TMED3

protein-coding

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

Gene summary

Predicted to be involved in Golgi organization; endoplasmic reticulum to Golgi vesicle-mediated transport; and intracellular protein transport. Located in Golgi apparatus; endoplasmic reticulum; and endoplasmic reticulum-Golgi intermediate compartment. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C15orf22

MANE transcript

NM_007364.4

Inheritance

—

ClinVar variants

U:36B:4

Top phenotype

TMED3-related disorder

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr15:79,311,112-79,427,432

External References & Databases

Ensembl (ENSG00000166557)

Transcript & Mutation Effects

hg38 • Region Span ~116.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TMED3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 31

TMED3-related disorderTotal: 3

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007364.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			30 clinvar	1 clinvar	1 clinvar	32
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar	1 clinvar		4
Total	0	0	36	3	1	40

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007364.4	RefSeq	NP_031390.1	3	MANE Select
ENST00000299705.10	Ensembl	ENSP00000299705.5	3	MANE Select
NM_001301203.3	RefSeq	NP_001288132.1	3	Standard
NM_001330376.2	RefSeq	NP_001317305.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000299705
Coding exons: 3
Length: 100931
Individuals with no LoFs: 124872
Homozygous LoFs: 2
Heterozygous LoFs: 874
Defined: 125748
p: 0.00349

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.303	120	130	0.925	0.00000762	1409
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00056	0.00049	rare
Latino/Admixed American	0.0021	0.0021	notable
Ashkenazi Jewish	0.0047	0.0045	notable
East Asian	0	0.0	absent
Finnish	0.0089	0.0083	notable
European (Non-Finnish)	0.0048	0.0044	notable
South Asian	0.0014	0.0014	notable
Other	0.0055	0.0052	notable

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.118

Intolerance Scores

RVIS EVS: 0.15
RVIS percentile EVS: 64.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.797

Gene Damage Prediction

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