TRAPPC3

protein-coding

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

Gene summary

This gene encodes a component of the trafficking protein particle complex, which tethers transport vesicles to the cis-Golgi membrane. The encoded protein participates in the regulation of transport from the endoplasmic reticulum to the Golgi apparatus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

MANE transcript

NM_014408.5

Inheritance

—

ClinVar variants

P:1U:34B:6

Top phenotype

Bardet-Biedl syndrome

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr1:36,136,570-36,156,053

External References & Databases

Ensembl (ENSG00000054116)

Transcript & Mutation Effects

hg38 • Region Span ~19.5 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 TRAPPC3 variants in ClinVar

3 Conditions Cataloged

not providedTotal: 36

not specifiedTotal: 19

Bardet-Biedl syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014408.5. 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				4 clinvar	2 clinvar	6
missense		1 clinvar	32 clinvar			33
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	34	4	2	41

Highest pathogenic variant AF is 0.000016728976

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014408.5	RefSeq	NP_055223.1	5	MANE Select
ENST00000373166.8	Ensembl	ENSP00000362261.3	5	MANE Select
NM_001270894.2	RefSeq	NP_001257823.1	5	Standard
NM_001270895.2	RefSeq	NP_001257824.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Post-translational protein modification
Metabolism of proteins
Transport to the Golgi and subsequent modification

Biological Process

endoplasmic reticulum to Golgi vesicle-mediated transport
intra-Golgi vesicle-mediated transport
COPII vesicle coating

Molecular Function

protein binding
Rab guanyl-nucleotide exchange factor activity

Cellular Component

Golgi membrane
endoplasmic reticulum
Golgi apparatus
cytosol
TRAPP complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373166
Coding exons: 5
Length: 12926
Individuals with no LoFs: 125709
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125711
p: 0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.20	69	103	0.667	0.00000566	1190
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.136

Intolerance Scores

LoFtool: 0.233
RVIS EVS: -0.01
RVIS percentile EVS: 52.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.890

Gene Damage Prediction

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