TRAPPC3

trafficking protein particle complex subunit 3, the group of Trafficking protein particle complex subunits

Basic information

Region (hg38): 1:36136570-36156053

Links

ENSG00000054116 ∙ NCBI:27095 ∙ OMIM:610955 ∙ HGNC:19942 ∙ Uniprot:O43617 ∙ 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 TRAPPC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC3 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			16			16
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				5	1	6
Total	0	0	17	5	3

Variants in TRAPPC3

This is a list of pathogenic ClinVar variants found in the TRAPPC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-36137225-T-C			Uncertain significance (Jan 04, 2024)
1-36137238-G-A			Uncertain significance (May 03, 2022)
1-36137245-G-C		not specified	Uncertain significance (Jan 31, 2024)
1-36137271-C-T			Uncertain significance (May 09, 2023)
1-36137308-C-CA			Uncertain significance (Nov 03, 2022)
1-36137342-C-T			Benign (Jan 31, 2024)
1-36137812-C-T			Uncertain significance (Jan 15, 2024)
1-36137826-C-A			Uncertain significance (Jun 03, 2023)
1-36137833-T-C			Uncertain significance (Feb 13, 2023)
1-36137882-C-A			Uncertain significance (Nov 06, 2021)
1-36137903-T-C			Uncertain significance (Jan 22, 2024)
1-36137935-T-G		not specified	Uncertain significance (Jun 11, 2024)
1-36137945-T-C		not specified	Uncertain significance (Nov 18, 2023)
1-36137983-C-A			Likely benign (Jun 24, 2022)
1-36137988-G-A			Likely benign (Aug 11, 2023)
1-36137997-C-T			Likely benign (May 11, 2023)
1-36139701-G-T			Likely benign (May 12, 2023)
1-36139735-C-T			Benign (Jan 18, 2024)
1-36139746-G-A			Uncertain significance (May 24, 2022)
1-36139757-C-T		not specified	Uncertain significance (Jun 17, 2022)
1-36139776-G-A		Bardet-Biedl syndrome	Likely pathogenic (-)
1-36140081-T-C		not specified	Uncertain significance (Nov 08, 2022)
1-36140085-T-C			Uncertain significance (Mar 04, 2022)
1-36140109-A-T			Uncertain significance (Sep 12, 2022)
1-36140175-G-C			Likely benign (Dec 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAPPC3	protein_coding	protein_coding	ENST00000373166	5	12926

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.251	0.723	125709	0	2	125711	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	69	103	0.667	0.00000566	1190
Missense in Polyphen		19	38.389	0.49493		434
Synonymous	1.31	28	38.4	0.730	0.00000195	345
Loss of Function	1.87	2	7.54	0.265	3.16e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000625	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
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)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.233
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.497
• hipred: N
• hipred_score: 0.439
• ghis: 0.657

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.890

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trappc3

Gene ontology

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