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.

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.

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	2
missense			14	5	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding					1	1
Total	0	0	14	6	3

Variants in TRAPPC6A

This is a list of pathogenic ClinVar variants found in the TRAPPC6A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-45163182-C-T		TRAPPC6A-related disorder	Benign (May 08, 2019)
19-45163202-G-A		not specified	Uncertain significance (May 13, 2024)
19-45163202-G-C		not specified	Uncertain significance (Jun 13, 2023)
19-45163208-A-G		not specified	Uncertain significance (May 07, 2024)
19-45163230-G-A		TRAPPC6A-related disorder	Likely benign (Jun 06, 2019)
19-45163919-C-T		not specified	Uncertain significance (Jul 21, 2021)
19-45163943-T-C		not specified	Uncertain significance (Jan 31, 2022)
19-45163970-A-T		not specified	Uncertain significance (Oct 12, 2022)
19-45163979-C-T		not specified	Uncertain significance (Dec 13, 2021)
19-45163981-C-T		TRAPPC6A-related disorder	Likely benign (Sep 13, 2022)
19-45164183-T-C		not specified	Uncertain significance (Jan 11, 2023)
19-45164187-G-T		not specified	Uncertain significance (Feb 05, 2024)
19-45164238-C-T		not specified	Uncertain significance (Nov 15, 2021)
19-45164241-A-T		TRAPPC6A-related disorder	Uncertain significance (-)
19-45164243-G-A		TRAPPC6A-related disorder	Likely benign (Apr 04, 2022)
19-45164896-G-A		not specified	Uncertain significance (Apr 13, 2022)
19-45164900-C-T		TRAPPC6A-related disorder	Benign (Sep 18, 2019)
19-45164934-C-T		TRAPPC6A-related disorder	Benign (May 08, 2019)
19-45164955-C-T		TRAPPC6A-related disorder	Likely benign (Apr 01, 2019)
19-45164956-G-A		not specified	Likely benign (Dec 01, 2022)
19-45165119-G-A		TRAPPC6A-related disorder	Likely benign (Apr 29, 2019)
19-45165152-G-A		not specified	Uncertain significance (Jul 09, 2021)
19-45165188-T-C		TRAPPC6A-related disorder	Likely benign (Jul 25, 2022)
19-45178103-C-T		not specified	Uncertain significance (Jan 03, 2022)
19-45178147-G-T		not specified	Uncertain significance (Apr 25, 2023)

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