TRAPPC1

trafficking protein particle complex subunit 1, the group of Trafficking protein particle complex subunits

Basic information

Region (hg38): 17:7930345-7932123

Links

ENSG00000170043 ∙ NCBI:58485 ∙ OMIM:610969 ∙ HGNC:19894 ∙ Uniprot:Q9Y5R8 ∙ 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 TRAPPC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC1 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in TRAPPC1

This is a list of pathogenic ClinVar variants found in the TRAPPC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7931531-C-T		not specified	Uncertain significance (May 08, 2023)
17-7931546-A-G		not specified	Uncertain significance (Aug 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAPPC1	protein_coding	protein_coding	ENST00000303731	4	1779

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0865	0.875	125696	0	52	125748	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	55	89.0	0.618	0.00000515	940
Missense in Polyphen		21	28.475	0.73748		340
Synonymous	-0.822	43	36.7	1.17	0.00000204	292
Loss of Function	1.77	3	8.59	0.349	5.36e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000499	0.000499
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000299	0.000299
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in vesicular transport from endoplasmic reticulum to Golgi.
• Pathway: Neutrophil degranulation;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;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

• loftool: 0.491
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.411
• hipred: Y
• hipred_score: 0.516
• ghis: 0.653

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Trappc1

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;neutrophil degranulation;COPII vesicle coating
• Cellular component: Golgi membrane;extracellular region;endoplasmic reticulum;cytosol;TRAPP complex;azurophil granule lumen
• Molecular function: Rab guanyl-nucleotide exchange factor activity