TRAPPC9

trafficking protein particle complex subunit 9, the group of Trafficking protein particle complex subunits

Basic information

Region (hg38): 8:139727725-140458579

Links

ENSG00000167632

∙ NCBI:83696 ∙ OMIM:611966 ∙ HGNC:30832 ∙ Uniprot:Q96Q05 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

intellectual disability, autosomal recessive 13 (Definitive), mode of inheritance: AR
autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
intellectual disability-obesity-brain malformations-facial dysmorphism syndrome (Supportive), mode of inheritance: AR
intellectual disability, autosomal recessive 13 (Moderate), mode of inheritance: AR
intellectual disability, autosomal recessive 13 (Strong), mode of inheritance: AR
intellectual disability-obesity-brain malformations-facial dysmorphism syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 13	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	Craniofacial; Endocrine; Neurologic	17120046; 20004765; 20004763; 20004764; 21629298; 22549410; 22989526

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRAPPC9 gene.

not_provided (674 variants)
Inborn_genetic_diseases (258 variants)
not_specified (106 variants)
Intellectual_disability,_autosomal_recessive_13 (100 variants)
Intellectual_Disability,_Recessive (46 variants)
TRAPPC9-related_disorder (43 variants)
Intellectual_disability (9 variants)
Abnormality_of_the_nervous_system (3 variants)
Intellectual_disability-obesity-brain_malformations-facial_dysmorphism_syndrome (2 variants)
Autosomal_recessive_non-syndromic_intellectual_disability (1 variants)
Autism_spectrum_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001160372.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	241 clinvar	3 clinvar	249
missense		2 clinvar	340 clinvar	26 clinvar		368
nonsense	18 clinvar	7 clinvar	1 clinvar			26
start loss						0
frameshift	19 clinvar	9 clinvar	3 clinvar			31
splice donor/acceptor (+/-2bp)	3 clinvar	11 clinvar	1 clinvar			15
Total	40	29	350	267	3

Highest pathogenic variant AF is 0.0000501887

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAPPC9	protein_coding	protein_coding	ENST00000389328	23	726093

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.29e-14	1.00	125646	0	102	125748	0.000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.48	626	739	0.847	0.0000489	8073
Missense in Polyphen		331	398.34	0.83096		4318
Synonymous	-1.64	353	316	1.12	0.0000231	2503
Loss of Function	3.23	32	58.7	0.545	0.00000318	650

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00144	0.00142
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000276	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000382	0.000378
Middle Eastern	0.000276	0.000272
South Asian	0.000196	0.000196
Other	0.000672	0.000652

dbNSFP

Source: dbNSFP

Function: FUNCTION: Functions as an activator of NF-kappa-B through increased phosphorylation of the IKK complex. May function in neuronal cells differentiation. May play a role in vesicular transport from endoplasmic reticulum to Golgi. {ECO:0000269|PubMed:15951441}.;
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)

Intolerance Scores

loftool: 0.0201
rvis_EVS: -1.65
rvis_percentile_EVS: 2.77

Haploinsufficiency Scores

pHI: 0.167
hipred: Y
hipred_score: 0.526
ghis: 0.610

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.380

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Trappc9
Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; muscle phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); respiratory system phenotype; liver/biliary system phenotype; immune system phenotype; skeleton phenotype; renal/urinary system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype;

Gene ontology

Biological process: cerebral cortex development;neuron differentiation;COPII vesicle coating;positive regulation of NF-kappaB transcription factor activity
Cellular component: Golgi membrane;endoplasmic reticulum;trans-Golgi network;cytosol;TRAPP complex
Molecular function: protein binding;Rab guanyl-nucleotide exchange factor activity