TRAPPC3L

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

Basic information

Region (hg38): 6:116494988-116545684

Previous symbols: [ "BET3L" ]

Links

ENSG00000173626 ∙ NCBI:100128327 ∙ OMIM:614137 ∙ HGNC:21090 ∙ Uniprot:Q5T215 ∙ 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 TRAPPC3L gene.

• Inborn genetic diseases (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC3L 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1		3
Total	0	0	12	2	0

Variants in TRAPPC3L

This is a list of pathogenic ClinVar variants found in the TRAPPC3L region.

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

Position	Type	Phenotype	Significance	ClinVar
6-116496965-C-T		not specified	Likely benign (Jun 18, 2021)
6-116496989-T-C		not specified	Uncertain significance (Jan 18, 2023)
6-116497003-A-C		not specified	Uncertain significance (Mar 14, 2023)
6-116497043-G-T		not specified	Uncertain significance (Jun 09, 2022)
6-116497063-G-A		not specified	Uncertain significance (Jan 23, 2023)
6-116500533-G-A		not specified	Uncertain significance (Jun 12, 2023)
6-116500539-C-T		not specified	Uncertain significance (Mar 24, 2023)
6-116500620-T-G		not specified	Uncertain significance (Mar 01, 2023)
6-116500652-C-T		not specified	Uncertain significance (Jan 22, 2024)
6-116500653-A-G		not specified	Uncertain significance (Mar 07, 2023)
6-116500654-T-C		not specified	Uncertain significance (May 31, 2023)
6-116511877-G-C		not specified	Uncertain significance (Jul 30, 2023)
6-116511884-T-C		not specified	Uncertain significance (Jan 02, 2024)
6-116511890-T-C		not specified	Likely benign (Feb 10, 2023)
6-116511966-A-T		not specified	Uncertain significance (Dec 14, 2023)
6-116512006-A-G		not specified	Uncertain significance (Sep 01, 2021)
6-116512039-C-G		not specified	Uncertain significance (Mar 11, 2022)
6-116512083-G-A		not specified	Uncertain significance (Jul 06, 2021)
6-116512169-G-A		not specified	Uncertain significance (Apr 15, 2022)
6-116512208-T-C		not specified	Uncertain significance (Jan 23, 2024)
6-116512226-C-T		not specified	Uncertain significance (Jul 21, 2021)
6-116515616-T-C		not specified	Uncertain significance (Apr 06, 2022)
6-116515628-C-T		not specified	Uncertain significance (Aug 12, 2021)
6-116515631-C-G		not specified	Uncertain significance (Dec 21, 2022)
6-116515663-C-T		not specified	Uncertain significance (Oct 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAPPC3L	protein_coding	protein_coding	ENST00000368602	5	50622

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000157	0.437	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.664	70	87.5	0.800	0.00000461	1172
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
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. {ECO:0000250}.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

• pHI: 0.269
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trappc3l

Gene ontology

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