TRAPPC3L

protein-coding

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

Gene summary

Predicted to contribute to guanyl-nucleotide exchange factor activity. Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport and intra-Golgi vesicle-mediated transport. Part of TRAPP complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

BET3L

MANE transcript

NM_001139444.3

Inheritance

—

ClinVar variants

U:32B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.85

Max pathogenic AF

—

Genomic locus

chr6:116,494,989-116,545,684

External References & Databases

Ensembl (ENSG00000173626)

NCBI Gene (100128327)

Transcript & Mutation Effects

hg38 • Region Span ~50.7 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 TRAPPC3L variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 85

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001139444.3. 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			1 clinvar			1
missense			31 clinvar	2 clinvar		33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	2	0	34

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001139444.3	RefSeq	NP_001132916.1	5	MANE Select
ENST00000368602.4	Ensembl	ENSP00000357591.3	5	MANE Select
ENST00000356128.4	Ensembl	ENSP00000348445.4	2	Standard
ENST00000437098.5	Ensembl	ENSP00000395769.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

endoplasmic reticulum to Golgi vesicle-mediated transport
intra-Golgi vesicle-mediated transport
biological_process

Molecular Function

protein binding
Rab guanyl-nucleotide exchange factor activity

Cellular Component

endoplasmic reticulum
Golgi apparatus
cytosol
TRAPP complex
cis-Golgi network membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368602
Coding exons: 5
Length: 50622
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.664	70	87.5	0.800	0.00000461	1172
Missense (PolyPhen)		24	28.586	0.83959		415
Synonymous	0.163	31	32.2	0.964	0.00000171	343
Loss of Function	0.441	8	9.47	0.845	6.16e-7	119

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
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	0.0	absent
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. {ECO:0000250}.;

Recessive Scores

pRec: 0.115

Intolerance Scores

RVIS EVS: -0.19
RVIS percentile EVS: 39.68

Essentials

Essential (CRISPR): N
Essential (gene trap): N

Gene Damage Prediction

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