TMED7-TICAM2

TMED7-TICAM2 readthrough

Basic information

Region (hg38): 5:115578642-115626161

Links

ENSG00000251201 ∙ NCBI:100302736 ∙ ∙ HGNC:33945 ∙ ∙ ∙ 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 TMED7-TICAM2 gene.

• not provided (76 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMED7-TICAM2 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	22	2	25
missense			30		2	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			2	3	1	6
splice region						0
non coding			2	9	2	13
Total	0	0	35	34	7

Variants in TMED7-TICAM2

This is a list of pathogenic ClinVar variants found in the TMED7-TICAM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-115580654-T-G			Benign (Aug 16, 2018)
5-115580986-C-G		not specified	Uncertain significance (Sep 25, 2023)
5-115581066-C-T			Benign (Aug 16, 2018)
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)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMED7-TICAM2	protein_coding	protein_coding	ENST00000282382	4	47520

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00259	0.984	124520	0	72	124592	0.000289

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.831	171	204	0.836	0.0000100	2648
Missense in Polyphen		60	93.613	0.64094		1256
Synonymous	-0.327	83	79.3	1.05	0.00000398	765
Loss of Function	2.17	7	16.5	0.423	0.00000109	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000278	0.000278
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000570	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000443	0.000440
Middle Eastern	0.0000570	0.0000544
South Asian	0.000440	0.000425
Other	0.000328	0.000327

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.

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.195
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

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