TMED5

protein-coding

transmembrane p24 trafficking protein 5, the group of Transmembrane p24 trafficking proteins

Gene summary

Involved in Golgi ribbon formation. Located in cis-Golgi network; endoplasmic reticulum exit site; and endoplasmic reticulum-Golgi intermediate compartment. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_016040.5

Inheritance

—

ClinVar variants

U:24B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.12

Max pathogenic AF

—

Genomic locus

chr1:93,149,742-93,180,516

External References & Databases

Ensembl (ENSG00000117500)

Transcript & Mutation Effects

hg38 • Region Span ~30.8 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 TMED5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 22

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016040.5. 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
missense			22 clinvar		1 clinvar	23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	24	0	2	26

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016040.5	RefSeq	NP_057124.3	4	MANE Select
ENST00000370282.8	Ensembl	ENSP00000359305.3	4	MANE Select
NM_001167830.2	RefSeq	NP_001161302.1	5	Standard
NM_001410825.1	RefSeq	NP_001397754.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

intracellular protein transport
endoplasmic reticulum to Golgi vesicle-mediated transport
Golgi organization
Golgi ribbon formation

Molecular Function

protein binding

Cellular Component

endoplasmic reticulum
endoplasmic reticulum membrane
endoplasmic reticulum-Golgi intermediate compartment
Golgi apparatus
cis-Golgi network

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370282
Coding exons: 4
Length: 30987
Individuals with no LoFs: 125702
Homozygous LoFs: 0
Heterozygous LoFs: 46
Defined: 125748
p: 0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.666	100	121	0.829	0.00000545	1514
Missense (PolyPhen)		23	34.803	0.66087		470
Synonymous	-0.403	49	45.5	1.08	0.00000199	428
Loss of Function	-0.353	12	10.8	1.12	6.15e-7	116

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00071	0.00071	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00020	0.00020	rare
South Asian	0.00017	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Potential role in vesicular protein trafficking, mainly in the early secretory pathway. Required for the maintenance of the Golgi apparatus; involved in protein exchange between Golgi stacks during assembly. Probably not required for COPI-vesicle- mediated retrograde transport. {ECO:0000269|PubMed:19948005}.;

Recessive Scores

pRec: 0.0973

Intolerance Scores

LoFtool: 0.748
RVIS EVS: 0.08
RVIS percentile EVS: 60.09

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High