TRAPPC13

trafficking protein particle complex subunit 13, the group of Trafficking protein particle complex subunits

Basic information

Region (hg38): 5:65624789-65666233

Previous symbols: [ "C5orf44" ]

Links

ENSG00000113597 ∙ NCBI:80006 ∙ ∙ HGNC:25828 ∙ Uniprot:A5PLN9 ∙ 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 TRAPPC13 gene.

• not_specified (32 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024941.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			32			32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAPPC13	protein_coding	protein_coding	ENST00000438419	13	41518

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00241	0.995	124622	0	15	124637	0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.80	128	199	0.642	0.00000957	2717
Missense in Polyphen		20	54.698	0.36564		795
Synonymous	0.281	68	71.0	0.958	0.00000353	765
Loss of Function	2.59	8	20.7	0.386	8.71e-7	316

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000278	0.000277
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000467	0.0000464
European (Non-Finnish)	0.0000628	0.0000531
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.591
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• 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: Trappc13

Gene ontology

• Cellular component: cytosol
• Molecular function: protein binding;Rab guanyl-nucleotide exchange factor activity