TRIM54

tripartite motif containing 54, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 2:27282428-27307439

Previous symbols: [ "RNF30" ]

Links

ENSG00000138100 ∙ NCBI:57159 ∙ OMIM:606474 ∙ HGNC:16008 ∙ Uniprot:Q9BYV2 ∙ 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 TRIM54 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM54 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				2	3	5
missense			22	1		23
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			2			2
splice region			1		1	2
non coding				1		1
Total	0	0	25	4	3

Variants in TRIM54

This is a list of pathogenic ClinVar variants found in the TRIM54 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27282741-A-G		not specified	Uncertain significance (Jun 22, 2023)
2-27282787-A-G		not specified	Uncertain significance (May 16, 2024)
2-27282812-C-T		TRIM54-related disorder	Benign (Aug 26, 2019)
2-27282887-C-T			Likely benign (Mar 01, 2024)
2-27282890-C-T		TRIM54-related disorder	Benign (Feb 22, 2019)
2-27298664-G-A		not specified	Uncertain significance (Jul 06, 2021)
2-27298699-G-A		not specified	Uncertain significance (Mar 07, 2023)
2-27298710-T-G		not specified	Uncertain significance (Dec 12, 2023)
2-27299297-G-T			Uncertain significance (Mar 01, 2020)
2-27299307-A-G		not specified	Uncertain significance (May 09, 2023)
2-27299399-A-G		not specified	Uncertain significance (Sep 28, 2022)
2-27299408-C-T		not specified	Uncertain significance (Apr 23, 2024)
2-27299415-AG-A			Uncertain significance (Aug 01, 2018)
2-27299425-CAG-C		TRIM54-related disorder	Likely benign (Mar 25, 2019)
2-27299637-G-T		not specified	Uncertain significance (Dec 28, 2023)
2-27304982-G-A		TRIM54-related disorder	Benign (Feb 19, 2019)
2-27305004-C-T		not specified	Uncertain significance (Nov 15, 2021)
2-27305007-G-A		not specified	Uncertain significance (Mar 16, 2022)
2-27305029-T-G			Uncertain significance (Feb 01, 2024)
2-27305578-T-G			Uncertain significance (Feb 01, 2024)
2-27305683-C-T		not specified	Uncertain significance (Jan 17, 2024)
2-27305708-G-A		not specified	Uncertain significance (Feb 27, 2024)
2-27305710-G-A		not specified	Uncertain significance (Apr 27, 2023)
2-27305716-G-A		not specified	Uncertain significance (Jan 18, 2022)
2-27305725-C-A		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM54	protein_coding	protein_coding	ENST00000296098	9	25048

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.51e-18	0.000909	125495	0	253	125748	0.00101

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.487	226	248	0.913	0.0000157	2603
Missense in Polyphen		55	58.855	0.9345		626
Synonymous	0.307	100	104	0.962	0.00000680	776
Loss of Function	-0.865	24	19.8	1.21	9.27e-7	236

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000676	0.000676
Ashkenazi Jewish	0.00	0.00
East Asian	0.00580	0.00572
Finnish	0.000656	0.000647
European (Non-Finnish)	0.000852	0.000844
Middle Eastern	0.00580	0.00572
South Asian	0.000511	0.000490
Other	0.000493	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May bind and stabilize microtubules during myotubes formation. {ECO:0000250}.

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.841
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.45

Haploinsufficiency Scores

• pHI: 0.133
• hipred: N
• hipred_score: 0.338
• ghis: 0.667

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.844

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim54
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; muscle phenotype

Gene ontology

• Biological process: microtubule-based process;negative regulation of microtubule depolymerization;signal transduction;multicellular organism development;muscle cell development
• Cellular component: microtubule;microtubule associated complex;Z disc
• Molecular function: protein binding;microtubule binding;zinc ion binding