TRAPPC2L

trafficking protein particle complex subunit 2L, the group of Trafficking protein particle complex subunits

Basic information

Region (hg38): 16:88856220-88862686

Links

ENSG00000167515 ∙ NCBI:51693 ∙ OMIM:610970 ∙ HGNC:30887 ∙ Uniprot:Q9UL33 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• encephalopathy, progressive, early-onset, with episodic rhabdomyolysis (Limited), mode of inheritance: AR
• encephalopathy, progressive, early-onset, with episodic rhabdomyolysis (Limited), mode of inheritance: AR
• encephalopathy, progressive, early-onset, with episodic rhabdomyolysis (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Encephalopathy, progressive, early-onset, with episodic rhabdomyolysis	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Neurologic	30120216

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRAPPC2L gene.

• Mucopolysaccharidosis, MPS-IV-A (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC2L 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					1	1
missense		1	14	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region			2	1		3
non coding	11	5	33	45	9	103
Total	11	7	47	46	11

Highest pathogenic variant AF is 0.00000669

Variants in TRAPPC2L

This is a list of pathogenic ClinVar variants found in the TRAPPC2L region.

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

Position	Type	Phenotype	Significance	ClinVar
16-88856269-G-A			Likely benign (May 01, 2021)
16-88856712-T-G			Benign (Aug 19, 2020)
16-88856728-GCCCTGCCCCGT-G		Mucopolysaccharidosis, MPS-IV-A	Likely benign (Nov 28, 2023)
16-88856738-G-A		Mucopolysaccharidosis, MPS-IV-A	Likely benign (Apr 03, 2023)
16-88856739-T-G		Mucopolysaccharidosis, MPS-IV-A	Likely benign (Oct 03, 2023)
16-88856744-C-T		Mucopolysaccharidosis, MPS-IV-A	Likely benign (Jan 18, 2024)
16-88856745-C-A		Mucopolysaccharidosis, MPS-IV-A	Likely benign (May 09, 2023)
16-88856745-C-G		Mucopolysaccharidosis, MPS-IV-A	Likely benign (Oct 05, 2023)
16-88856745-C-T		Mucopolysaccharidosis, MPS-IV-A	Benign (Jan 19, 2024)
16-88856746-G-A		Mucopolysaccharidosis, MPS-IV-A	Likely benign (Nov 13, 2023)
16-88856746-G-C		Mucopolysaccharidosis, MPS-IV-A	Likely benign (Apr 30, 2023)
16-88856749-C-A		Mucopolysaccharidosis, MPS-IV-A	Likely benign (Sep 03, 2023)
16-88856750-G-C		Mucopolysaccharidosis, MPS-IV-A	Likely benign (Jan 31, 2024)
16-88856754-T-C		Mucopolysaccharidosis, MPS-IV-A	Uncertain significance (Sep 07, 2023)
16-88856757-C-G		Mucopolysaccharidosis, MPS-IV-A	Pathogenic (Mar 21, 2023)
16-88856757-C-T		Mucopolysaccharidosis, MPS-IV-A	Pathogenic (May 02, 2023)
16-88856759-T-C		Mucopolysaccharidosis, MPS-IV-A	Uncertain significance (Feb 01, 2021)
16-88856760-C-A		Mucopolysaccharidosis, MPS-IV-A	Uncertain significance (Jul 26, 2022)
16-88856760-C-G		Mucopolysaccharidosis, MPS-IV-A	Pathogenic (Aug 31, 2021)
16-88856760-C-T		Mucopolysaccharidosis, MPS-IV-A	Conflicting classifications of pathogenicity (Jan 24, 2023)
16-88856761-GTC-G		Mucopolysaccharidosis, MPS-IV-A	Pathogenic (Jul 30, 2021)
16-88856762-T-C		Mucopolysaccharidosis, MPS-IV-A	Pathogenic/Likely pathogenic (Feb 14, 2023)
16-88856763-C-A		Mucopolysaccharidosis, MPS-IV-A • not specified	Uncertain significance (Sep 27, 2024)
16-88856765-A-C			Uncertain significance (Mar 01, 2019)
16-88856766-T-G		Mucopolysaccharidosis, MPS-IV-A	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAPPC2L	protein_coding	protein_coding	ENST00000301021	5	6467

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.68e-11	0.00703	125701	0	43	125744	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.384	102	91.7	1.11	0.00000565	925
Missense in Polyphen		25	26.892	0.92963		335
Synonymous	-2.20	56	38.6	1.45	0.00000278	255
Loss of Function	-1.69	13	7.89	1.65	5.00e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000335	0.000308
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.000464	0.000462
European (Non-Finnish)	0.000182	0.000176
Middle Eastern	0.000326	0.000326
South Asian	0.0000745	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in vesicular transport from endoplasmic reticulum to Golgi. {ECO:0000269|PubMed:19416478}.
• 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: 0.113

Intolerance Scores

• loftool: 0.384
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.168
• hipred: N
• hipred_score: 0.197
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trappc2l

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;COPII vesicle coating;protein complex oligomerization
• Cellular component: Golgi membrane;endoplasmic reticulum;cytosol;TRAPP complex;intracellular membrane-bounded organelle;perinuclear region of cytoplasm
• Molecular function: protein binding;Rab guanyl-nucleotide exchange factor activity