TRAPPC1

protein-coding

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

Gene summary

This gene product plays a role in vesicular transport of proteins to the Golgi apparatus from the endoplasmic reticulum. The encoded protein is a component of the multisubunit transport protein particle (TRAPP) complex. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Oct 2009]

MANE transcript

NM_021210.5

Inheritance

—

ClinVar variants

U:21

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr17:7,930,345-7,932,123

External References & Databases

Ensembl (ENSG00000170043)

Transcript & Mutation Effects

hg38 • Region Span ~1.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TRAPPC1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 13

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021210.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar			5
missense			13 clinvar			13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	21	0	0	21

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021210.5	RefSeq	NP_067033.1	4	MANE Select
ENST00000303731.9	Ensembl	ENSP00000302783.4	4	MANE Select
NM_001166621.1	RefSeq	NP_001160093.1	4	Standard
ENST00000540486.5	Ensembl	ENSP00000441130.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neutrophil degranulation
Vesicle-mediated transport
Membrane Trafficking
Post-translational protein modification
Metabolism of proteins

Biological Process

endoplasmic reticulum to Golgi vesicle-mediated transport
neutrophil degranulation
COPII vesicle coating

Molecular Function

Rab guanyl-nucleotide exchange factor activity

Cellular Component

Golgi membrane
extracellular region
endoplasmic reticulum
cytosol
TRAPP complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000303731
Coding exons: 4
Length: 1779
Individuals with no LoFs: 125696
Homozygous LoFs: 0
Heterozygous LoFs: 52
Defined: 125748
p: 0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.28	55	89.0	0.618	0.00000515	940
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00030	0.00030	rare
South Asian	0	0.0	absent
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in vesicular transport from endoplasmic reticulum to Golgi.;

Intolerance Scores

LoFtool: 0.491
RVIS EVS: -0.1
RVIS percentile EVS: 46.2

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.508

Gene Damage Prediction

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