TRIM42

protein-coding

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

Gene summary

This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, namely a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. [provided by RefSeq, Jul 2008]

MANE transcript

NM_152616.5

Inheritance

—

ClinVar variants

U:106B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr3:140,678,064-140,701,150

External References & Databases

Ensembl (ENSG00000155890)

Transcript & Mutation Effects

hg38 • Region Span ~23.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TRIM42 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 107

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152616.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			105 clinvar	3 clinvar		108
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	106	5	0	111

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152616.5	RefSeq	NP_689829.3	5	MANE Select
ENST00000286349.4	Ensembl	ENSP00000286349.3	5	MANE Select
XM_011512740.4	RefSeq	XP_011511042.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
zinc ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000286349
Coding exons: 5
Length: 23112
Individuals with no LoFs: 125609
Homozygous LoFs: 0
Heterozygous LoFs: 139
Defined: 125748
p: 0.000553

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.392	399	422	0.946	0.0000260	4833
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00050	0.00049	rare
Latino/Admixed American	0.00072	0.00072	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.00027	0.00027	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00077	0.00074	rare
South Asian	0.00027	0.00026	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0972

Intolerance Scores

LoFtool: 0.931
RVIS EVS: 0.38
RVIS percentile EVS: 75.65

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.171

Gene Damage Prediction

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