TRAPPC2B

trafficking protein particle complex subunit 2B

Basic information

Region (hg38): 19:57363550-57365405

Previous symbols: [ "SEDLP", "TRAPPC2P1" ]

Links

ENSG00000256060 ∙ NCBI:10597 ∙ ∙ HGNC:10710 ∙ Uniprot:P0DI82 ∙ 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 TRAPPC2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC2B 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	0

Variants in TRAPPC2B

This is a list of pathogenic ClinVar variants found in the TRAPPC2B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57365022-T-C			Likely benign (Jul 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAPPC2B	protein_coding	protein_coding	ENST00000543226	1	1843

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0295	0.607	124535	1	54	124590	0.000221

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0118	78	77.7	1.00	0.00000414	950
Missense in Polyphen		22	19.516	1.1273		286
Synonymous	0.638	23	27.2	0.845	0.00000169	236
Loss of Function	0.175	2	2.29	0.875	9.75e-8	29

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00221	0.00219
East Asian	0.0000560	0.0000556
Finnish	0.0000467	0.0000464
European (Non-Finnish)	0.000179	0.000168
Middle Eastern	0.0000560	0.0000556
South Asian	0.000230	0.000229
Other	0.000667	0.000661

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Prevents transcriptional repression and induction of cell death by ENO1. May play a role in vesicular transport from endoplasmic reticulum to Golgi. {ECO:0000269|PubMed:11134351}.
• 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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.215
• ghis: 0.523

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport
• Cellular component: nucleus;nucleoplasm;endoplasmic reticulum;endoplasmic reticulum-Golgi intermediate compartment;intracellular membrane-bounded organelle;perinuclear region of cytoplasm