TRAPPC8

trafficking protein particle complex subunit 8, the group of Trafficking protein particle complex subunits

Basic information

Region (hg38): 18:31829197-31953136

Previous symbols: [ "KIAA1012" ]

Links

ENSG00000153339 ∙ NCBI:22878 ∙ OMIM:614136 ∙ HGNC:29169 ∙ Uniprot:Q9Y2L5 ∙ 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 TRAPPC8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC8 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				2		2
missense			103	1	1	105
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					2	2
Total	0	0	103	3	3

Variants in TRAPPC8

This is a list of pathogenic ClinVar variants found in the TRAPPC8 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-31830814-C-G		not specified	Uncertain significance (Jul 14, 2022)
18-31830828-G-A		not specified	Uncertain significance (Feb 23, 2023)
18-31830838-C-A		not specified	Uncertain significance (Dec 25, 2024)
18-31830847-T-C		not specified	Uncertain significance (Jan 26, 2025)
18-31830850-G-C		not specified	Uncertain significance (Sep 30, 2024)
18-31830919-T-G		not specified	Uncertain significance (Sep 14, 2023)
18-31830937-A-G		not specified	Uncertain significance (Sep 27, 2021)
18-31830957-G-A		not specified	Uncertain significance (Jan 23, 2025)
18-31830969-T-C		not specified	Uncertain significance (Mar 07, 2025)
18-31830985-C-T		not specified	Uncertain significance (Jun 02, 2023)
18-31832138-T-C		not specified	Uncertain significance (Feb 17, 2023)
18-31839419-T-C			Likely benign (Apr 01, 2024)
18-31846747-C-T		not specified	Uncertain significance (Jun 02, 2023)
18-31846750-A-G		not specified	Uncertain significance (Oct 11, 2024)
18-31846753-G-A		not specified	Uncertain significance (Jun 24, 2022)
18-31846763-T-C		not specified	Likely benign (Aug 09, 2021)
18-31846768-T-C		not specified	Uncertain significance (Aug 04, 2024)
18-31846798-C-G		not specified	Uncertain significance (Dec 02, 2024)
18-31849585-T-C		not specified	Uncertain significance (Jan 07, 2025)
18-31849630-T-C		not specified	Uncertain significance (Jul 06, 2022)
18-31849658-G-C		not specified	Uncertain significance (Nov 13, 2024)
18-31849666-G-T		not specified	Uncertain significance (Jan 30, 2024)
18-31849670-G-C		not specified	Uncertain significance (Aug 28, 2023)
18-31849702-T-A		not specified	Uncertain significance (Jan 26, 2025)
18-31852612-C-T		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAPPC8	protein_coding	protein_coding	ENST00000283351	29	123964

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.05e-9	125731	0	6	125737	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	634	726	0.874	0.0000360	9388
Missense in Polyphen		138	232.51	0.59351		3045
Synonymous	-1.59	283	251	1.13	0.0000123	2695
Loss of Function	7.55	5	76.0	0.0658	0.00000409	954

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000692	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in endoplasmic reticulum to Golgi apparatus trafficking at a very early stage. {ECO:0000269|PubMed:21525244}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

• pRec: 0.0963

Intolerance Scores

• rvis_EVS: 0.72
• rvis_percentile_EVS: 85.86

Haploinsufficiency Scores

• pHI: 0.150
• hipred: Y
• hipred_score: 0.676
• ghis: 0.499

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trappc8

Gene ontology

• Biological process: autophagosome assembly;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;autophagy of peroxisome;protein localization by the Cvt pathway;protein localization to phagophore assembly site
• Cellular component: phagophore assembly site;cytosol;TRAPP complex;cytoplasmic vesicle;TRAPPIII protein complex
• Molecular function: protein binding;Rab guanyl-nucleotide exchange factor activity