TRAPPC5

trafficking protein particle complex subunit 5, the group of Trafficking protein particle complex subunits

Basic information

Region (hg38): 19:7680833-7687703

Links

ENSG00000181029 ∙ NCBI:126003 ∙ ∙ HGNC:23067 ∙ Uniprot:Q8IUR0 ∙ 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 TRAPPC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC5 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	1
missense			16	1	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	2

Variants in TRAPPC5

This is a list of pathogenic ClinVar variants found in the TRAPPC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-7682282-C-T		not specified	Uncertain significance (Nov 15, 2024)
19-7682297-G-A		not specified	Uncertain significance (Sep 24, 2024)
19-7682300-C-G		not specified	Uncertain significance (Aug 15, 2023)
19-7682306-C-T		not specified	Likely benign (Dec 20, 2022)
19-7682376-G-C		not specified	Uncertain significance (Nov 08, 2024)
19-7682407-T-G			Benign (Dec 03, 2021)
19-7682411-G-A		not specified	Uncertain significance (Dec 15, 2023)
19-7682456-C-G		not specified	Uncertain significance (Feb 13, 2024)
19-7682467-C-T		not specified	Uncertain significance (May 13, 2024)
19-7682470-G-A		not specified	Uncertain significance (Jul 13, 2021)
19-7682548-G-A		not specified	Uncertain significance (Feb 14, 2023)
19-7682549-G-T		not specified	Uncertain significance (Jan 09, 2024)
19-7682559-G-A			Benign (Dec 03, 2021)
19-7682588-C-T		not specified	Uncertain significance (Jun 02, 2023)
19-7682602-A-G		not specified	Uncertain significance (Nov 21, 2024)
19-7682675-G-T		not specified	Uncertain significance (Aug 15, 2023)
19-7682684-C-T		not specified	Uncertain significance (Oct 14, 2023)
19-7682692-G-T		not specified	Uncertain significance (Oct 06, 2021)
19-7682791-G-A		not specified	Uncertain significance (Sep 15, 2021)
19-7682801-G-C			Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAPPC5	protein_coding	protein_coding	ENST00000317378	1	2016

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.228	0.656	124521	0	2	124523	0.00000803

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.40	56	134	0.418	0.0000106	1156
Missense in Polyphen		15	54.508	0.27519		551
Synonymous	0.613	63	69.5	0.906	0.00000624	408
Loss of Function	1.12	1	3.14	0.319	1.34e-7	39

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)	0.0000178	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in vesicular transport from endoplasmic reticulum to Golgi.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport (Consensus)

Intolerance Scores

• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.471
• ghis: 0.445

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.530

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trappc5

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;COPII vesicle coating
• Cellular component: Golgi membrane;endoplasmic reticulum;cytosol;TRAPP complex;TRAPPI protein complex;TRAPPII protein complex;TRAPPIII protein complex
• Molecular function: protein binding;Rab guanyl-nucleotide exchange factor activity