TARBP2
TARBP2 subunit of RISC loading complex, the group of RISC loading complex
Basic information
Region (hg38): 12:53500921-53506431
Links
Phenotypes
GenCC
Source:
No genCC data.
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 TARBP2 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 | 0 | |||||
| missense | 15 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 2 | 2 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 0 | 0 |
Variants in TARBP2
This is a list of pathogenic ClinVar variants found in the TARBP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-53501433-G-A | not specified | Uncertain significance (Aug 21, 2023) | ||
| 12-53501445-G-A | not specified | Uncertain significance (Jun 10, 2024) | ||
| 12-53501452-G-A | not specified | Uncertain significance (Sep 20, 2023) | ||
| 12-53501455-T-C | not specified | Uncertain significance (Mar 03, 2022) | ||
| 12-53501460-A-G | not specified | Uncertain significance (Apr 25, 2022) | ||
| 12-53502176-G-A | not specified | Uncertain significance (Apr 24, 2024) | ||
| 12-53503072-T-A | not specified | Uncertain significance (Apr 07, 2023) | ||
| 12-53503101-A-G | not specified | Uncertain significance (Feb 28, 2023) | ||
| 12-53504394-C-G | Benign (Dec 31, 2019) | |||
| 12-53504404-C-T | not specified | Uncertain significance (Apr 08, 2024) | ||
| 12-53504717-G-C | not specified | Uncertain significance (May 14, 2024) | ||
| 12-53504722-C-T | not specified | Uncertain significance (Mar 01, 2023) | ||
| 12-53504801-G-A | not specified | Uncertain significance (Dec 08, 2023) | ||
| 12-53505793-C-T | not specified | Uncertain significance (Dec 08, 2023) | ||
| 12-53505849-T-C | Benign (Dec 31, 2019) | |||
| 12-53506024-T-C | not specified | Uncertain significance (Apr 22, 2022) | ||
| 12-53506030-A-T | not specified | Uncertain significance (Jul 17, 2023) | ||
| 12-53506045-C-T | not specified | Uncertain significance (Dec 06, 2023) | ||
| 12-53506047-G-A | not specified | Uncertain significance (Apr 07, 2023) | ||
| 12-53506097-G-C | not specified | Uncertain significance (Nov 17, 2022) | ||
| 12-53506104-C-T | not specified | Uncertain significance (Dec 08, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TARBP2 | protein_coding | protein_coding | ENST00000266987 | 9 | 5511 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.466 | 0.533 | 125735 | 0 | 8 | 125743 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.77 | 146 | 220 | 0.664 | 0.0000132 | 2334 |
| Missense in Polyphen | 31 | 94.362 | 0.32852 | 1014 | ||
| Synonymous | -0.0712 | 91 | 90.1 | 1.01 | 0.00000523 | 788 |
| Loss of Function | 3.17 | 4 | 18.8 | 0.212 | 0.00000110 | 192 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000153 | 0.000152 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000553 | 0.0000544 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.0000553 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Required for formation of the RNA induced silencing complex (RISC). Component of the RISC loading complex (RLC), also known as the micro-RNA (miRNA) loading complex (miRLC), which is composed of DICER1, AGO2 and TARBP2. Within the RLC/miRLC, DICER1 and TARBP2 are required to process precursor miRNAs (pre-miRNAs) to mature miRNAs and then load them onto AGO2. AGO2 bound to the mature miRNA constitutes the minimal RISC and may subsequently dissociate from DICER1 and TARBP2. May also play a role in the production of short interfering RNAs (siRNAs) from double-stranded RNA (dsRNA) by DICER1. Binds to the HIV-1 TAR RNA which is located in the long terminal repeat (LTR) of HIV-1, and stimulates translation of TAR-containing RNAs. This is achieved in part at least by binding to and inhibiting EIF2AK2/PKR, thereby reducing phosphorylation and inhibition of EIF2S1/eIF-2-alpha. May also promote translation of TAR-containing RNAs independently of EIF2AK2/PKR. {ECO:0000255|HAMAP-Rule:MF_03034, ECO:0000269|PubMed:12475984, ECO:0000269|PubMed:15973356, ECO:0000269|PubMed:16142218, ECO:0000269|PubMed:16271387, ECO:0000269|PubMed:16357216, ECO:0000269|PubMed:16424907, ECO:0000269|PubMed:17452327, ECO:0000269|PubMed:18178619, ECO:0000269|PubMed:19219043}.;
- Pathway
- Gene expression (Transcription);MicroRNA (miRNA) biogenesis;Small interfering RNA (siRNA) biogenesis;Gene Silencing by RNA
(Consensus)
Recessive Scores
- pRec
- 0.147
Intolerance Scores
- loftool
- 0.219
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.37
Haploinsufficiency Scores
- pHI
- 0.198
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.575
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.811
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tarbp2
- 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); reproductive system phenotype; 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); muscle phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- negative regulation of protein kinase activity;spermatid development;single fertilization;miRNA metabolic process;production of siRNA involved in RNA interference;targeting of mRNA for destruction involved in RNA interference;pre-miRNA processing;siRNA loading onto RISC involved in RNA interference;production of miRNAs involved in gene silencing by miRNA;multicellular organism growth;miRNA loading onto RISC involved in gene silencing by miRNA;skeletal muscle tissue regeneration;positive regulation of viral genome replication;positive regulation of translation;regulation of viral transcription;negative regulation of defense response to virus by host;positive regulation of muscle cell differentiation;neural precursor cell proliferation;regulation of production of siRNA involved in RNA interference;regulation of production of miRNAs involved in gene silencing by miRNA
- Cellular component
- nucleoplasm;cytoplasm;cytosol;RISC complex;nuclear body;micro-ribonucleoprotein complex;perinuclear region of cytoplasm;RISC-loading complex
- Molecular function
- double-stranded RNA binding;protein binding;enzyme binding;siRNA binding;miRNA binding;pre-mRNA binding;identical protein binding;protein homodimerization activity;protein N-terminus binding;pre-miRNA binding