TRIM2

tripartite motif containing 2, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 4:153152162-153339319

Links

ENSG00000109654 ∙ NCBI:23321 ∙ OMIM:614141 ∙ HGNC:15974 ∙ Uniprot:Q9C040 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Charcot-Marie-Tooth disease type 2R (Limited), mode of inheritance: AR
• Charcot-Marie-Tooth disease type 2R (Supportive), mode of inheritance: AR
• Charcot-Marie-Tooth disease type 2R (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Charcot-Marie-Tooth disease, axonal, type 2R	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	Neurologic	23562820; 25893792

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRIM2 gene.

• Charcot-Marie-Tooth disease type 2R (345 variants)
• not provided (67 variants)
• Inborn genetic diseases (13 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM2 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			5	129	5	139
missense		1	157	3	1	162
nonsense			2			2
start loss						0
frameshift		1	5			6
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			3	11		14
non coding			3	44	18	65
Total	0	2	173	176	24

Highest pathogenic variant AF is 0.0000197

Variants in TRIM2

This is a list of pathogenic ClinVar variants found in the TRIM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-153204194-G-A			Likely benign (Aug 07, 2018)
4-153204283-T-C			Benign (Jul 06, 2018)
4-153204529-C-T		TRIM2-related disorder	Likely benign (May 24, 2019)
4-153204530-G-GATGC			Likely pathogenic (Jul 01, 2016)
4-153204556-C-T		not specified	Uncertain significance (Dec 16, 2023)
4-153204846-T-C			Benign (Jul 05, 2018)
4-153270074-G-A			Benign (Jul 15, 2018)
4-153270118-C-T			Benign (Jul 31, 2018)
4-153270129-T-C			Benign (Jul 15, 2018)
4-153270361-C-T		TRIM2-related disorder	Likely benign (Jun 11, 2019)
4-153270384-G-T			Uncertain significance (Dec 21, 2021)
4-153270385-G-C		not specified	Uncertain significance (Jun 16, 2023)
4-153270389-G-T		Charcot-Marie-Tooth disease type 2R	Uncertain significance (Oct 23, 2023)
4-153270395-G-A		Charcot-Marie-Tooth disease type 2R	Uncertain significance (Apr 04, 2022)
4-153270399-G-A		Charcot-Marie-Tooth disease type 2R	Uncertain significance (Mar 04, 2022)
4-153270410-C-A		Charcot-Marie-Tooth disease type 2R	Uncertain significance (May 24, 2021)
4-153270415-T-A		Charcot-Marie-Tooth disease type 2R	Uncertain significance (Jan 17, 2024)
4-153270418-T-G		Charcot-Marie-Tooth disease type 2R	Likely benign (Mar 14, 2019)
4-153270421-G-C		Charcot-Marie-Tooth disease type 2R • TRIM2-related disorder	Likely benign (Jun 22, 2023)
4-153270423-T-C		Charcot-Marie-Tooth disease type 2R	Uncertain significance (Apr 18, 2023)
4-153270425-C-T		Charcot-Marie-Tooth disease type 2R	Uncertain significance (Feb 25, 2023)
4-153270426-G-A		Charcot-Marie-Tooth disease type 2R • TRIM2-related disorder	Likely benign (Jan 31, 2024)
4-153270429-A-C		Charcot-Marie-Tooth disease type 2R	Uncertain significance (Mar 05, 2022)
4-153270448-G-C		Charcot-Marie-Tooth disease type 2R	Likely benign (Oct 28, 2023)
4-153270457-T-C		Charcot-Marie-Tooth disease type 2R	Likely benign (Jun 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM2	protein_coding	protein_coding	ENST00000338700	12	186979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00397	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.57	248	465	0.534	0.0000277	5092
Missense in Polyphen		58	156.07	0.37162		1720
Synonymous	1.19	176	197	0.892	0.0000138	1515
Loss of Function	4.76	4	34.0	0.118	0.00000194	372

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000548	0.0000544
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.0000548	0.0000544
South Asian	0.0000391	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: UBE2D1-dependent E3 ubiquitin-protein ligase that mediates the ubiquitination of NEFL and of phosphorylated BCL2L11. Plays a neuroprotective function. May play a role in neuronal rapid ischemic tolerance. {ECO:0000250|UniProtKB:Q9ESN6}.
• Disease: DISEASE: Charcot-Marie-Tooth disease 2R (CMT2R) [MIM:615490]: An axonal form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot-Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Neuropathies of the CMT2 group are characterized by signs of axonal degeneration in the absence of obvious myelin alterations, normal or slightly reduced nerve conduction velocities, and progressive distal muscle weakness and atrophy. {ECO:0000269|PubMed:23562820}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.266
• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.78

Haploinsufficiency Scores

• pHI: 0.654
• hipred: Y
• hipred_score: 0.724
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.738

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye 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)

Zebrafish Information Network

• Gene name: trim2a
• Affected structure: myeloid cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: protein polyubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;regulation of neuron apoptotic process
• Cellular component: cytoplasm
• Molecular function: ubiquitin-protein transferase activity;protein binding;zinc ion binding;ubiquitin protein ligase activity