TMED1

transmembrane p24 trafficking protein 1, the group of Transmembrane p24 trafficking proteins

Basic information

Region (hg38): 19:10832067-10836318

Links

ENSG00000099203 ∙ NCBI:11018 ∙ OMIM:605395 ∙ HGNC:17291 ∙ Uniprot:Q13445 ∙ 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 TMED1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMED1 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						0
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in TMED1

This is a list of pathogenic ClinVar variants found in the TMED1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-10833129-T-G		not specified	Uncertain significance (Jan 10, 2023)
19-10833191-G-A		not specified	Uncertain significance (Jun 11, 2024)
19-10833194-C-T		not specified	Uncertain significance (Jun 11, 2024)
19-10833195-G-A		not specified	Uncertain significance (Mar 31, 2024)
19-10835077-C-T		not specified	Uncertain significance (Aug 28, 2023)
19-10835260-G-A		not specified	Uncertain significance (Feb 17, 2024)
19-10835287-T-C		not specified	Uncertain significance (Jan 23, 2024)
19-10835316-A-T		not specified	Uncertain significance (Nov 17, 2022)
19-10836094-T-G		not specified	Uncertain significance (Jun 16, 2023)
19-10836118-C-T		not specified	Uncertain significance (Feb 05, 2024)
19-10836155-A-C		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMED1	protein_coding	protein_coding	ENST00000214869	4	3881

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000116	0.208	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.521	124	141	0.877	0.00000945	1451
Missense in Polyphen		44	46.867	0.93882		472
Synonymous	-0.240	66	63.6	1.04	0.00000443	470
Loss of Function	-0.0367	9	8.88	1.01	4.79e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000138	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000133	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.000545	0.000490
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential role in vesicular protein trafficking, mainly in the early secretory pathway. May act as a cargo receptor at the lumenal side for incorporation of secretory cargo molecules into transport vesicles and may be involved in vesicle coat formation at the cytoplasmic side.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.808
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.280
• hipred: N
• hipred_score: 0.282
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmed1

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;signal transduction;cell-cell signaling
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;plasma membrane;integral component of membrane;COPII-coated ER to Golgi transport vesicle;endoplasmic reticulum-Golgi intermediate compartment membrane
• Molecular function: signaling receptor binding;protein binding