TMED3

transmembrane p24 trafficking protein 3, the group of Transmembrane p24 trafficking proteins

Basic information

Region (hg38): 15:79311112-79427432

Previous symbols: [ "C15orf22" ]

Links

ENSG00000166557 ∙ NCBI:23423 ∙ ∙ HGNC:28889 ∙ Uniprot:Q9Y3Q3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMED3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMED3 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				1		1
missense			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding				1		1
Total	0	0	15	4	1

Variants in TMED3

This is a list of pathogenic ClinVar variants found in the TMED3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-79311263-T-C		not specified	Likely benign (Jul 25, 2023)
15-79311266-C-T		not specified	Uncertain significance (Aug 16, 2022)
15-79311352-G-C		not specified	Uncertain significance (Dec 26, 2023)
15-79311362-A-T		not specified	Uncertain significance (Jan 02, 2024)
15-79311418-G-A			Likely benign (Apr 01, 2023)
15-79313812-A-T		not specified	Uncertain significance (Oct 20, 2023)
15-79313817-A-G		not specified	Uncertain significance (Sep 23, 2023)
15-79313821-A-G		not specified	Uncertain significance (May 27, 2022)
15-79313830-C-T		not specified	Uncertain significance (Feb 06, 2023)
15-79313860-G-A		TMED3-related disorder	Benign (Jun 10, 2019)
15-79313921-C-T		TMED3-related disorder	Likely benign (May 27, 2022)
15-79313928-G-A		not specified	Uncertain significance (Jan 03, 2024)
15-79313947-T-C		not specified	Uncertain significance (Aug 01, 2022)
15-79314004-A-G		not specified	Uncertain significance (Sep 20, 2023)
15-79321987-G-A		not specified	Uncertain significance (May 04, 2022)
15-79321994-T-C		not specified	Uncertain significance (Aug 15, 2023)
15-79322066-G-T		not specified	Uncertain significance (Dec 26, 2023)
15-79322093-G-T		not specified	Uncertain significance (May 04, 2023)
15-79322099-C-T		not specified	Uncertain significance (Mar 27, 2023)
15-79322120-C-T		not specified	Uncertain significance (Apr 06, 2024)
15-79322219-G-A		TMED3-related disorder	Likely benign (May 11, 2020)
15-79411441-C-T		TMED3-related disorder	Likely benign (Mar 29, 2021)
15-79411474-C-A		TMED3-related disorder	Likely benign (Mar 21, 2023)
15-79411508-A-G		TMED3-related disorder	Likely benign (May 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMED3	protein_coding	protein_coding	ENST00000299705	3	100931

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0226	0.918	124872	2	874	125748	0.00349

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.303	120	130	0.925	0.00000762	1409
Missense in Polyphen		22	30.437	0.7228		362
Synonymous	-0.0404	60	59.6	1.01	0.00000383	439
Loss of Function	1.61	4	9.29	0.431	5.69e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00267	0.00260
Ashkenazi Jewish	0.00472	0.00447
East Asian	0.00	0.00
Finnish	0.00892	0.00835
European (Non-Finnish)	0.00483	0.00438
Middle Eastern	0.00	0.00
South Asian	0.00142	0.00137
Other	0.00548	0.00523

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential role in vesicular protein trafficking, mainly in the early secretory pathway. Contributes to the coupled localization of TMED2 and TMED10 in the cis-Golgi network. {ECO:0000269|PubMed:10852829}.
• Pathway: 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;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: 0.118

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.251
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.797

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tmed3

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;Golgi organization
• Cellular component: Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;integral component of membrane;COPI vesicle coat;transport vesicle;COPII-coated ER to Golgi transport vesicle;Golgi cisterna membrane;endoplasmic reticulum-Golgi intermediate compartment membrane