TMED6

transmembrane p24 trafficking protein 6, the group of Transmembrane p24 trafficking proteins

Basic information

Region (hg38): 16:69343250-69351786

Links

ENSG00000157315 ∙ NCBI:146456 ∙ ∙ HGNC:28331 ∙ Uniprot:Q8WW62 ∙ 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 TMED6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMED6 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in TMED6

This is a list of pathogenic ClinVar variants found in the TMED6 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-69343448-T-C		not specified	Uncertain significance (Sep 22, 2023)
16-69343456-C-T		not specified	Uncertain significance (Jun 03, 2022)
16-69343604-T-C		not specified	Uncertain significance (Nov 21, 2023)
16-69343615-T-C		not specified	Uncertain significance (Jun 12, 2023)
16-69347897-A-G		not specified	Uncertain significance (Feb 06, 2024)
16-69349554-C-T		not specified	Uncertain significance (Nov 18, 2022)
16-69349564-C-A		not specified	Uncertain significance (Nov 06, 2023)
16-69349587-C-T		not specified	Uncertain significance (Dec 14, 2022)
16-69349615-C-T		not specified	Likely benign (Dec 28, 2023)
16-69349639-C-T		not specified	Uncertain significance (Sep 26, 2022)
16-69351599-C-T		not specified	Uncertain significance (Jan 03, 2022)
16-69351616-G-C		not specified	Uncertain significance (Dec 15, 2023)
16-69351641-C-T		not specified	Uncertain significance (Jun 29, 2023)
16-69351654-G-A		not specified	Uncertain significance (Oct 30, 2023)
16-69351689-T-G		not specified	Uncertain significance (Jun 02, 2024)
16-69351749-G-C		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMED6	protein_coding	protein_coding	ENST00000288025	4	8562

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000863	0.792	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.523	156	139	1.13	0.00000793	1583
Missense in Polyphen		47	43.781	1.0735		501
Synonymous	-0.867	59	51.1	1.15	0.00000289	457
Loss of Function	1.16	8	12.4	0.644	6.85e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000383	0.000383
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000246	0.000237
Middle Eastern	0.000326	0.000326
South Asian	0.000327	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.905
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.25

Haploinsufficiency Scores

• pHI: 0.0521
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.229

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmed6

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;integral component of membrane;COPII-coated ER to Golgi transport vesicle