TMED7

transmembrane p24 trafficking protein 7, the group of Transmembrane p24 trafficking proteins

Basic information

Region (hg38): 5:115613210-115632992

Links

ENSG00000134970 ∙ NCBI:51014 ∙ OMIM:619990 ∙ HGNC:24253 ∙ Uniprot:Q9Y3B3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinal disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMED7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMED7 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				30	2	32
missense			42		1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	3		4
non coding				6	2	8
Total	0	0	42	36	5

Variants in TMED7

This is a list of pathogenic ClinVar variants found in the TMED7 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-115616212-T-A			Likely benign (Apr 10, 2022)
5-115616223-GA-AT			Uncertain significance (Sep 29, 2022)
5-115616228-G-C		not specified	Uncertain significance (Apr 23, 2024)
5-115616229-T-C			Uncertain significance (Mar 25, 2023)
5-115616262-A-G			Likely benign (Aug 07, 2023)
5-115616272-C-T			Likely benign (Apr 06, 2022)
5-115616281-G-A			Likely benign (Dec 26, 2022)
5-115616312-A-G			Uncertain significance (Sep 17, 2023)
5-115616314-T-A			Benign (Jan 31, 2024)
5-115616332-T-G			Likely benign (Feb 27, 2023)
5-115616342-T-A			Uncertain significance (Aug 10, 2022)
5-115616357-C-T			Uncertain significance (Jul 09, 2022)
5-115616387-G-T			Uncertain significance (Jun 29, 2022)
5-115616392-A-G			Likely benign (Apr 18, 2022)
5-115616436-C-G			Uncertain significance (Jan 12, 2024)
5-115616456-A-G			Likely benign (Feb 28, 2022)
5-115616459-T-C			Likely benign (Aug 27, 2022)
5-115616462-T-C			Likely benign (Feb 27, 2022)
5-115616465-G-A			Likely benign (Oct 10, 2021)
5-115620415-T-C			Likely benign (Nov 27, 2023)
5-115620417-G-A			Likely benign (Jul 09, 2022)
5-115620421-A-AT			Benign (Dec 08, 2021)
5-115620421-A-ATT			Benign (Jan 29, 2024)
5-115620428-T-A			Likely benign (Jul 14, 2022)
5-115620437-G-T			Uncertain significance (May 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMED7	protein_coding	protein_coding	ENST00000456936	3	19485

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.480	0.516	124564	0	4	124568	0.0000161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	67	112	0.601	0.00000548	1433
Missense in Polyphen		20	47.817	0.41826		681
Synonymous	-0.967	52	43.9	1.19	0.00000209	451
Loss of Function	2.37	2	10.2	0.197	7.40e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000191	0.0000179
Middle Eastern	0.00	0.00
South Asian	0.0000768	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential role in vesicular protein trafficking, mainly in the early secretory pathway. Appears to play a role in the biosynthesis of secreted cargo including processing and post- translational modifications.
• Pathway: Regulation of toll-like receptor signaling pathway;miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous 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: 0.100

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.371
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.192

Mouse Genome Informatics

• Gene name: Tmed7

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;COPII vesicle coat;transport vesicle;COPII-coated ER to Golgi transport vesicle;endoplasmic reticulum-Golgi intermediate compartment membrane