TRAPPC11

trafficking protein particle complex subunit 11, the group of Trafficking protein particle complex subunits

Basic information

Region (hg38): 4:183659267-183713594

Previous symbols: [ "C4orf41" ]

Links

ENSG00000168538 ∙ NCBI:60684 ∙ OMIM:614138 ∙ HGNC:25751 ∙ Uniprot:Q7Z392 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive limb-girdle muscular dystrophy type R18 (Definitive), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type R18 (Strong), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type R18 (Strong), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type R18 (Strong), mode of inheritance: AR
• triple-A syndrome (Supportive), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type R18 (Supportive), mode of inheritance: AR
• intellectual disability-hyperkinetic movement-truncal ataxia syndrome (Supportive), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Muscular dystrophy, limb-girdle, autosomal recessive, 18	AR	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; Neurologic	23830518; 27707803; 28827486

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRAPPC11 gene.

• Autosomal recessive limb-girdle muscular dystrophy type R18 (27 variants)
• not provided (4 variants)
• Autosomal recessive limb-girdle muscular dystrophy (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 TRAPPC11 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			6	179	4	189
missense		2	373	12	6	393
nonsense	15	4	3			22
start loss			1			1
frameshift	12	12		1		25
inframe indel			4			4
splice donor/acceptor (+/-2bp)	1	10				11
splice region	1	1	26	30	1	59
non coding			3	136	81	220
Total	28	28	390	328	91

Highest pathogenic variant AF is 0.0000329

Variants in TRAPPC11

This is a list of pathogenic ClinVar variants found in the TRAPPC11 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-183663736-G-GT			Benign (Nov 14, 2019)
4-183663736-G-GTT			Benign (Sep 02, 2019)
4-183663860-T-C		TRAPPC11-related disorder	Likely benign (Sep 12, 2018)
4-183663862-G-A		not specified	Benign (Aug 17, 2018)
4-183663870-G-A		Autosomal recessive limb-girdle muscular dystrophy type R18	Uncertain significance (Aug 09, 2022)
4-183663883-T-C		Autosomal recessive limb-girdle muscular dystrophy type R18	Uncertain significance (Aug 02, 2023)
4-183663891-C-A		Autosomal recessive limb-girdle muscular dystrophy type R18	Uncertain significance (Oct 05, 2023)
4-183663910-C-T		Autosomal recessive limb-girdle muscular dystrophy type R18	Uncertain significance (Aug 09, 2022)
4-183663911-G-A		Autosomal recessive limb-girdle muscular dystrophy type R18	Uncertain significance (Aug 20, 2021)
4-183663916-A-C		Autosomal recessive limb-girdle muscular dystrophy type R18	Uncertain significance (Mar 08, 2022)
4-183663919-G-A		Autosomal recessive limb-girdle muscular dystrophy type R18	Uncertain significance (May 13, 2022)
4-183663920-C-T		Autosomal recessive limb-girdle muscular dystrophy type R18	Uncertain significance (Aug 03, 2022)
4-183663933-A-G		Autosomal recessive limb-girdle muscular dystrophy type R18	Likely benign (Sep 07, 2022)
4-183663936-G-A			Uncertain significance (Aug 27, 2021)
4-183663942-G-A		Autosomal recessive limb-girdle muscular dystrophy type R18	Likely benign (Dec 10, 2022)
4-183663953-A-G		Autosomal recessive limb-girdle muscular dystrophy type R18	Uncertain significance (Mar 23, 2019)
4-183663963-C-G		Autosomal recessive limb-girdle muscular dystrophy type R18	Likely benign (Mar 26, 2018)
4-183663967-C-A		Autosomal recessive limb-girdle muscular dystrophy type R18	Likely benign (Oct 27, 2019)
4-183663967-C-T		Autosomal recessive limb-girdle muscular dystrophy type R18	Pathogenic (Oct 23, 2023)
4-183663973-G-A		Autosomal recessive limb-girdle muscular dystrophy type R18	Uncertain significance (Jul 27, 2022)
4-183663973-G-C		Autosomal recessive limb-girdle muscular dystrophy type R18	Uncertain significance (Jul 26, 2022)
4-183663981-C-T		Autosomal recessive limb-girdle muscular dystrophy type R18	Likely benign (Jan 02, 2024)
4-183663984-C-G		not specified • Autosomal recessive limb-girdle muscular dystrophy type R18	Benign/Likely benign (Jan 18, 2024)
4-183663993-A-T			Uncertain significance (Nov 01, 2023)
4-183663997-C-T		Autosomal recessive limb-girdle muscular dystrophy type R18	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAPPC11	protein_coding	protein_coding	ENST00000334690	29	54326

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.56e-10	1.00	125670	0	78	125748	0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.932	534	598	0.893	0.0000300	7426
Missense in Polyphen		68	92.014	0.73902		1085
Synonymous	0.533	209	219	0.954	0.0000119	2132
Loss of Function	4.46	28	67.5	0.415	0.00000349	814

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000614	0.000610
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000336	0.000326
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000391	0.000387
Middle Eastern	0.000336	0.000326
South Asian	0.000306	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in endoplasmic reticulum to Golgi apparatus trafficking at a very early stage. {ECO:0000269|PubMed:21525244, ECO:0000269|PubMed:27862579}.
• Disease: DISEASE: Limb-girdle muscular dystrophy 2S (LGMD2S) [MIM:615356]: A form of limb-girdle muscular dystrophy characterized by proximal muscle weakness with childhood onset, resulting in gait abnormalities and scapular winging. Serum creatine kinase is increased. A subset of patients may show a hyperkinetic movement disorder with chorea, ataxia, or dystonia and global developmental delay. {ECO:0000269|PubMed:23830518}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• rvis_EVS: -0.97
• rvis_percentile_EVS: 8.99

Haploinsufficiency Scores

• pHI: 0.0922
• hipred: Y
• hipred_score: 0.544
• ghis: 0.664

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trappc11

Zebrafish Information Network

• Gene name: trappc11
• Affected structure: hepatocyte
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;protein complex oligomerization;regulation of protein complex stability
• Cellular component: Golgi apparatus;cytosol;TRAPP complex
• Molecular function: protein binding;Rab guanyl-nucleotide exchange factor activity