TRIM71
tripartite motif containing 71, the group of Tripartite motif family|Ring finger proteins
Basic information
Region (hg38): 3:32817997-32897824
Links
Phenotypes
GenCC
Source:
- hydrocephalus, congenital communicating, 1 (Limited), mode of inheritance: AD
- hydrocephalus, congenital communicating, 1 (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Hydrocephalus, congenital, 4 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 29983323 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM71 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 | 11 | |||||
| missense | 44 | 48 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 4 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 2 | 47 | 12 | 2 |
Variants in TRIM71
This is a list of pathogenic ClinVar variants found in the TRIM71 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-32818093-C-G | not specified | Uncertain significance (May 17, 2023) | ||
| 3-32818094-C-G | not specified | Uncertain significance (Mar 25, 2024) | ||
| 3-32818111-A-G | not specified | Uncertain significance (May 24, 2024) | ||
| 3-32818179-G-C | TRIM71-related disorder | Likely benign (Feb 24, 2023) | ||
| 3-32818199-C-T | not specified | Uncertain significance (Mar 31, 2023) | ||
| 3-32818279-C-A | Hydrocephalus, congenital communicating, 1 • not specified | Uncertain significance (Mar 02, 2023) | ||
| 3-32818299-C-CCGGCTGCCGGCGGCGGG | Non-obstructive azoospermia | Likely pathogenic (Mar 01, 2021) | ||
| 3-32818310-C-G | not specified | Uncertain significance (May 30, 2022) | ||
| 3-32818317-C-T | Likely benign (Jul 16, 2018) | |||
| 3-32818328-C-T | Cryptozoospermia | Uncertain significance (Mar 01, 2021) | ||
| 3-32818419-C-T | TRIM71-related disorder | Likely benign (Jun 07, 2022) | ||
| 3-32818448-T-C | Cryptozoospermia | Uncertain significance (Mar 01, 2021) | ||
| 3-32818454-C-T | not specified | Uncertain significance (Jan 29, 2024) | ||
| 3-32818489-G-GCCGGCGCT | Hydrocephalus, congenital communicating, 1 | Uncertain significance (Dec 28, 2021) | ||
| 3-32818527-C-G | not specified | Uncertain significance (Jun 16, 2024) | ||
| 3-32818535-A-C | not specified | Uncertain significance (Jul 13, 2022) | ||
| 3-32818538-C-T | not specified | Uncertain significance (Sep 29, 2023) | ||
| 3-32818565-C-T | not specified | Uncertain significance (Jul 12, 2023) | ||
| 3-32818633-G-T | Non-obstructive azoospermia | Likely benign (Mar 01, 2021) | ||
| 3-32818643-C-A | not specified | Uncertain significance (Sep 27, 2021) | ||
| 3-32818652-T-A | not specified | Uncertain significance (Jun 18, 2024) | ||
| 3-32818663-C-A | not specified | Uncertain significance (Jan 06, 2023) | ||
| 3-32818680-C-G | not specified | Uncertain significance (May 20, 2024) | ||
| 3-32818702-G-A | not specified | Uncertain significance (Nov 21, 2022) | ||
| 3-32818787-A-G | TRIM71-related disorder | Likely pathogenic (Feb 09, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TRIM71 | protein_coding | protein_coding | ENST00000383763 | 4 | 79809 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000310 | 112519 | 0 | 1 | 112520 | 0.00000444 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.28 | 295 | 502 | 0.588 | 0.0000305 | 5581 |
| Missense in Polyphen | 31 | 158.33 | 0.1958 | 1537 | ||
| Synonymous | -3.53 | 294 | 226 | 1.30 | 0.0000142 | 1867 |
| Loss of Function | 4.69 | 1 | 27.6 | 0.0363 | 0.00000164 | 265 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000101 | 0.0000101 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase that cooperates with the microRNAs (miRNAs) machinery and promotes embryonic stem cells proliferation and maintenance (Probable). Binds to miRNAs and associates with AGO2, participating in post-transcriptional repression of transcripts such as CDKN1A (By similarity). In addition, participates in post-transcriptional mRNA repression in a miRNA independent mechanism (PubMed:23125361). Facilitates the G1-S transition to promote rapid embryonic stem cell self-renewal by repressing CDKN1A expression. Required to maintain proliferation and prevent premature differentiation of neural progenitor cells during early neural development: positively regulates FGF signaling by controlling the stability of SHCBP1 (By similarity). Specific regulator of miRNA biogenesis. Binds to miRNA MIR29A hairpin and postranscriptionally modulates MIR29A levels, which indirectly regulates TET proteins expression (PubMed:28431233). {ECO:0000250|UniProtKB:Q1PSW8, ECO:0000269|PubMed:23125361, ECO:0000269|PubMed:28431233, ECO:0000305|PubMed:24239284}.;
- Pathway
- MicroRNAs in cancer - Homo sapiens (human);Mesodermal Commitment Pathway;let-7 inhibition of ES cell reprogramming;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation
(Consensus)
Recessive Scores
- pRec
- 0.127
Intolerance Scores
- loftool
- 0.00448
- rvis_EVS
- -1.13
- rvis_percentile_EVS
- 6.43
Haploinsufficiency Scores
- pHI
- 0.379
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.478
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.512
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Trim71
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype; respiratory system phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- trim71
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- sigmoid
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;protein polyubiquitination;neural tube closure;fibroblast growth factor receptor signaling pathway;miRNA metabolic process;posttranscriptional regulation of gene expression;negative regulation of translation;neural tube development;production of miRNAs involved in gene silencing by miRNA;miRNA mediated inhibition of translation;proteasome-mediated ubiquitin-dependent protein catabolic process;protein autoubiquitination;regulation of gene silencing by miRNA;3'-UTR-mediated mRNA destabilization;stem cell proliferation;regulation of neural precursor cell proliferation;positive regulation of gene silencing by miRNA
- Cellular component
- P-body
- Molecular function
- ubiquitin-protein transferase activity;protein binding;zinc ion binding;translation repressor activity;miRNA binding;ubiquitin protein ligase activity