24 trafficking proteins

Basic information

Region (hg38): 7:44576392-44582287

Links

ENSG00000158604NCBI:222068OMIM:612038HGNC:22301Uniprot:Q7Z7H5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMED4 gene.

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
clinvar
1
clinvar
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)2402568
7-44579616-G-A not specified Uncertain significance (Feb 12, 2024)3178358
7-44581128-C-T not specified Uncertain significance (Mar 11, 2022)2278379
7-44581457-C-T not specified Uncertain significance (Jul 25, 2023)2593025
7-44581466-A-C not specified Uncertain significance (Apr 07, 2022)2282111
7-44581775-G-A not specified Uncertain significance (Mar 06, 2023)2461954
7-44582104-C-G not specified Uncertain significance (Feb 02, 2022)3178356
7-44582121-C-G not specified Uncertain significance (Aug 09, 2021)2302019
7-44582190-G-A not specified Uncertain significance (Jan 29, 2024)3178357
7-44582194-C-A not specified Uncertain significance (Jun 06, 2022)2294212
7-44582194-C-G not specified Likely benign (Nov 12, 2021)2401352

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TMED4protein_codingprotein_codingENST00000457408 54394
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.2430.7511257340131257470.0000517
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7381171420.8260.000008131482
Missense in Polyphen2340.1910.57226395
Synonymous0.3215356.10.9450.00000311442
Loss of Function2.37311.80.2555.91e-7113

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009040.0000904
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00008800.0000879
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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