TRIM52

tripartite motif containing 52, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 5:181254076-181261150

Links

ENSG00000183718 ∙ NCBI:84851 ∙ OMIM:619265 ∙ HGNC:19024 ∙ Uniprot:Q96A61 ∙ 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 TRIM52 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM52 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			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in TRIM52

This is a list of pathogenic ClinVar variants found in the TRIM52 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-181257472-A-G		not specified	Likely benign (Jul 11, 2023)
5-181257488-T-C		not specified	Uncertain significance (Jun 10, 2024)
5-181260006-A-G		not specified	Uncertain significance (May 03, 2023)
5-181260011-T-C		not specified	Uncertain significance (Jan 03, 2022)
5-181260021-C-T		not specified	Uncertain significance (Jun 16, 2024)
5-181260176-G-A		not specified	Uncertain significance (Nov 07, 2022)
5-181260254-C-T		not specified	Uncertain significance (May 26, 2022)
5-181260259-C-A		not specified	Uncertain significance (Dec 12, 2023)
5-181260334-G-T		not specified	Uncertain significance (Jun 02, 2023)
5-181260347-G-T		not specified	Likely benign (Dec 27, 2022)
5-181260349-T-A		not specified	Uncertain significance (Aug 10, 2021)
5-181260398-A-C		not specified	Uncertain significance (Nov 21, 2022)
5-181260407-A-G		not specified	Uncertain significance (Mar 15, 2024)
5-181260476-T-C		not specified	Uncertain significance (Aug 28, 2023)
5-181260516-C-T		not specified	Uncertain significance (Apr 20, 2024)
5-181260526-G-C		not specified	Uncertain significance (Feb 28, 2024)
5-181260560-A-G		not specified	Uncertain significance (Apr 09, 2024)
5-181260578-T-A		not specified	Uncertain significance (Jan 26, 2022)
5-181260602-G-A		not specified	Uncertain significance (Nov 07, 2022)
5-181260670-C-A		not specified	Uncertain significance (May 16, 2024)
5-181260737-T-G		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM52	protein_coding	protein_coding	ENST00000327767	2	6703

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.14e-9	0.0522	125643	1	104	125748	0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.113	151	155	0.975	0.00000721	1998
Missense in Polyphen		36	34.058	1.057		426
Synonymous	0.250	55	57.4	0.958	0.00000274	518
Loss of Function	-0.349	13	11.7	1.11	5.55e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00123	0.00123
Ashkenazi Jewish	0.000201	0.000198
East Asian	0.00201	0.00201
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000238	0.000229
Middle Eastern	0.00201	0.00201
South Asian	0.000131	0.000131
Other	0.000978	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.736
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.09

Haploinsufficiency Scores

• pHI: 0.0744
• hipred: N
• hipred_score: 0.180
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: positive regulation of NF-kappaB transcription factor activity
• Cellular component: nuclear body
• Molecular function: zinc ion binding