TMED5

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

Basic information

Region (hg38): 1:93149741-93180516

Links

ENSG00000117500 ∙ NCBI:50999 ∙ OMIM:616876 ∙ HGNC:24251 ∙ Uniprot:Q9Y3A6 ∙ 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 TMED5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMED5 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			5		1	6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	2

Variants in TMED5

This is a list of pathogenic ClinVar variants found in the TMED5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-93154751-T-C			Benign (Dec 13, 2017)
1-93154761-A-G			Benign (Mar 01, 2018)
1-93154771-A-T		not specified	Uncertain significance (Sep 16, 2021)
1-93154827-C-G		not specified	Uncertain significance (Sep 27, 2021)
1-93156301-A-C		not specified	Uncertain significance (Nov 17, 2022)
1-93156385-A-G		not specified	Uncertain significance (May 09, 2024)
1-93156385-A-T		not specified	Uncertain significance (Feb 23, 2023)
1-93180063-G-C		not specified	Uncertain significance (Apr 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMED5	protein_coding	protein_coding	ENST00000370282	4	30987

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.27e-9	0.0664	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.666	100	121	0.829	0.00000545	1514
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000873	0.0000873
Ashkenazi Jewish	0.00	0.00
East Asian	0.000714	0.000707
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.000714	0.000707
South Asian	0.000168	0.000163
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.243
• hipred: N
• hipred_score: 0.292
• ghis: 0.639

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmed5

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;Golgi ribbon formation
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;cis-Golgi network;integral component of membrane;COPII-coated ER to Golgi transport vesicle;endoplasmic reticulum-Golgi intermediate compartment membrane;endoplasmic reticulum exit site
• Molecular function: protein binding