TRAPPC2

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

Basic information

Region (hg38): X:13712244-13734635

Previous symbols: [ "SEDL" ]

Links

ENSG00000196459 ∙ NCBI:6399 ∙ OMIM:300202 ∙ HGNC:23068 ∙ Uniprot:P0DI81 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spondyloepiphyseal dysplasia tarda, X-linked (Strong), mode of inheritance: XL
• spondyloepiphyseal dysplasia tarda (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spondyloepiphyseal dysplasia tarda, X-linked	XL	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	10431248; 14755465; 15316971; 19002213; 19417549; 19766614; 20301324; 22563562; 23656395

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRAPPC2 gene.

• not provided (10 variants)
• Spondyloepiphyseal dysplasia tarda (5 variants)
• Spondyloepiphyseal dysplasia tarda, X-linked (3 variants)
• Hereditary spastic paraplegia 4 (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC2 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	5	4	10
missense		2	12		2	16
nonsense	3	1				4
start loss						0
frameshift	8	3	1			12
inframe indel						0
splice donor/acceptor (+/-2bp)	1	1	2			4
splice region	1		4	3		8
non coding			31	15	28	74
Total	12	7	47	20	34

Variants in TRAPPC2

This is a list of pathogenic ClinVar variants found in the TRAPPC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-13712297-T-TCA		Spondyloepiphyseal dysplasia congenita	Benign (Jun 14, 2016)
X-13712347-C-T		Spondyloepiphyseal dysplasia tarda	Uncertain significance (Jan 12, 2018)
X-13712372-G-A		Spondyloepiphyseal dysplasia tarda	Benign (Jan 13, 2018)
X-13712444-T-C		Spondyloepiphyseal dysplasia tarda	Benign (Jan 12, 2018)
X-13712558-A-AT		Spondyloepiphyseal dysplasia congenita	Likely benign (Jun 14, 2016)
X-13712668-G-C		Spondyloepiphyseal dysplasia tarda	Benign (Apr 27, 2017)
X-13712773-C-A		Spondyloepiphyseal dysplasia tarda	Benign (Jan 12, 2018)
X-13712808-A-G		Spondyloepiphyseal dysplasia tarda	Benign (Jan 13, 2018)
X-13712921-C-T		Spondyloepiphyseal dysplasia tarda	Uncertain significance (Jan 12, 2018)
X-13712964-C-T		Spondyloepiphyseal dysplasia tarda	Benign (Jan 12, 2018)
X-13712965-G-A		Spondyloepiphyseal dysplasia tarda	Uncertain significance (Jan 13, 2018)
X-13712971-G-A		Spondyloepiphyseal dysplasia tarda	Uncertain significance (Jan 12, 2018)
X-13712971-G-C		Spondyloepiphyseal dysplasia tarda	Benign (Jan 12, 2018)
X-13713103-CA-C		Spondyloepiphyseal dysplasia congenita	Benign (Jun 14, 2016)
X-13713119-A-C		Spondyloepiphyseal dysplasia tarda	Uncertain significance (Jan 12, 2018)
X-13713120-C-A		Spondyloepiphyseal dysplasia tarda	Uncertain significance (Apr 27, 2017)
X-13713178-G-A		Spondyloepiphyseal dysplasia tarda	Likely benign (Apr 27, 2017)
X-13713216-G-A		Spondyloepiphyseal dysplasia tarda	Uncertain significance (Jan 12, 2018)
X-13713279-G-A		Spondyloepiphyseal dysplasia tarda	Benign (Jan 12, 2018)
X-13713355-A-G		Spondyloepiphyseal dysplasia tarda	Benign (Apr 27, 2017)
X-13713357-G-A		Spondyloepiphyseal dysplasia tarda	Likely benign (Apr 27, 2017)
X-13713375-A-G		Spondyloepiphyseal dysplasia tarda	Uncertain significance (Jan 13, 2018)
X-13713418-C-A		Spondyloepiphyseal dysplasia tarda	Uncertain significance (Jan 12, 2018)
X-13713449-T-TAAAAAAA		Spondyloepiphyseal dysplasia congenita	Uncertain significance (Jun 14, 2016)
X-13713450-C-CA		Spondyloepiphyseal dysplasia congenita	Uncertain significance (Jun 14, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAPPC2	protein_coding	protein_coding	ENST00000458511	5	22392

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00241	0.557	115758	0	2	115760	0.00000864

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	24	56.4	0.426	0.00000404	1169
Missense in Polyphen		4	13.921	0.28734		333
Synonymous	-0.429	24	21.5	1.12	0.00000178	290
Loss of Function	0.275	4	4.64	0.862	3.36e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000813	0.0000585
Finnish	0.00	0.00
European (Non-Finnish)	0.0000141	0.00000964
Middle Eastern	0.0000813	0.0000585
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Prevents transcriptional repression and induction of cell death by ENO1 (By similarity). May play a role in vesicular transport from endoplasmic reticulum to Golgi. {ECO:0000250}.
• 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: 0.355

Intolerance Scores

• rvis_EVS: 0.12
• rvis_percentile_EVS: 62.38

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.469
• ghis: 0.624

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trappc2
• Phenotype: reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: skeletal system development;regulation of transcription, DNA-templated;endoplasmic reticulum to Golgi vesicle-mediated transport;COPII vesicle coating
• Cellular component: Golgi membrane;nucleus;nucleoplasm;endoplasmic reticulum;endoplasmic reticulum-Golgi intermediate compartment;cytosol;TRAPP complex;intracellular membrane-bounded organelle;perinuclear region of cytoplasm
• Molecular function: protein binding;transcription factor binding;Rab guanyl-nucleotide exchange factor activity;ion channel binding