TRIM9

tripartite motif containing 9, the group of Fibronectin type III domain containing|Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 14:50975261-51096061

Links

ENSG00000100505 ∙ NCBI:114088 ∙ OMIM:606555 ∙ HGNC:16288 ∙ Uniprot:Q9C026 ∙ 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 TRIM9 gene.

• Inborn genetic diseases (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM9 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						0
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in TRIM9

This is a list of pathogenic ClinVar variants found in the TRIM9 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-50979477-A-C		not specified	Uncertain significance (Jan 29, 2024)
14-50979517-A-G		not specified	Uncertain significance (Aug 08, 2022)
14-50981868-G-T		not specified	Uncertain significance (Jan 17, 2024)
14-50998073-G-A		not specified	Uncertain significance (Oct 27, 2022)
14-50998094-C-A		not specified	Uncertain significance (Jan 20, 2023)
14-50998110-C-A		not specified	Uncertain significance (Dec 27, 2022)
14-51000689-T-G		not specified	Uncertain significance (Nov 15, 2021)
14-51000733-C-T		not specified	Uncertain significance (Jul 12, 2023)
14-51009085-A-C		not specified	Uncertain significance (Nov 07, 2023)
14-51009178-C-T		not specified	Uncertain significance (Mar 24, 2023)
14-51009185-C-T		not specified	Uncertain significance (Apr 15, 2022)
14-51022869-G-A		not specified	Uncertain significance (Sep 12, 2023)
14-51022951-T-C		not specified	Uncertain significance (Oct 27, 2022)
14-51025287-C-T		not specified	Uncertain significance (Mar 04, 2024)
14-51025303-A-G		not specified	Uncertain significance (Jan 20, 2023)
14-51025336-C-T		not specified	Uncertain significance (Sep 17, 2021)
14-51094153-C-G		not specified	Uncertain significance (Apr 04, 2023)
14-51094204-T-C		not specified	Uncertain significance (Sep 12, 2023)
14-51094318-G-A		not specified	Uncertain significance (Nov 10, 2022)
14-51094459-T-C		not specified	Uncertain significance (Jul 20, 2021)
14-51094554-G-A		not specified	Uncertain significance (Feb 17, 2023)
14-51094626-G-A		not specified	Uncertain significance (Jun 17, 2022)
14-51094698-T-C		not specified	Uncertain significance (Sep 20, 2023)
14-51094736-C-T		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM9	protein_coding	protein_coding	ENST00000298355	10	120800

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000267	125744	0	2	125746	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.01	241	413	0.583	0.0000223	4673
Missense in Polyphen		57	122.82	0.46408		1395
Synonymous	0.564	166	176	0.946	0.0000107	1393
Loss of Function	4.72	1	28.0	0.0358	0.00000127	326

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase which ubiquitinates itself in cooperation with an E2 enzyme UBE2D2/UBC4 and serves as a targeting signal for proteasomal degradation. May play a role in regulation of neuronal functions and may also participate in the formation or breakdown of abnormal inclusions in neurodegenerative disorders. May act as a regulator of synaptic vesicle exocytosis by controlling the availability of SNAP25 for the SNARE complex formation. {ECO:0000269|PubMed:20085810}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.172

Intolerance Scores

• loftool: 0.0372
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.51

Haploinsufficiency Scores

• pHI: 0.259
• hipred: Y
• hipred_score: 0.818
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim9
• 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); cellular phenotype

Gene ontology

• Biological process: synaptic vesicle exocytosis;protein ubiquitination;negative regulation of SNARE complex assembly;proteasome-mediated ubiquitin-dependent protein catabolic process;negative regulation of calcium ion-dependent exocytosis
• Cellular component: cytoplasm;cytosol;cytoskeleton;synaptic vesicle;cell junction;dendrite;presynaptic cytosol
• Molecular function: SNARE binding;ubiquitin-protein transferase activity;protein binding;zinc ion binding;protein domain specific binding;protein homodimerization activity