TRIM48

tripartite motif containing 48, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 11:55262155-55271114

Links

ENSG00000150244 ∙ NCBI:79097 ∙ ∙ HGNC:19021 ∙ Uniprot:Q8IWZ4 ∙ 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 TRIM48 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM48 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				1		1
missense			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	1	0

Variants in TRIM48

This is a list of pathogenic ClinVar variants found in the TRIM48 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-55262275-G-A		not specified	Uncertain significance (Dec 17, 2024)
11-55262281-T-A		not specified	Uncertain significance (Jan 30, 2024)
11-55262287-T-A		not specified	Uncertain significance (Mar 07, 2023)
11-55262287-T-C		not specified	Uncertain significance (Oct 03, 2022)
11-55262293-C-A		not specified	Uncertain significance (Apr 09, 2024)
11-55264911-C-A		not specified	Uncertain significance (Dec 06, 2021)
11-55264953-T-C		not specified	Uncertain significance (Sep 14, 2022)
11-55264979-G-T		not specified	Uncertain significance (Sep 25, 2023)
11-55264992-G-A		not specified	Uncertain significance (Jan 10, 2022)
11-55265002-C-G		not specified	Uncertain significance (Jul 13, 2022)
11-55265009-A-G		not specified	Uncertain significance (Apr 19, 2024)
11-55265042-C-A		not specified	Uncertain significance (Aug 16, 2022)
11-55265042-C-T		not specified	Uncertain significance (Sep 08, 2024)
11-55265057-T-C		not specified	Uncertain significance (May 24, 2023)
11-55265071-A-G		not specified	Uncertain significance (Jul 09, 2024)
11-55265115-A-C		not specified	Uncertain significance (Oct 13, 2023)
11-55265117-A-C		not specified	Uncertain significance (Jan 31, 2023)
11-55265129-C-A		not specified	Uncertain significance (Apr 15, 2024)
11-55265147-C-A		not specified	Uncertain significance (Aug 20, 2024)
11-55265155-A-G			Likely benign (Dec 01, 2022)
11-55265186-A-G		not specified	Uncertain significance (Jul 13, 2021)
11-55265285-C-T		not specified	Uncertain significance (Nov 09, 2024)
11-55265301-C-T		not specified	Uncertain significance (Jun 16, 2024)
11-55265625-C-G		not specified	Uncertain significance (Sep 16, 2021)
11-55265637-A-C		not specified	Uncertain significance (Oct 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM48	protein_coding	protein_coding	ENST00000417545	5	8938

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.10e-27	1.72e-7	123049	28	98	123175	0.000512

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.49	220	115	1.92	0.00000548	1474
Missense in Polyphen		24	18.924	1.2682		261
Synonymous	-4.52	78	41.1	1.90	0.00000206	389
Loss of Function	-4.25	31	13.9	2.23	7.81e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00160	0.00146
Ashkenazi Jewish	0.000604	0.000503
East Asian	0.000462	0.000400
Finnish	0.0000929	0.0000927
European (Non-Finnish)	0.000466	0.000382
Middle Eastern	0.000462	0.000400
South Asian	0.00175	0.00123
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Pathway: Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon Signaling (Consensus)

Intolerance Scores

• loftool: 0.475
• rvis_EVS: 1.84
• rvis_percentile_EVS: 97.09

Haploinsufficiency Scores

• pHI: 0.0519
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Gene ontology

• Molecular function: zinc ion binding