TRIM29

tripartite motif containing 29, the group of Tripartite motif family

Basic information

Region (hg38): 11:120111286-120185529

Links

ENSG00000137699

∙ NCBI:23650 ∙ OMIM:610658 ∙ HGNC:17274 ∙ Uniprot:Q14134 ∙ 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 TRIM29 gene.

not_specified (93 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM29 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012101.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			93 clinvar			93
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	93	0	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM29	protein_coding	protein_coding	ENST00000341846	9	74255

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.12e-8	0.910	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.305	350	366	0.955	0.0000242	3868
Missense in Polyphen		93	109.84	0.8467		1215
Synonymous	-0.458	166	159	1.05	0.0000114	1124
Loss of Function	1.75	15	24.3	0.618	0.00000113	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000380	0.000380
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000505	0.0000462
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.000164	0.000163
South Asian	0.000262	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays a crucial role in the regulation of macrophage activation in response to viral or bacterial infections within the respiratory tract. Mechanistically, TRIM29 interacts with IKBKG/NEMO in the lysosome where it induces its 'Lys-48' ubiquitination and subsequent degradation. In turn, the expression of type I interferons and the production of proinflammatory cytokines are inhibited. Additionally, induces the 'Lys-48' ubiquitination of TMEM173/STING in a similar way, leading to its degradation. {ECO:0000269|PubMed:27695001, ECO:0000269|PubMed:29038422}.;
Pathway: Hematopoietic Stem Cell Differentiation;Cytokine Signaling in Immune system;Immune System;EGFR1;Interferon gamma signaling;Interferon Signaling (Consensus)

Recessive Scores

pRec: 0.117

Intolerance Scores

loftool: 0.628
rvis_EVS: -0.06
rvis_percentile_EVS: 48.84

Haploinsufficiency Scores

pHI: 0.509
hipred: N
hipred_score: 0.373
ghis: 0.577

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Trim29
Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;innate immune response;cell-cell adhesion;negative regulation of protein localization to nucleus
Cellular component: lysosome;cell-cell adherens junction
Molecular function: p53 binding;DNA-binding transcription factor activity;protein binding;zinc ion binding;identical protein binding;cadherin binding involved in cell-cell adhesion