TRIM42

tripartite motif containing 42, the group of Tripartite motif family|Ring finger proteins|Fibronectin type III domain containing|Protein phosphatase 1 regulatory subunits|Minor histocompatibility antigens

Basic information

Region (hg38): 3:140678064-140701150

Links

ENSG00000155890 ∙ NCBI:287015 ∙ ∙ HGNC:19014 ∙ Uniprot:Q8IWZ5 ∙ 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 TRIM42 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM42 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		2
missense			46	2		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	4	0

Variants in TRIM42

This is a list of pathogenic ClinVar variants found in the TRIM42 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-140678242-A-T		not specified	Uncertain significance (Mar 25, 2024)
3-140678372-G-A		not specified	Uncertain significance (Apr 16, 2024)
3-140678379-C-G		not specified	Uncertain significance (Mar 23, 2022)
3-140678389-C-T		not specified	Uncertain significance (Apr 10, 2023)
3-140678433-C-G		not specified	Uncertain significance (Aug 31, 2022)
3-140678434-T-G		not specified	Uncertain significance (Mar 30, 2024)
3-140678510-G-A		not specified	Uncertain significance (May 26, 2024)
3-140678519-G-A		not specified	Uncertain significance (Jan 06, 2023)
3-140678548-C-A		not specified	Uncertain significance (Mar 25, 2024)
3-140678567-C-A		not specified	Uncertain significance (Sep 15, 2021)
3-140682479-G-A		not specified	Uncertain significance (May 30, 2024)
3-140682499-C-G		not specified	Uncertain significance (Oct 20, 2021)
3-140682530-A-G		not specified	Uncertain significance (Sep 20, 2023)
3-140682578-G-T		not specified	Uncertain significance (Jan 04, 2022)
3-140682649-G-A		not specified	Uncertain significance (May 15, 2024)
3-140682652-G-A		not specified	Uncertain significance (May 25, 2022)
3-140682689-T-G		not specified	Uncertain significance (Jul 06, 2021)
3-140682725-A-C		not specified	Uncertain significance (May 03, 2023)
3-140682769-C-A		not specified	Uncertain significance (Jan 03, 2024)
3-140682770-G-A		not specified	Uncertain significance (Oct 26, 2021)
3-140682799-T-G		not specified	Uncertain significance (Jun 16, 2023)
3-140682811-C-G		not specified	Uncertain significance (Dec 21, 2023)
3-140682815-C-T		not specified	Uncertain significance (Sep 06, 2023)
3-140682839-T-A		not specified	Uncertain significance (Apr 19, 2024)
3-140682858-C-T			Likely benign (Jul 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM42	protein_coding	protein_coding	ENST00000286349	5	23112

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.07e-19	0.00440	125609	0	139	125748	0.000553

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.392	399	422	0.946	0.0000260	4833
Missense in Polyphen		111	129.76	0.8554		1666
Synonymous	-0.679	178	167	1.07	0.0000110	1322
Loss of Function	0.162	29	30.0	0.968	0.00000173	329

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00122	0.00122
Ashkenazi Jewish	0.000497	0.000496
East Asian	0.000272	0.000272
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000766	0.000739
Middle Eastern	0.000272	0.000272
South Asian	0.000273	0.000261
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0972

Intolerance Scores

• loftool: 0.931
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.65

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.171

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim42

Gene ontology

• Molecular function: protein binding;zinc ion binding