TRAPPC6A

trafficking protein particle complex subunit 6A, the group of Trafficking protein particle complex subunits

Basic information

Region (hg38): 19:45162928-45178237

Links

ENSG00000007255 ∙ NCBI:79090 ∙ OMIM:610396 ∙ HGNC:23069 ∙ Uniprot:O75865 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRAPPC6A gene.

• not_specified (27 variants)
• TRAPPC6A-related_disorder (9 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC6A gene is commonly pathogenic or not. These statistics are base on transcript: NM_001270891.2. 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				1	1	2
missense			21	5	1	27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	6	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAPPC6A	protein_coding	protein_coding	ENST00000006275	6	15310

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.15e-8	0.0684	125716	0	28	125744	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0215	105	104	1.01	0.00000612	1100
Missense in Polyphen		23	29.219	0.78716		354
Synonymous	-0.0581	47	46.5	1.01	0.00000298	347
Loss of Function	-0.676	10	7.94	1.26	3.38e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000375	0.000359
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000626	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000303	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in vesicular transport during the biogenesis of melanosomes. {ECO:0000250|UniProtKB:Q78XR0}.
• 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: 0.105

Intolerance Scores

• loftool: 0.597
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• pHI: 0.223
• hipred: N
• hipred_score: 0.197
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.890

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trappc6a
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); pigmentation phenotype; vision/eye phenotype

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;regulation of GTPase activity;COPII vesicle coating;melanosome assembly
• Cellular component: Golgi membrane;endoplasmic reticulum;cis-Golgi network;trans-Golgi network;cytosol
• Molecular function: protein binding;Rab guanyl-nucleotide exchange factor activity